From fe055761212107043f4a0c3d5ac77b8721dad60f Mon Sep 17 00:00:00 2001
From: mh17 <mh17>
Date: Tue, 8 Jun 2010 08:31:23 +0000
Subject: [PATCH] removed g_datalist from styles and speeded up access to
parameters
---
src/include/ZMap/zmapConfigIni.h | 4 +-
src/include/ZMap/zmapConfigStrings.h | 5 +-
src/include/ZMap/zmapFeature.h | 30 +-
src/include/ZMap/zmapGFF.h | 10 +-
src/include/ZMap/zmapServerProtocol.h | 6 +-
src/include/ZMap/zmapStyle.h | 475 +++++++++++--
src/include/ZMap/zmapUtilsDebug.h | 77 ++-
src/include/ZMap/zmapView.h | 4 +-
src/include/ZMap/zmapWindow.h | 44 +-
src/include/ZMap/zmapWindowNavigator.h | 18 +-
src/zmapConfig/zmapConfigLoader.c | 11 +-
src/zmapFeature/zmapFeature.c | 17 +-
src/zmapFeature/zmapFeatureContext.c | 4 +-
src/zmapFeature/zmapFeatureOutput.c | 22 +-
src/zmapFeature/zmapFeatureTypes.c | 642 +++---------------
src/zmapFeature/zmapFeatureUtils.c | 14 +-
src/zmapFeature/zmapFeature_P.h | 8 +-
src/zmapFeature/zmapStyle.c | 20 +-
src/zmapFeature/zmapStyleUtils.c | 12 +-
src/zmapFeature/zmapStyle_I.h | 296 +-------
src/zmapGFF/gffparser.c | 32 +-
src/zmapGFF/zmapGFF2Dumper.c | 146 ++--
src/zmapGFF/zmapGFF2parser.c | 41 +-
src/zmapGFF/zmapGFF_P.h | 13 +-
src/zmapServer/acedb/acedbServer.c | 42 +-
src/zmapServer/das/dasServer.c | 34 +-
src/zmapServer/das/dasServer_P.h | 11 +-
src/zmapServer/pipe/pipeServer.c | 14 +-
src/zmapServer/zmapServer.c | 8 +-
src/zmapServer/zmapServer.h | 12 +-
src/zmapServer/zmapServerProtocolHandler.c | 16 +-
src/zmapServer/zmapServerPrototype.h | 8 +-
src/zmapUtils/zmapGLibUtils.c | 47 +-
src/zmapUtils/zmapUtils.c | 36 +-
src/zmapUtils/zmapUtilsConfig.c | 26 +-
src/zmapView/zmapView.c | 96 +--
src/zmapView/zmapViewRemoteReceive.c | 6 +-
src/zmapView/zmapView_P.h | 4 +-
.../items/zmapWindowAlignmentFeature.c | 6 +-
.../items/zmapWindowAlignmentFeature.h | 15 +-
.../items/zmapWindowAssemblyFeature.h | 15 +-
src/zmapWindow/items/zmapWindowBasicFeature.c | 17 +-
src/zmapWindow/items/zmapWindowBasicFeature.h | 15 +-
src/zmapWindow/items/zmapWindowCanvasItem.c | 28 +-
src/zmapWindow/items/zmapWindowCanvasItem.h | 17 +-
.../items/zmapWindowContainerAlignment.h | 15 +-
.../items/zmapWindowContainerBlock.h | 23 +-
.../items/zmapWindowContainerChildren.h | 15 +-
.../items/zmapWindowContainerContext.h | 15 +-
.../items/zmapWindowContainerFeatureSet.c | 18 +-
.../items/zmapWindowContainerFeatureSet.h | 19 +-
.../zmapWindowContainerFeatureSetUtils.c | 18 +-
.../items/zmapWindowContainerGroup.c | 160 ++---
.../items/zmapWindowContainerGroup.h | 30 +-
.../items/zmapWindowContainerStrand.h | 15 +-
src/zmapWindow/items/zmapWindowGlyphItem.h | 8 +-
src/zmapWindow/items/zmapWindowLongItem.h | 17 +-
.../items/zmapWindowSequenceFeature.h | 15 +-
src/zmapWindow/items/zmapWindowTextFeature.h | 15 +-
src/zmapWindow/items/zmapWindowTextItem.h | 22 +-
.../items/zmapWindowTranscriptFeature.h | 15 +-
src/zmapWindow/zmapWindow.c | 41 +-
src/zmapWindow/zmapWindowColBump.c | 5 +-
src/zmapWindow/zmapWindowDraw.c | 44 +-
src/zmapWindow/zmapWindowDrawFeatures.c | 45 +-
src/zmapWindow/zmapWindowDump.c | 4 +-
src/zmapWindow/zmapWindowFeature.c | 8 +-
src/zmapWindow/zmapWindowItemFactory.c | 5 +-
src/zmapWindow/zmapWindowNavigator.c | 316 ++++-----
src/zmapWindow/zmapWindowRemoteReceive.c | 100 +--
src/zmapWindow/zmapWindowSearch.c | 68 +-
src/zmapWindow/zmapWindowUtils.c | 27 +-
src/zmapWindow/zmapWindow_P.h | 112 +--
73 files changed, 1753 insertions(+), 1866 deletions(-)
diff --git a/src/include/ZMap/zmapConfigIni.h b/src/include/ZMap/zmapConfigIni.h
index 527a6f68c..8e4c79a40 100755
--- a/src/include/ZMap/zmapConfigIni.h
+++ b/src/include/ZMap/zmapConfigIni.h
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: May 26 14:53 2009 (edgrif)
* Created: Thu Sep 11 10:40:13 2008 (rds)
- * CVS info: $Id: zmapConfigIni.h,v 1.14 2010-05-17 14:41:15 mh17 Exp $
+ * CVS info: $Id: zmapConfigIni.h,v 1.15 2010-06-08 08:31:23 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -144,7 +144,7 @@ GList *zMapConfigIniContextGetSources(ZMapConfigIniContext context) ;
GList *zMapConfigIniContextGetNamed(ZMapConfigIniContext context, char *stanza_name) ;
GList *zMapConfigIniContextGetStyleList(ZMapConfigIniContext context,char *styles_list_in);
-gboolean zMapConfigIniGetStylesFromFile(char *styles_list, char *styles_file, GData **styles_out);
+gboolean zMapConfigIniGetStylesFromFile(char *styles_list, char *styles_file, GHashTable **styles_out);
GHashTable *zMapConfigIniGetFeatureset2Column(ZMapConfigIniContext context,GHashTable *hash,GHashTable *hdesc);
GHashTable *zMapConfigIniGetGlyph(ZMapConfigIniContext context);
diff --git a/src/include/ZMap/zmapConfigStrings.h b/src/include/ZMap/zmapConfigStrings.h
index a53cb501b..03ce1232c 100755
--- a/src/include/ZMap/zmapConfigStrings.h
+++ b/src/include/ZMap/zmapConfigStrings.h
@@ -40,7 +40,7 @@
* HISTORY:
* Last edited: Mar 2 14:19 2010 (edgrif)
* Created: Tue Apr 25 14:36:16 2006 (edgrif)
- * CVS info: $Id: zmapConfigStrings.h,v 1.31 2010-05-17 14:41:15 mh17 Exp $
+ * CVS info: $Id: zmapConfigStrings.h,v 1.32 2010-06-08 08:31:23 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_CONFIG_STRINGS_H
@@ -193,7 +193,7 @@
//#define ZMAPSTANZA_APP_STYLESFILE "stylesfile"
#define ZMAPSTANZA_APP_LEGACY_STYLES "legacy-styles"
#define ZMAPSTANZA_APP_XREMOTE_DEBUG "xremote-debug"
-#define ZMAPSTANZA_APP_COLUMNS "columns"
+#define ZMAPSTANZA_APP_COLUMNS "columns"
/*! @addtogroup config_stanzas
@@ -717,6 +717,7 @@
#define ZMAPSTANZA_DEBUG_APP_THREADS "threads"
#define ZMAPSTANZA_DEBUG_APP_FEATURE2STYLE "feature2style"
#define ZMAPSTANZA_DEBUG_APP_STYLES "styles"
+#define ZMAPSTANZA_DEBUG_APP_TIMING "timing" // output timing of various things to STDOUT
/*! @addtogroup config_stanzas
diff --git a/src/include/ZMap/zmapFeature.h b/src/include/ZMap/zmapFeature.h
index dbf2fef9e..adcfee459 100755
--- a/src/include/ZMap/zmapFeature.h
+++ b/src/include/ZMap/zmapFeature.h
@@ -27,7 +27,7 @@
* HISTORY:
* Last edited: Mar 3 13:40 2010 (edgrif)
* Created: Fri Jun 11 08:37:19 2004 (edgrif)
- * CVS info: $Id: zmapFeature.h,v 1.174 2010-04-22 14:31:52 mh17 Exp $
+ * CVS info: $Id: zmapFeature.h,v 1.175 2010-06-08 08:31:23 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_FEATURE_H
@@ -410,6 +410,8 @@ typedef struct ZMapFeatureSetStruct_
set of ZMapFeatureStruct. */
char *description ; /* As it says... */
+ ZMapFeatureTypeStyle style;
+
} ZMapFeatureSetStruct, *ZMapFeatureSet ;
@@ -546,9 +548,13 @@ typedef struct ZMapFeatureStruct_
"trans_splice_acceptor_site", this
might be recognised SO term or not. */
+ // style id tp be removed when style fully working
GQuark style_id ; /* Style defining how this feature is processed.
(use Styles _unique_ id.) */
+ ZMapFeatureTypeStyle style; // pointer to the style structure
+
+
/* coords are _always_ with reference to forward strand, i.e. x1 <= x2, strand flag gives the
* strand of the feature. */
Coord x1, x2 ;
@@ -685,7 +691,7 @@ typedef ZMapFeatureContextExecuteStatus (*ZMapGDataRecurseFunc)(GQuark key_id,
char **error);
typedef gboolean (*ZMapFeatureDumpFeatureFunc)(ZMapFeatureAny feature_any,
- GData *styles,
+ GHashTable *styles,
GString *dump_string_in_out,
GError **error,
gpointer user_data);
@@ -697,7 +703,7 @@ ZMapFeatureAny zMapFeatureAnyCreate(ZMapStyleMode feature_type) ;
ZMapFeatureAny zMapFeatureAnyCopy(ZMapFeatureAny orig_feature_any) ;
gboolean zMapFeatureAnyFindFeature(ZMapFeatureAny feature_set, ZMapFeatureAny feature) ;
ZMapFeatureAny zMapFeatureAnyGetFeatureByID(ZMapFeatureAny feature_set, GQuark feature_id) ;
-gboolean zMapFeatureAnyAddModesToStyles(ZMapFeatureAny feature_any, GData *styles) ;
+gboolean zMapFeatureAnyAddModesToStyles(ZMapFeatureAny feature_any, GHashTable *styles) ;
gboolean zMapFeatureAnyRemoveFeature(ZMapFeatureAny feature_set, ZMapFeatureAny feature) ;
void zMapFeatureAnyDestroy(ZMapFeatureAny feature) ;
@@ -773,7 +779,7 @@ gboolean zMapFeatureAddAssemblyPathData(ZMapFeature feature,
gboolean zMapFeatureSetCoords(ZMapStrand strand, int *start, int *end,
int *query_start, int *query_end) ;
void zMapFeature2MasterCoords(ZMapFeature feature, double *feature_x1, double *feature_x2) ;
-void zMapFeatureReverseComplement(ZMapFeatureContext context, GData *styles) ;
+void zMapFeatureReverseComplement(ZMapFeatureContext context, GHashTable *styles) ;
ZMapFrame zMapFeatureFrame(ZMapFeature feature) ;
gboolean zMapFeatureAddURL(ZMapFeature feature, char *url) ;
gboolean zMapFeatureAddLocus(ZMapFeature feature, GQuark locus_id) ;
@@ -926,35 +932,35 @@ char *zMapFeatureName(ZMapFeatureAny any_feature) ;
char *zMapFeatureCanonName(char *feature_name) ;
ZMapFeatureTypeStyle zMapFeatureGetStyle(ZMapFeatureAny feature) ;
gboolean zMapSetListEqualStyles(GList **feature_set_names, GList **styles) ;
-gboolean zMapFeatureAnyForceModesToStyles(ZMapFeatureAny feature_any, GData *styles) ;
+gboolean zMapFeatureAnyForceModesToStyles(ZMapFeatureAny feature_any, GHashTable *styles) ;
/* Probably should be merged at some time.... */
-gboolean zMapFeatureDumpStdOutFeatures(ZMapFeatureContext feature_context, GData *styles, GError **error_out) ;
-gboolean zMapFeatureDumpToFileName(ZMapFeatureContext feature_context,char *filename,char *header, GData *styles, GError **error_out);
-gboolean zMapFeatureContextDump(ZMapFeatureContext feature_context, GData *styles,
+gboolean zMapFeatureDumpStdOutFeatures(ZMapFeatureContext feature_context, GHashTable *styles, GError **error_out) ;
+gboolean zMapFeatureDumpToFileName(ZMapFeatureContext feature_context,char *filename,char *header, GHashTable *styles, GError **error_out);
+gboolean zMapFeatureContextDump(ZMapFeatureContext feature_context, GHashTable *styles,
GIOChannel *file, GError **error_out) ;
gboolean zMapFeatureContextDumpToFile(ZMapFeatureAny feature_any,
- GData *styles,
+ GHashTable *styles,
ZMapFeatureDumpFeatureFunc dump_func,
gpointer dump_user_data,
GIOChannel *dump_file,
GError **dump_error_out);
gboolean zMapFeatureContextRangeDumpToFile(ZMapFeatureAny dump_set,
- GData *styles,
+ GHashTable *styles,
ZMapSpan span_data,
ZMapFeatureDumpFeatureFunc dump_func,
gpointer dump_user_data,
GIOChannel *dump_file,
GError **dump_error_out) ;
gboolean zMapFeatureListDumpToFile(GList *feature_list,
- GData *styles,
+ GHashTable *styles,
ZMapFeatureDumpFeatureFunc dump_func,
gpointer dump_user_data,
GIOChannel *dump_file,
GError **dump_error_out);
gboolean zMapFeatureListForeachDumperCreate(ZMapFeatureDumpFeatureFunc dump_func,
- GData *styles,
+ GHashTable *styles,
gpointer dump_user_data,
GDestroyNotify dump_user_free,
GIOChannel *dump_file,
diff --git a/src/include/ZMap/zmapGFF.h b/src/include/ZMap/zmapGFF.h
index 5c9970606..82a594796 100755
--- a/src/include/ZMap/zmapGFF.h
+++ b/src/include/ZMap/zmapGFF.h
@@ -30,7 +30,7 @@
* HISTORY:
* Last edited: Apr 21 18:23 2010 (edgrif)
* Created: Sat May 29 13:18:32 2004 (edgrif)
- * CVS info: $Id: zmapGFF.h,v 1.23 2010-05-19 13:15:31 mh17 Exp $
+ * CVS info: $Id: zmapGFF.h,v 1.24 2010-06-08 08:31:23 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_GFF_H
@@ -104,7 +104,7 @@ typedef struct
ZMapGFFParser zMapGFFCreateParser(void) ;
-gboolean zMapGFFParserInitForFeatures(ZMapGFFParser parser, GData *sources, gboolean parse_only) ;
+gboolean zMapGFFParserInitForFeatures(ZMapGFFParser parser, GHashTable *sources, gboolean parse_only) ;
gboolean zMapGFFParseHeader(ZMapGFFParser parser, char *line, gboolean *header_finished) ;
gboolean zMapGFFParseLine(ZMapGFFParser parser, char *line) ;
gboolean zMapGFFParseLineLength(ZMapGFFParser parser, char *line, gsize line_length) ;
@@ -128,10 +128,10 @@ gboolean zMapGFFTerminated(ZMapGFFParser parser) ;
void zMapGFFSetFreeOnDestroy(ZMapGFFParser parser, gboolean free_on_destroy) ;
void zMapGFFDestroyParser(ZMapGFFParser parser) ;
-gboolean zMapGFFDump(ZMapFeatureAny dump_set, GData *styles, GIOChannel *file, GError **error_out);
-gboolean zMapGFFDumpRegion(ZMapFeatureAny dump_set, GData *styles,
+gboolean zMapGFFDump(ZMapFeatureAny dump_set, GHashTable *styles, GIOChannel *file, GError **error_out);
+gboolean zMapGFFDumpRegion(ZMapFeatureAny dump_set, GHashTable *styles,
ZMapSpan region_span, GIOChannel *file, GError **error_out) ;
-gboolean zMapGFFDumpForeachList(ZMapFeatureAny first_feature, GData *styles,
+gboolean zMapGFFDumpForeachList(ZMapFeatureAny first_feature, GHashTable *styles,
GIOChannel *file, GError **error_out,
char *sequence,
GFunc *list_func_out, gpointer *list_data_out) ;
diff --git a/src/include/ZMap/zmapServerProtocol.h b/src/include/ZMap/zmapServerProtocol.h
index 74774b3a3..8f05cb984 100755
--- a/src/include/ZMap/zmapServerProtocol.h
+++ b/src/include/ZMap/zmapServerProtocol.h
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Jan 14 09:49 2010 (edgrif)
* Created: Wed Feb 2 11:47:16 2005 (edgrif)
- * CVS info: $Id: zmapServerProtocol.h,v 1.33 2010-05-17 14:41:15 mh17 Exp $
+ * CVS info: $Id: zmapServerProtocol.h,v 1.34 2010-06-08 08:31:23 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_PROTOCOL_H
@@ -182,7 +182,7 @@ typedef struct
* themseleves. This is completely data source dependent. */
gboolean server_styles_have_mode ;
- GData *styles_out ; /* List of prespecified styles or NULL
+ GHashTable *styles_out ; /* List of prespecified styles or NULL
to get all available styles. */
} ZMapServerReqStylesStruct, *ZMapServerReqStyles ;
@@ -204,7 +204,7 @@ typedef struct
ZMapServerReqType type ;
ZMapServerResponseType response ;
- GData *styles ; /* Needed for some features to control
+ GHashTable *styles ; /* Needed for some features to control
how they are fetched. */
ZMapFeatureContext context ; /* Returned feature sets. */
diff --git a/src/include/ZMap/zmapStyle.h b/src/include/ZMap/zmapStyle.h
index f57a7d925..e254e7463 100755
--- a/src/include/ZMap/zmapStyle.h
+++ b/src/include/ZMap/zmapStyle.h
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: Jan 26 08:42 2010 (edgrif)
* Created: Mon Feb 26 09:28:26 2007 (edgrif)
- * CVS info: $Id: zmapStyle.h,v 1.57 2010-05-26 12:02:49 mh17 Exp $
+ * CVS info: $Id: zmapStyle.h,v 1.58 2010-06-08 08:31:23 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_STYLE_H
@@ -453,16 +453,337 @@ ZMAP_DEFINE_ENUM(ZMapStyleMergeMode, ZMAP_STYLE_MERGE_MODE_LIST) ;
/* Note the naming here in the macros. ZMAP_TYPE_FEATURE_TYPE_STYLE seemed confusing... */
#define ZMAP_TYPE_FEATURE_STYLE (zMapFeatureTypeStyleGetType())
+
+#if GOBJ_CAST
+#define ZMAP_FEATURE_STYLE(obj) ((ZMapFeatureTypeStyle) obj)
+#define ZMAP_FEATURE_STYLE_CONST(obj) ((ZMapFeatureTypeStyle const) obj)
+#else
#define ZMAP_FEATURE_STYLE(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_FEATURE_STYLE, zmapFeatureTypeStyle))
#define ZMAP_FEATURE_STYLE_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_FEATURE_STYLE, zmapFeatureTypeStyle const))
+#endif
+
#define ZMAP_FEATURE_STYLE_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_FEATURE_STYLE, zmapFeatureTypeStyleClass))
#define ZMAP_IS_FEATURE_STYLE(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_FEATURE_STYLE))
#define ZMAP_FEATURE_STYLE_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_FEATURE_STYLE, zmapFeatureTypeStyleClass))
-/* Instance */
-typedef struct _zmapFeatureTypeStyleStruct zmapFeatureTypeStyle, *ZMapFeatureTypeStyle ;
+// ----- style structs moved here for faster access ------
+
+/*! @addtogroup zmapstyles
+ * @{
+ * */
+
+
+/*! @struct ZMapStyleColour zmapStyle_P.h
+ * @brief ZMap object colours
+ *
+ * All ZMap objects can potentially have a border colour, a fill colour and a draw colour
+ * which can be used to "draw" over the fill colour. */
+
+typedef struct
+{
+ struct
+ {
+ unsigned int draw : 1 ;
+ unsigned int fill : 1 ;
+ unsigned int border : 1 ;
+ } fields_set ;
+
+ GdkColor draw ; /* Overlaid on fill colour. */
+ GdkColor fill ; /* Fill/background colour. */
+ GdkColor border ; /* Surround/line colour. */
+} ZMapStyleColourStruct, *ZMapStyleColour ;
+
+
+/*! @struct ZMapStyleFullColour zmapStyle_P.h
+ * @brief ZMap feature colours
+ *
+ * All features in ZMap can be selected and hence must have both "normal" and "selected"
+ * colours. */
+typedef struct
+{
+ ZMapStyleColourStruct normal ;
+ ZMapStyleColourStruct selected ;
+} ZMapStyleFullColourStruct, *ZMapStyleFullColour ;
+
+/* At most 6 colour specs can be given for any one field (i.e. all the combinations of selected,
+ * normal and draw, fill, border. */
+enum {ZMAPSTYLE_MAX_COLOUR_SPECS = 6} ;/* Instance */
+
+
+
+
+/*! Styles have different modes, e.g. graph, alignment etc, information specific to a particular
+ * style is held in its own struct. */
+
+
+/*! @struct ZMapBasicGraph zmapStyle_P.h
+ * @brief Basic feature
+ *
+ * < currently this is empty > */
+typedef struct
+{
+ char *dummy ;
+
+} ZMapStyleBasicStruct, *ZMapStyleBasic ;
+
+/*! @struct ZMapSequenceGraph zmapStyle_P.h
+ * @brief Sequence feature
+ *
+ * (currently this is empty) */
+typedef struct
+{
+ char *dummy ;
+
+} ZMapStyleSequenceStruct, *ZMapStyleSequence ;
+
+/*! @struct ZMapTextGraph zmapStyle_P.h
+ * @brief Text feature
+ *
+ * (currently this is empty) */
+typedef struct
+{
+ char *font;
+
+} ZMapStyleTextStruct, *ZMapStyleText ;
+
+
+
+/*! @struct ZMapStyleGraph zmapStyle_P.h
+ * @brief Graph feature
+ *
+ * Draws a feature as a graph, the feature must contain graph points. */
+typedef struct
+{
+ ZMapStyleGraphMode mode ; /*!< Graph style. */
+
+ double baseline ; /*!< zero level for graph. */
+
+} ZMapStyleGraphStruct, *ZMapStyleGraph ;
+
+
+
+
+
+/*! @struct ZMapStyleGlyph zmapStyle_P.h
+ * @brief Glyph feature
+ *
+ * Draws shapes of various kinds, e.g. splice site indicators etc. */
+typedef struct
+{
+ // sub feature glyphs or glyphs for glyph mode
+ GQuark glyph_name,glyph_name_5,glyph_name_3;
+ ZMapStyleGlyphShapeStruct glyph; // single glyph or unspecified 5' or 3' end
+ ZMapStyleGlyphShapeStruct glyph5; // shape for 5' end
+ ZMapStyleGlyphShapeStruct glyph3; // shape for 3' end
+ ZMapStyleFullColourStruct glyph_alt_colours;
+ ZMapStyleGlyphStrand glyph_strand;
+ ZMapStyleGlyphAlign glyph_align;
+ guint glyph_threshold;
+
+} ZMapStyleGlyphStruct, *ZMapStyleGlyph ;
+
+
+
+/*! @struct ZMapStyleAlignment zmapStyle_P.h
+ * @brief Alignment feature
+ *
+ * Draws an alignment as a series of blocks joined by straight lines. The lines can be coloured
+ * to indicate colinearity between adjacent blocks. */
+typedef struct
+ {
+ /* If set then blixem will be run with nucleotide or peptide sequences for the features. */
+ ZMapStyleBlixemType blixem_type ;
+
+ gboolean pfetchable ; /* TRUE => alignments have pfetch entries. */
+
+ gboolean allow_misalign; /* TRUE => ref and match sequences
+ don't have to be exactly same
+ length, ref coords dominate. */
+
+ /*! Allowable align errors, used to decide whether a match should be classified as "perfect".
+ * between_align_error is used to assess several alignments (e.g. for exon matches) if join_homols = TRUE
+ *
+ * Number is allowable number of missing bases between blocks/alignments, default is 0. */
+ unsigned int between_align_error ;
+
+ /*! Colours for bars joining up intra/inter alignment gaps. */
+ ZMapStyleFullColourStruct perfect ;
+ ZMapStyleFullColourStruct colinear ;
+ ZMapStyleFullColourStruct noncolinear ;
+ ZMapStyleColumnDisplayState unmarked_colinear; /* paint colinear lines even if not marked */
+
+ /* Options for processing gapped aligns. */
+ gboolean parse_gaps ; /* TRUE means parse gaps from input data, */
+ gboolean show_gaps ; /* TRUE means gaps within alignment are displayed,
+ otherwise alignment is displayed as a single block. */
+
+} ZMapStyleAlignmentStruct, *ZMapStyleAlignment ;
+
+
+/*! @struct ZMapStyleTranscript zmapStyle_P.h
+ * @brief Transcript feature
+ *
+ * Draws a transcript as a series of boxes joined by angled lines. */
+typedef struct
+{
+ ZMapStyleFullColourStruct CDS_colours ; /*!< Colour for CDS part of feature. */
+
+} ZMapStyleTranscriptStruct, *ZMapStyleTranscript ;
+
+
+/*! @struct ZMapStyleAssemblyPath zmapStyle_P.h
+ * @brief AssemblyPath feature
+ *
+ * Draws an assembly path as a series of boxes placed alternately to form a tiling path. */
+typedef struct
+{
+ ZMapStyleFullColourStruct non_path_colours ; /*!< Colour for non-assembly part of feature. */
+
+} ZMapStyleAssemblyPathStruct, *ZMapStyleAssemblyPath ;
+
+
+/* THIS STRUCT NEEDS A MAGIC PTR, ONCE IT HAS ONE THEN ADD A TEST TO zmapStyleIsValid() FOR IT.... */
+
+/*! @struct ZMapFeatureTypeStyle zmapStyle_P.h
+ * @brief ZMap Style
+ *
+ * ZMap Style definition, the style must have a mode which specifies what sort of
+ * of feature the style represents. */
+typedef struct //_zmapFeatureTypeStyleStruct
+{
+ GObject __parent__;
+
+#define STYLE_IS_SET_SIZE ((_STYLE_PROP_N_ITEMS + 7) / 8)
+ guchar is_set[STYLE_IS_SET_SIZE]; // flags to say whether fields are set
+ // includes mode dependant fields
+ // but colours have thier own flags
+
+ /*! _All_ styles must have these fields set, no other fields are compulsory. */
+ GQuark original_id ; /*!< Original name. */
+ GQuark unique_id ; /*!< Name normalised to be unique. */
+
+
+ /*! Data fields for the style. */
+
+
+ GQuark parent_id ; /*!< Styles can inherit from other
+ styles, the parent style _must_ be
+ identified by its unique id. */
+
+ char *description ; /*!< Description of what this style
+ represents. */
+
+ ZMapStyleMode mode ; /*!< Specifies how features that
+ reference this style will be processed. */
+ // must be set before setting mode dependant fields
+ // and may not be unset/changed afterwards
+
+ GQuark sub_features[ZMAPSTYLE_SUB_FEATURE_MAX]; // style ID quarks indexed by SUBFEATURE ENUM
+
+ ZMapStyleFullColourStruct colours ; /*!< Main feature colours. */
+
+ /*! Colours for when feature is shown in frames. */
+ ZMapStyleFullColourStruct frame0_colours ;
+ ZMapStyleFullColourStruct frame1_colours ;
+ ZMapStyleFullColourStruct frame2_colours ;
+
+ /*! Colours for when feature is shown stranded by colour */
+ ZMapStyleFullColourStruct strand_rev_colours;
+
+
+ ZMapStyleColumnDisplayState col_display_state ; /* Controls how/when col is displayed. */
+
+ ZMapStyleBumpMode default_bump_mode ; /*!< Allows return to original bump mode. */
+ ZMapStyleBumpMode curr_bump_mode ; /*!< Controls how features are grouped
+ into sub columns within a column. */
+ double bump_spacing ; /*!< gap between bumped features. */
+
+ ZMapStyle3FrameMode frame_mode ; /*!< Controls how frame sensitive
+ features are displayed. */
+
+ double min_mag ; /*!< Don't display if fewer bases/line */
+ double max_mag ; /*!< Don't display if more bases/line */
+
+ double width ; /*!< column width */
+
+ ZMapStyleScoreMode score_mode ; /*!< Controls width of features that
+ have scores. */
+ double min_score, max_score ; /*!< Min/max for score width calc. */
+
+
+ /*! GFF feature dumping, allows specifying of source/feature types independently of feature
+ * attributes. */
+ GQuark gff_source ;
+ GQuark gff_feature ;
+
+
+ /*! State information for the style. */
+ gboolean displayable; /* FALSE means never, ever display,
+ for TRUE see col_display_state. */
+
+
+ gboolean show_when_empty; /*!< If FALSE, features' column is
+ displayed even if there are no features. */
+ gboolean bump_fixed; /*!< If TRUE then bump mode cannot be changed. */
+
+ gboolean showText; /*!< Should feature text be displayed. */
+
+ /*! Strand, show reverse and frame are all linked: something that is frame specific must be
+ * strand specific as well.... */
+ gboolean strand_specific; /*!< Feature that is on one strand of the dna. */
+ gboolean show_rev_strand; /*!< Only display the feature on the
+ reverse strand if this is set. */
+ gboolean hide_fwd_strand; /* don't show the fwd strand when revcomp'd */
+ gboolean show_only_in_separator;
+
+ gboolean directional_end; /*!< Display pointy ends on exons etc. */
+
+ gboolean deferred; /* flag for to say if this style is deferred loaded */
+
+ gboolean loaded; /* flag to say if we're loaded */
+
+ gboolean inherited; // style has inherited it's parents
+
+ /*! Mode specific fields, see docs for individual structs. */
+ union
+ {
+ ZMapStyleBasicStruct basic ;
+ ZMapStyleSequenceStruct sequence ;
+ ZMapStyleTextStruct text ;
+ ZMapStyleTranscriptStruct transcript ;
+ ZMapStyleAssemblyPathStruct assembly_path ;
+ ZMapStyleAlignmentStruct alignment ;
+ ZMapStyleGraphStruct graph ;
+ ZMapStyleGlyphStruct glyph ;
+ } mode_data ;
+
+
+} zmapFeatureTypeStyleStruct,
+#ifdef ZMAPSTYLE_INTERNAL
+zmapFeatureTypeStyle, *ZMapFeatureTypeStyle;
+#else
+zmapFeatureTypeStyle;
+
+// non internal functions can ref style members but not change them
+// MH17: why have I never liked typedefs?
+// is it because they have to so finely balanced that you can't make them compile??
+// we need a pointer to a const style not a const pointer to a volatile style
+// typdefs are atomic and not text substitutions.
+// try 'google C typedef const pointer' for a few explanations
+typedef const zmapFeatureTypeStyle* ZMapFeatureTypeStyle ;
+#endif
+
+
+
+/* Instance */
+//#ifdef ZMAPSTYLE_INTERNAL
+//typedef struct _zmapFeatureTypeStyleStruct zmapFeatureTypeStyle, *ZMapFeatureTypeStyle ;
+//#else
+// read-only for the public
+//typedef struct _zmapFeatureTypeStyleStruct zmapFeatureTypeStyle, *ZMapFeatureTypeStyle const ;
+//#endif
/* Class */
typedef struct _zmapFeatureTypeStyleClassStruct zmapFeatureTypeStyleClass, *ZMapFeatureTypeStyleClass ;
@@ -471,6 +792,8 @@ typedef struct _zmapFeatureTypeStyleClassStruct zmapFeatureTypeStyleClass, *ZMa
+
+
/* Public funcs */
GType zMapFeatureTypeStyleGetType(void);
@@ -531,58 +854,85 @@ gboolean zMapStyleIsTrueFeature(ZMapFeatureTypeStyle style) ;
ZMapStyleGlyphShape zMapStyleGetGlyphShape(gchar *shape);
ZMapFeatureTypeStyle zMapStyleLegacyStyle(char *name);
-unsigned int zmapStyleGetWithinAlignError(ZMapFeatureTypeStyle style) ;
-GQuark zMapStyleGetUniqueID(ZMapFeatureTypeStyle style) ;
-GQuark zMapStyleGetID(ZMapFeatureTypeStyle style) ;
+//unsigned int zmapStyleGetWithinAlignError(ZMapFeatureTypeStyle style) ;
+#define zMapStyleGetWithinAlignError(style) (style->mode_data.alignment.between_align_error)
+//GQuark zMapStyleGetUniqueID(ZMapFeatureTypeStyle style) ;
+#define zMapStyleGetUniqueID(style) (style->unique_id)
+//GQuark zMapStyleGetID(ZMapFeatureTypeStyle style) ;
+#define zMapStyleGetID(style) (style->original_id)
+
GQuark zMapStyleGetSubFeature(ZMapFeatureTypeStyle style,ZMapStyleSubFeature i);
gboolean zMapStyleSetColours(ZMapFeatureTypeStyle style, ZMapStyleParamId target, ZMapStyleColourType type,
char *fill, char *draw, char *border) ;
void zMapStyleSetDisplay(ZMapFeatureTypeStyle style, ZMapStyleColumnDisplayState col_show) ;
void zMapStyleSetMode(ZMapFeatureTypeStyle style, ZMapStyleMode mode) ;
-ZMapStyleMode zMapStyleGetMode(ZMapFeatureTypeStyle style) ;
-const gchar *zMapStyleGetName(ZMapFeatureTypeStyle style) ;
-ZMapStyleScoreMode zMapStyleGetScoreMode(ZMapFeatureTypeStyle style);
-ZMapStyleBumpMode zMapStyleGetBumpMode(ZMapFeatureTypeStyle style) ;
+//ZMapStyleMode zMapStyleGetMode(ZMapFeatureTypeStyle style) ;
+#define zMapStyleGetMode(style) (style->mode)
+//const gchar *zMapStyleGetName(ZMapFeatureTypeStyle style) ;
+#define zMapStyleGetName(style) (g_quark_to_string(style->original_id))
+//ZMapStyleScoreMode zMapStyleGetScoreMode(ZMapFeatureTypeStyle style);
+#define zMapStyleGetScoreMode(style) (style->score_mode)
+//ZMapStyleBumpMode zMapStyleGetBumpMode(ZMapFeatureTypeStyle style) ;
+#define zMapStyleGetBumpMode(style) (style->curr_bump_mode)
void zMapStyleSetBumpMode(ZMapFeatureTypeStyle style, ZMapStyleBumpMode bump_mode) ;
-const gchar *zMapStyleGetGFFSource(ZMapFeatureTypeStyle style) ;
-const gchar *zMapStyleGetGFFFeature(ZMapFeatureTypeStyle style) ;
+//const gchar *zMapStyleGetGFFSource(ZMapFeatureTypeStyle style) ;
+#define zMapStyleGetGFFSource(style) g_quark_to_string(style->gff_source) // NULL quark gives NULL string
+//const gchar *zMapStyleGetGFFFeature(ZMapFeatureTypeStyle style) ;
+#define zMapStyleGetGFFFeature(style) g_quark_to_string(style->gff_feature)
void zMapStyleSetDescription(ZMapFeatureTypeStyle style, char *description) ;
-ZMapStyleBumpMode zMapStyleGetDefaultBumpMode(ZMapFeatureTypeStyle style);
-double zMapStyleGetWidth(ZMapFeatureTypeStyle style) ;
-double zMapStyleGetBumpSpace(ZMapFeatureTypeStyle style) ;
-ZMapStyleColumnDisplayState zMapStyleGetDisplay(ZMapFeatureTypeStyle style) ;
-
-ZMapStyleGlyphShape zMapStyleGlyphShape(ZMapFeatureTypeStyle style);
+//ZMapStyleBumpMode zMapStyleGetDefaultBumpMode(ZMapFeatureTypeStyle style);
+#define zMapStyleGetDefaultBumpMode(style) (style->default_bump_mode)
+//double zMapStyleGetWidth(ZMapFeatureTypeStyle style) ;
+#define zMapStyleGetWidth(style) (style->width)
+//double zMapStyleGetBumpSpace(ZMapFeatureTypeStyle style) ;
+#define zMapStyleGetBumpSpace(style) (style->bump_spacing)
+//ZMapStyleColumnDisplayState zMapStyleGetDisplay(ZMapFeatureTypeStyle style) ;
+#define zMapStyleGetDisplay(style) (style->col_display_state)
+
+//ZMapStyleGlyphShape zMapStyleGlyphShape(ZMapFeatureTypeStyle style);
+#define zMapStyleGlyphShape(style) (&style->mode_data.glyph.glyph)
ZMapStyleGlyphShape zMapStyleGlyphShape5(ZMapFeatureTypeStyle style);
ZMapStyleGlyphShape zMapStyleGlyphShape3(ZMapFeatureTypeStyle style);
void zMapStyleSetShowGaps(ZMapFeatureTypeStyle style, gboolean show_gaps) ;
void zMapStyleSetJoinAligns(ZMapFeatureTypeStyle style, unsigned int between_align_error) ;
-GQuark zMapStyleGetID(ZMapFeatureTypeStyle style) ;
-double zMapStyleGetMinMag(ZMapFeatureTypeStyle style) ;
-double zMapStyleGetMaxMag(ZMapFeatureTypeStyle style) ;
+
+//double zMapStyleGetMinMag(ZMapFeatureTypeStyle style) ;
+#define zMapStyleGetMinMag(style) (style->min_mag)
+//double zMapStyleGetMaxMag(ZMapFeatureTypeStyle style) ;
+#define zMapStyleGetMaxMag(style) (style->max_mag)
void zMapStyleGetStrandAttrs(ZMapFeatureTypeStyle type,
gboolean *strand_specific, gboolean *show_rev_strand, ZMapStyle3FrameMode *frame_mode) ;
-double zMapStyleGetMaxScore(ZMapFeatureTypeStyle style) ;
-double zMapStyleGetMinScore(ZMapFeatureTypeStyle style) ;
-gboolean zMapStyleGetShowWhenEmpty(ZMapFeatureTypeStyle style);
+//double zMapStyleGetMaxScore(ZMapFeatureTypeStyle style) ;
+#define zMapStyleGetMaxScore(style) (style->max_score)
+//double zMapStyleGetMinScore(ZMapFeatureTypeStyle style) ;
+#define zMapStyleGetMinScore(style) (style->min_score)
+//gboolean zMapStyleGetShowWhenEmpty(ZMapFeatureTypeStyle style);
+#define zMapStyleGetShowWhenEmpty(style) (style->show_when_empty)
gboolean zMapStyleGetColours(ZMapFeatureTypeStyle style, ZMapStyleParamId target, ZMapStyleColourType type,
GdkColor **fill, GdkColor **draw, GdkColor **border) ;
gboolean zMapStyleGetColoursDefault(ZMapFeatureTypeStyle style,
GdkColor **background, GdkColor **foreground, GdkColor **outline);
-char *zMapStyleGetDescription(ZMapFeatureTypeStyle style) ;
-double zMapStyleGetWidth(ZMapFeatureTypeStyle style) ;
+//char *zMapStyleGetDescription(ZMapFeatureTypeStyle style) ;
+#define zMapStyleGetDescription(style) (style->description)
+
+
+//int zMapStyleGlyphThreshold(ZMapFeatureTypeStyle style);
+#define zMapStyleGlyphThreshold(style) (style->mode_data.glyph.glyph_threshold)
-int zMapStyleGlyphThreshold(ZMapFeatureTypeStyle style);
+#define zMapStyleGetUnmarked(style) (style->mode_data.alignment.unmarked_colinear)
-ZMapStyleGlyphStrand zMapStyleGlyphStrand(ZMapFeatureTypeStyle style);
-ZMapStyleGlyphAlign zMapStyleGetAlign(ZMapFeatureTypeStyle style);
+//ZMapStyleGlyphStrand zMapStyleGlyphStrand(ZMapFeatureTypeStyle style);
+#define zMapStyleGlyphStrand(style) (style->mode_data.glyph.glyph_strand)
+//ZMapStyleGlyphAlign zMapStyleGetAlign(ZMapFeatureTypeStyle style);
+#define zMapStyleGetAlign(style) (style->mode_data.glyph.glyph_align)
-void zMapStyleGetGappedAligns(ZMapFeatureTypeStyle style, gboolean *parse_gaps, gboolean *show_gaps) ;
+//void zMapStyleGetGappedAligns(ZMapFeatureTypeStyle style, gboolean *parse_gaps, gboolean *show_gaps) ;
-double zMapStyleGetBumpWidth(ZMapFeatureTypeStyle style) ;
+//double zMapStyleGetBumpWidth(ZMapFeatureTypeStyle style) ;
+#define zMapStyleGetBumpWidth(style) (style->bump_spacing) // yes really
void zMapStyleSetParent(ZMapFeatureTypeStyle style, char *parent_name) ;
void zMapStyleSetMag(ZMapFeatureTypeStyle style, double min_mag, double max_mag) ;
void zMapStyleSetGraph(ZMapFeatureTypeStyle style, ZMapStyleGraphMode mode, double min, double max, double baseline) ;
@@ -598,7 +948,7 @@ void zMapStyleSetEndStyle(ZMapFeatureTypeStyle style, gboolean directional) ;
void zMapStyleSetGappedAligns(ZMapFeatureTypeStyle style, gboolean parse_gaps, gboolean show_gaps) ;
-gboolean zMapStyleGetJoinAligns(ZMapFeatureTypeStyle style, unsigned int *between_align_error) ;
+//gboolean zMapStyleGetJoinAligns(ZMapFeatureTypeStyle style, unsigned int *between_align_error) ;
void zMapStyleSetBumpSpace(ZMapFeatureTypeStyle style, double bump_spacing) ;
void zMapStyleSetShowWhenEmpty(ZMapFeatureTypeStyle style, gboolean show_when_empty) ;
void zMapStyleSetPfetch(ZMapFeatureTypeStyle style, gboolean pfetchable) ;
@@ -620,27 +970,36 @@ gboolean zMapStyleIsOutlineColour(ZMapFeatureTypeStyle style) ;
gboolean zMapStyleColourByStrand(ZMapFeatureTypeStyle style);
-ZMapStyleGlyphStrand zMapStyleGlyphStrand(ZMapFeatureTypeStyle style);
-gboolean zMapStyleIsDirectionalEnd(ZMapFeatureTypeStyle style) ;
+//gboolean zMapStyleIsDirectionalEnd(ZMapFeatureTypeStyle style) ;
+#define zMapStyleIsDirectionalEnd(style) (style->directional_end)
-gboolean zMapStyleIsDisplayable(ZMapFeatureTypeStyle style) ;
+//gboolean zMapStyleIsDisplayable(ZMapFeatureTypeStyle style) ;
+#define zMapStyleIsDisplayable(style) (style->displayable)
-gboolean zMapStyleIsDeferred(ZMapFeatureTypeStyle style) ;
+//gboolean zMapStyleIsDeferred(ZMapFeatureTypeStyle style) ;
+#define zMapStyleIsDeferred(style) (style->deferred)
-gboolean zMapStyleIsLoaded(ZMapFeatureTypeStyle style) ;
+//gboolean zMapStyleIsLoaded(ZMapFeatureTypeStyle style) ;
+#define zMapStyleIsLoaded(style) (style->loaded)
-gboolean zMapStyleIsHidden(ZMapFeatureTypeStyle style) ;
+//gboolean zMapStyleIsHidden(ZMapFeatureTypeStyle style) ;
+#define zMapStyleIsHidden(style) (style->col_display_state == ZMAPSTYLE_COLDISPLAY_HIDE)
-gboolean zMapStyleIsStrandSpecific(ZMapFeatureTypeStyle style) ;
-gboolean zMapStyleIsShowReverseStrand(ZMapFeatureTypeStyle style) ;
-gboolean zMapStyleIsHideForwardStrand(ZMapFeatureTypeStyle style) ;
+//gboolean zMapStyleIsStrandSpecific(ZMapFeatureTypeStyle style) ;
+#define zMapStyleIsStrandSpecific(style) (style->strand_specific)
+//gboolean zMapStyleIsShowReverseStrand(ZMapFeatureTypeStyle style) ;
+#define zMapStyleIsShowReverseStrand(style) (style->show_rev_strand)
+//gboolean zMapStyleIsHideForwardStrand(ZMapFeatureTypeStyle style) ;
+#define zMapStyleIsHideForwardStrand(style) (style->hide_fwd_strand)
gboolean zMapStyleIsFrameSpecific(ZMapFeatureTypeStyle style) ;
-gboolean zMapStyleIsFrameOneColumn(ZMapFeatureTypeStyle style) ;
+//gboolean zMapStyleIsFrameOneColumn(ZMapFeatureTypeStyle style) ;
+#define zMapStyleIsFrameOneColumn(style) (style->frame_mode == ZMAPSTYLE_3_FRAME_ONLY_1)
-double zMapStyleBaseline(ZMapFeatureTypeStyle style) ;
+//double zMapStyleBaseline(ZMapFeatureTypeStyle style) ;
+#define zMapStyleBaseline(style) (style->mode_data.graph.baseline)
gboolean zMapStyleIsMinMag(ZMapFeatureTypeStyle style, double *min_mag) ;
gboolean zMapStyleIsMaxMag(ZMapFeatureTypeStyle style, double *max_mag) ;
@@ -651,8 +1010,10 @@ ZMapFeatureTypeStyle zMapFeatureTypeCreate(char *name, char *description) ;
gboolean zMapStyleHasMode(ZMapFeatureTypeStyle style);
-gboolean zMapStyleIsParseGaps(ZMapFeatureTypeStyle style) ;
-gboolean zMapStyleIsShowGaps(ZMapFeatureTypeStyle style) ;
+//gboolean zMapStyleIsParseGaps(ZMapFeatureTypeStyle style) ;
+#define zMapStyleIsParseGaps(style) (style->mode_data.alignment.parse_gaps)
+//gboolean zMapStyleIsShowGaps(ZMapFeatureTypeStyle style) ;
+#define zMapStyleIsShowGaps(style) (style->mode_data.alignment.show_gaps)
char *zMapStyleCreateName(char *style_name) ;
@@ -660,7 +1021,6 @@ GQuark zMapStyleCreateID(char *style_name) ;
ZMapFeatureTypeStyle zMapStyleGetPredefined(char *style_name) ;
-gboolean zMapFeatureTypeSetAugment(GData **current, GData **new) ;
void zMapStyleInitBumpMode(ZMapFeatureTypeStyle style,
ZMapStyleBumpMode default_bump_mode, ZMapStyleBumpMode curr_bump_mode) ;
@@ -674,19 +1034,20 @@ gboolean zMapStyleMerge(ZMapFeatureTypeStyle curr_style, ZMapFeatureTypeStyle ne
-gboolean zMapStyleDisplayInSeparator(ZMapFeatureTypeStyle style);
+//gboolean zMapStyleDisplayInSeparator(ZMapFeatureTypeStyle style);
+#define zMapStyleDisplayInSeparator(style) (style->show_only_in_separator)
/* Style set functions... */
-gboolean zMapStyleSetAdd(GData **style_set, ZMapFeatureTypeStyle style) ;
-gboolean zMapStyleCopyAllStyles(GData **style_set, GData **copy_style_set_out) ;
-gboolean zMapStyleInheritAllStyles(GData **style_set) ;
+gboolean zMapStyleSetAdd(GHashTable *style_set, ZMapFeatureTypeStyle style) ;
+gboolean zMapStyleCopyAllStyles(GHashTable *style_set, GHashTable **copy_style_set_out) ;
+gboolean zMapStyleInheritAllStyles(GHashTable *style_set) ;
gboolean zMapStyleNameExists(GList *style_name_list, char *style_name) ;
-ZMapFeatureTypeStyle zMapFindStyle(GData *styles, GQuark style_id) ;
-GList *zMapStylesGetNames(GData *styles) ;
-GData *zMapStyleGetAllPredefined(void) ;
-GData *zMapStyleMergeStyles(GData *curr_styles, GData *new_styles, ZMapStyleMergeMode merge_mode) ;
-void zMapStyleDestroyStyles(GData **styles) ;
+ZMapFeatureTypeStyle zMapFindStyle(GHashTable *styles, GQuark style_id) ;
+GList *zMapStylesGetNames(GHashTable *styles) ;
+GHashTable *zMapStyleGetAllPredefined(void) ;
+GHashTable *zMapStyleMergeStyles(GHashTable *curr_styles, GHashTable *new_styles, ZMapStyleMergeMode merge_mode) ;
+void zMapStyleDestroyStyles(GHashTable *styles) ;
@@ -694,8 +1055,8 @@ void zMapStyleDestroyStyles(GData **styles) ;
void zMapStylePrint(ZMapIOOut dest, ZMapFeatureTypeStyle style, char *prefix, gboolean full) ;
-void zMapStyleSetPrintAll(ZMapIOOut dest, GData *type_set, char *user_string, gboolean full) ;
-void zMapStyleSetPrintAllStdOut(GData *type_set, char *user_string, gboolean full) ;
+void zMapStyleSetPrintAll(ZMapIOOut dest, GHashTable *type_set, char *user_string, gboolean full) ;
+void zMapStyleSetPrintAllStdOut(GHashTable *type_set, char *user_string, gboolean full) ;
void zMapStyleListPrintAll(ZMapIOOut dest, GList *styles, char *user_string, gboolean full) ;
diff --git a/src/include/ZMap/zmapUtilsDebug.h b/src/include/ZMap/zmapUtilsDebug.h
index 28c25f4a0..3fa8c204e 100755
--- a/src/include/ZMap/zmapUtilsDebug.h
+++ b/src/include/ZMap/zmapUtilsDebug.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,11 +23,11 @@
* Rob Clack (Sanger Institute, UK) rnc@sanger.ac.uk
*
* Description: Contains macros, functions etc. useful for testing/debugging.
- *
+ *
* HISTORY:
* Last edited: Mar 12 12:58 2010 (edgrif)
* Created: Mon Mar 29 16:51:28 2004 (edgrif)
- * CVS info: $Id: zmapUtilsDebug.h,v 1.11 2010-03-12 12:59:02 edgrif Exp $
+ * CVS info: $Id: zmapUtilsDebug.h,v 1.12 2010-06-08 08:31:23 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_UTILS_DEBUG_H
@@ -69,7 +69,7 @@ G_STMT_START{ \
/* Define debug messages more easily. */
-#ifdef __GNUC__
+#ifdef __GNUC__
#define zMapDebugPrint(BOOLEAN_VAR, FORMAT, ...) \
G_STMT_START \
{ \
@@ -88,12 +88,13 @@ G_STMT_START{ \
/* Timer functions, just simplifies printing etc a bit and provides a global timer if required.
* Just comment out #define ZMAP_DISABLE_TIMER to turn it all on.
*/
-#define ZMAP_DISABLE_TIMER
+// make this into a build option
+//#define ZMAP_DISABLE_TIMER
#ifdef ZMAP_DISABLE_TIMER
-
+// the void zero bit is so we can have a semicolon after the call.
#define zMapStartTimer(TIMER_PTR) (void)0
#define zMapPrintTimer(TIMER, TEXT) (void)0
#define zMapResetTimer(TIMER) (void)0
@@ -101,29 +102,51 @@ G_STMT_START{ \
#else
-/* Define reference to global timer. */
+/* Define reference to global timer from view creation */
#define ZMAP_GLOBAL_TIMER zmap_global_timer_G
extern GTimer *ZMAP_GLOBAL_TIMER ;
-
-/* A bit clumsy but couldn't see a neat way to allow just putting NULL for the timer to get
- * the global one.
- * Do this for the global one: zMapStartTimer(ZMAP_GLOBAL_TIMER) ;
- * and this for your one: zMapStartTimer(your_timer_ptr) ;
- * */
-#define zMapStartTimer(TIMER_PTR) \
-(TIMER_PTR) = g_timer_new()
-
+extern gboolean zmap_timing_G;
+
+#define zMapInitTimer() \
+ if(zmap_timing_G) \
+ { GTimeVal gtv; \
+ GDate gd; \
+ if(ZMAP_GLOBAL_TIMER) \
+ g_timer_reset(ZMAP_GLOBAL_TIMER); \
+ else \
+ ZMAP_GLOBAL_TIMER = g_timer_new();\
+ g_get_current_time(>v);\
+ g_date_set_time_val(&gd,>v);\
+ printf("# %s\t%02d/%02d/%4d\n",zMapConfigDirGetFile(),\
+ g_date_get_day (&gd), g_date_get_month(&gd),g_date_get_year(&gd));\
+ zMapPrintTime("Reset","Timer","");\
+ }
+
+
+// this output format is TAB delimited.
+// Func is Start or Stop
+// ID may be readable text but may not contain TABS.
+// OPT is another (descriptive) text string
+// timings in seconds.milliseconds
+// output is now configured from [ZMap] - can leave code compiled in
+// NULL args shoudl be ""
+#define zMapPrintTime(FUNC, ID, OPT) \
+ { if(ZMAP_GLOBAL_TIMER) \
+ printf("%s\t%.3f\t%s\t%s\n", \
+ FUNC,\
+ g_timer_elapsed(ZMAP_GLOBAL_TIMER, NULL),\
+ ID,OPT); \
+ }
+
+// can use start then stop, but stop on its own can be interpreted as previous event as start
+#define zMapStartTimer(TEXT,OPT) zMapPrintTime("Start",TEXT,OPT)
+#define zMapStopTimer(TEXT,OPT) zMapPrintTime("Stop",TEXT,OPT)
+
+
+// interface to legacy calls: removed to avoid clutter, redef the macro if you want them back
+// grep for PrintTimer to see them all (about 30)
/* Takes an optional Gtimer* and an optional char* (you must supply the args but either can be NULL */
-#define zMapPrintTimer(TIMER, TEXT) \
- printf(ZMAP_MSG_FORMAT_STRING " %s - elapsed time: %g\n", \
- ZMAP_MSG_FUNCTION_MACRO, \
- ((TEXT) ? (TEXT) : ""), \
- g_timer_elapsed(((TIMER) ? (TIMER) : ZMAP_GLOBAL_TIMER), NULL)) ;
-
-/* Takes an optional Gtimer* (you must supply the arg but it can be NULL */
-#define zMapResetTimer(TIMER) \
- g_timer_reset(((TIMER) ? (TIMER) : ZMAP_GLOBAL_TIMER))
-
+#define zMapPrintTimer(TIMER, TEXT) (void) 0 // zmapPrintTime(TEXT ? TEXT : "?","")
#endif /* ZMAP_DISABLE_TIMER */
diff --git a/src/include/ZMap/zmapView.h b/src/include/ZMap/zmapView.h
index 4fc9901a7..886aebe7c 100755
--- a/src/include/ZMap/zmapView.h
+++ b/src/include/ZMap/zmapView.h
@@ -31,7 +31,7 @@
* HISTORY:
* Last edited: Jun 12 14:36 2009 (edgrif)
* Created: Thu May 13 14:59:14 2004 (edgrif)
- * CVS info: $Id: zmapView.h,v 1.58 2010-04-22 14:31:52 mh17 Exp $
+ * CVS info: $Id: zmapView.h,v 1.59 2010-06-08 08:31:23 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAPVIEW_H
@@ -225,7 +225,7 @@ char *zMapViewGetStatusStr(ZMapViewState zmap_state) ;
gboolean zMapViewGetFeaturesSpan(ZMapView zmap_view, int *start, int *end) ;
ZMapWindow zMapViewGetWindow(ZMapViewWindow view_window) ;
ZMapView zMapViewGetView(ZMapViewWindow view_window) ;
-GData *zMapViewGetStyles(ZMapViewWindow view_window) ;
+GHashTable *zMapViewGetStyles(ZMapViewWindow view_window) ;
ZMapWindowNavigator zMapViewGetNavigator(ZMapView view);
int zMapViewNumWindows(ZMapViewWindow view_window) ;
diff --git a/src/include/ZMap/zmapWindow.h b/src/include/ZMap/zmapWindow.h
index 57d58ab7e..88e1c2e1d 100755
--- a/src/include/ZMap/zmapWindow.h
+++ b/src/include/ZMap/zmapWindow.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -24,11 +24,11 @@
*
* Description: Defines interface to code that creates/handles a
* window displaying genome data.
- *
+ *
* HISTORY:
* Last edited: May 5 17:27 2010 (edgrif)
* Created: Thu Jul 24 15:21:56 2003 (edgrif)
- * CVS info: $Id: zmapWindow.h,v 1.110 2010-05-06 11:58:45 edgrif Exp $
+ * CVS info: $Id: zmapWindow.h,v 1.111 2010-06-08 08:31:23 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_WINDOW_H
@@ -134,13 +134,13 @@ typedef struct
-/*
+/*
* THIS IS GOING BACK TO HOW I ORIGINALLY ENVISAGED THE CALLBACK SYSTEM WHICH WAS AS A COMMAND
* FIELD FOLLOWED BY DIFFERENT INFO. STRUCTS...I.E. LIKE THE SIGNAL INTERFACE OF GTK ETC...
- *
+ *
* Data returned by the "command" callback, note all command structs must start with the
* CommandAny fields.
- *
+ *
*/
typedef enum
@@ -225,12 +225,12 @@ typedef struct _ZMapWindowCallbacksStruct
void zMapWindowInit(ZMapWindowCallbacks callbacks) ;
-ZMapWindow zMapWindowCreate(GtkWidget *parent_widget,
+ZMapWindow zMapWindowCreate(GtkWidget *parent_widget,
char *sequence, void *app_data,
GList *feature_set_names) ;
-ZMapWindow zMapWindowCopy(GtkWidget *parent_widget, char *sequence,
+ZMapWindow zMapWindowCopy(GtkWidget *parent_widget, char *sequence,
void *app_data, ZMapWindow old,
- ZMapFeatureContext features, GData *all_styles, GData *new_styles,
+ ZMapFeatureContext features, GHashTable *all_styles, GHashTable *new_styles,
ZMapWindowLockType window_locking) ;
void zMapWindowBusyFull(ZMapWindow window, gboolean busy, const char *file, const char *func) ;
@@ -244,16 +244,16 @@ void zMapWindowBusyFull(ZMapWindow window, gboolean busy, const char *file, cons
void zMapWindowDisplayData(ZMapWindow window, ZMapWindowState state,
ZMapFeatureContext current_features, ZMapFeatureContext new_features,
- GData *all_styles, GData *new_styles,
+ GHashTable *all_styles, GHashTable *new_styles,
GHashTable *new_featuresets_2_stylelist) ;
-void zMapWindowUnDisplayData(ZMapWindow window,
+void zMapWindowUnDisplayData(ZMapWindow window,
ZMapFeatureContext current_features,
ZMapFeatureContext new_features);
void zMapWindowMove(ZMapWindow window, double start, double end) ;
void zMapWindowReset(ZMapWindow window) ;
void zMapWindowRedraw(ZMapWindow window) ;
void zMapWindowFeatureRedraw(ZMapWindow window, ZMapFeatureContext feature_context,
- GData *all_styles, GData *new_styles,
+ GHashTable *all_styles, GHashTable *new_styles,
gboolean reversed) ;
void zMapWindowZoom(ZMapWindow window, double zoom_factor) ;
ZMapWindowZoomStatus zMapWindowGetZoomStatus(ZMapWindow window) ;
@@ -266,7 +266,7 @@ double zMapWindowGetZoomMaxDNAInWrappedColumn(ZMapWindow window);
gboolean zMapWindowZoomToFeature(ZMapWindow window, ZMapFeature feature) ;
void zMapWindowZoomToWorldPosition(ZMapWindow window, gboolean border,
- double rootx1, double rooty1,
+ double rootx1, double rooty1,
double rootx2, double rooty2);
gboolean zMapWindowGetMark(ZMapWindow window, int *start, int *end) ;
@@ -274,7 +274,7 @@ gboolean zMapWindowGetMark(ZMapWindow window, int *start, int *end) ;
gboolean zMapWindowGetDNAStatus(ZMapWindow window);
void zMapWindowStats(ZMapWindow window,GString *text) ;
void zMapWindowToggle3Frame(ZMapWindow window) ;
-void zMapWindowToggleDNAProteinColumns(ZMapWindow window,
+void zMapWindowToggleDNAProteinColumns(ZMapWindow window,
GQuark align_id, GQuark block_id,
gboolean dna, gboolean protein,
gboolean force_to, gboolean force);
@@ -289,8 +289,8 @@ void zMapWindowSiblingWasRemoved(ZMapWindow window); /* For when a window in
/* Remove this to use Ed's version */
//PangoFont *zMapWindowGetFixedWidthFont(ZMapWindow window);
#endif
-PangoFontDescription *zMapWindowZoomGetFixedWidthFontInfo(ZMapWindow window,
- double *width_out,
+PangoFontDescription *zMapWindowZoomGetFixedWidthFontInfo(ZMapWindow window,
+ double *width_out,
double *height_out);
void zMapWindowGetVisible(ZMapWindow window, double *top_out, double *bottom_out) ;
@@ -307,7 +307,7 @@ gboolean zMapWindowPrint(ZMapWindow window) ;
FooCanvasItem *zMapWindowFeatureAdd(ZMapWindow window,
FooCanvasGroup *feature_group, ZMapFeature feature) ;
FooCanvasItem *zMapWindowFeatureSetAdd(ZMapWindow window,
- FooCanvasGroup *block_group,
+ FooCanvasGroup *block_group,
char *feature_set_name) ;
FooCanvasItem *zMapWindowFeatureReplace(ZMapWindow zmap_window,
FooCanvasItem *curr_feature_item,
@@ -335,10 +335,10 @@ void zMapWindowMergeInFeatureSetNames(ZMapWindow window, GList *feature_set_name
GList *zMapWindowGetSpawnedPIDList(ZMapWindow window);
void zMapWindowDestroy(ZMapWindow window) ;
-void zMapWindowMenuAlignBlockSubMenus(ZMapWindow window,
- ZMapGUIMenuItem each_align,
- ZMapGUIMenuItem each_block,
- char *root,
+void zMapWindowMenuAlignBlockSubMenus(ZMapWindow window,
+ ZMapGUIMenuItem each_align,
+ ZMapGUIMenuItem each_block,
+ char *root,
GArray **items_array_out);
char *zMapWindowRemoteReceiveAccepts(ZMapWindow window);
void zMapWindowSetupXRemote(ZMapWindow window, GtkWidget *widget);
diff --git a/src/include/ZMap/zmapWindowNavigator.h b/src/include/ZMap/zmapWindowNavigator.h
index d09ab1359..989c3c125 100755
--- a/src/include/ZMap/zmapWindowNavigator.h
+++ b/src/include/ZMap/zmapWindowNavigator.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,18 +23,18 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Jun 10 09:44 2009 (rds)
* Created: Thu Sep 7 09:10:32 2006 (rds)
- * CVS info: $Id: zmapWindowNavigator.h,v 1.10 2010-03-04 15:15:31 mh17 Exp $
+ * CVS info: $Id: zmapWindowNavigator.h,v 1.11 2010-06-08 08:31:23 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_WINDOW_NAVIGATOR_H
-#define ZMAP_WINDOW_NAVIGATOR_H
+#define ZMAP_WINDOW_NAVIGATOR_H
#include <ZMap/zmapWindow.h>
@@ -51,15 +51,15 @@ typedef struct _ZMapNavigatorCallbackStruct
ZMapWindowNavigator zMapWindowNavigatorCreate(GtkWidget *canvas_widget);
-void zMapWindowNavigatorFocus(ZMapWindowNavigator navigate,
+void zMapWindowNavigatorFocus(ZMapWindowNavigator navigate,
gboolean true_eq_focus);
void zMapWindowNavigatorSetCurrentWindow(ZMapWindowNavigator navigate, ZMapWindow window);
-void zMapWindowNavigatorMergeInFeatureSetNames(ZMapWindowNavigator navigate,
+void zMapWindowNavigatorMergeInFeatureSetNames(ZMapWindowNavigator navigate,
GList *navigator_sets);
void zMapWindowNavigatorSetStrand(ZMapWindowNavigator navigate, gboolean is_revesed);
-void zMapWindowNavigatorDrawFeatures(ZMapWindowNavigator navigate,
+void zMapWindowNavigatorDrawFeatures(ZMapWindowNavigator navigate,
ZMapFeatureContext full_context,
- GData *styles);
+ GHashTable *styles);
void zMapWindowNavigatorDrawLocator(ZMapWindowNavigator navigate,
double top, double bottom);
void zMapWindowNavigatorReset(ZMapWindowNavigator navigate);
diff --git a/src/zmapConfig/zmapConfigLoader.c b/src/zmapConfig/zmapConfigLoader.c
index 17ae412f4..7fbc48a92 100644
--- a/src/zmapConfig/zmapConfigLoader.c
+++ b/src/zmapConfig/zmapConfigLoader.c
@@ -31,7 +31,7 @@
* HISTORY:
* Last edited: Mar 2 14:47 2010 (edgrif)
* Created: Thu Sep 25 14:12:05 2008 (rds)
- * CVS info: $Id: zmapConfigLoader.c,v 1.22 2010-05-26 12:02:50 mh17 Exp $
+ * CVS info: $Id: zmapConfigLoader.c,v 1.23 2010-06-08 08:31:23 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -523,10 +523,10 @@ GQuark zMapStyleQuark(gchar *str)
// get style stanzas in styles_list of all from the file
-gboolean zMapConfigIniGetStylesFromFile(char *styles_list, char *styles_file, GData **styles_out)
+gboolean zMapConfigIniGetStylesFromFile(char *styles_list, char *styles_file, GHashTable **styles_out)
{
gboolean result = FALSE ;
- GData *styles = NULL ;
+ GHashTable *styles = NULL ;
GList *settings_list = NULL, *free_this_list = NULL;
ZMapConfigIniContext context ;
GHashTable *shapes = NULL;
@@ -548,7 +548,7 @@ gboolean zMapConfigIniGetStylesFromFile(char *styles_list, char *styles_file, GD
{
free_this_list = settings_list ;
- g_datalist_init(&styles) ;
+ styles = g_hash_table_new(NULL,NULL);
do
{
@@ -684,7 +684,7 @@ gboolean zMapConfigIniGetStylesFromFile(char *styles_list, char *styles_file, GD
if ((new_style = zMapStyleCreateV(num_params, params)))
{
- if (!zMapStyleSetAdd(&styles, new_style))
+ if (!zMapStyleSetAdd(styles, new_style))
{
/* Free style, report error and move on. */
zMapStyleDestroy(new_style) ;
@@ -1064,6 +1064,7 @@ static ZMapConfigIniContextKeyEntry get_debug_group_data(char **stanza_name, cha
{ ZMAPSTANZA_DEBUG_APP_THREADS, G_TYPE_BOOLEAN, NULL, FALSE },
{ ZMAPSTANZA_DEBUG_APP_FEATURE2STYLE, G_TYPE_BOOLEAN, NULL, FALSE },
{ ZMAPSTANZA_DEBUG_APP_STYLES, G_TYPE_BOOLEAN, NULL, FALSE },
+ { ZMAPSTANZA_DEBUG_APP_TIMING, G_TYPE_BOOLEAN, NULL, FALSE },
{ NULL }
};
static char *name = ZMAPSTANZA_DEBUG_CONFIG;
diff --git a/src/zmapFeature/zmapFeature.c b/src/zmapFeature/zmapFeature.c
index 40efdcca5..c369d6603 100755
--- a/src/zmapFeature/zmapFeature.c
+++ b/src/zmapFeature/zmapFeature.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Dec 14 11:20 2009 (edgrif)
* Created: Fri Jul 16 13:05:58 2004 (edgrif)
- * CVS info: $Id: zmapFeature.c,v 1.129 2010-04-26 14:29:42 mh17 Exp $
+ * CVS info: $Id: zmapFeature.c,v 1.130 2010-06-08 08:31:23 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -116,7 +116,7 @@ typedef struct
typedef struct _HackForForcingStyleModeStruct
{
gboolean force;
- GData *styles ;
+ GHashTable *styles ;
ZMapFeatureSet feature_set;
} HackForForcingStyleModeStruct, *HackForForcingStyleMode;
@@ -288,7 +288,7 @@ gboolean zMapFeatureAnyRemoveFeature(ZMapFeatureAny feature_parent, ZMapFeatureA
* in our styles...
*
* */
-gboolean zMapFeatureAnyAddModesToStyles(ZMapFeatureAny feature_any, GData *styles)
+gboolean zMapFeatureAnyAddModesToStyles(ZMapFeatureAny feature_any, GHashTable *styles)
{
gboolean result = TRUE;
ZMapFeatureContextExecuteStatus status = ZMAP_CONTEXT_EXEC_STATUS_OK;
@@ -315,7 +315,7 @@ gboolean zMapFeatureAnyAddModesToStyles(ZMapFeatureAny feature_any, GData *style
* mode to basic for featureset where there are no features to get the
* mode from... When adding new features to these once empty
* columns, we must force the styles... */
-gboolean zMapFeatureAnyForceModesToStyles(ZMapFeatureAny feature_any, GData *styles)
+gboolean zMapFeatureAnyForceModesToStyles(ZMapFeatureAny feature_any, GHashTable *styles)
{
gboolean result = TRUE;
ZMapFeatureContextExecuteStatus status = ZMAP_CONTEXT_EXEC_STATUS_OK;
@@ -546,7 +546,7 @@ ZMapFeature zMapFeatureCreateEmpty(void)
* Because the contents of this are quite a lot of work. Useful for
* creating single features, but be warned that usually you will need
* to keep track of uniqueness, so for large parser the GFF style of
- * doing things is better (assuming we get a fix for g_datalist!).
+ * doing things is better
* ==================================================================
*/
ZMapFeature zMapFeatureCreateFromStandardData(char *name, char *sequence, char *ontology,
@@ -608,6 +608,7 @@ gboolean zMapFeatureAddStandardData(ZMapFeature feature, char *feature_name_id,
feature->type = feature_type ;
feature->ontology = g_quark_from_string(ontology) ;
feature->style_id = zMapStyleGetUniqueID(style) ;
+ feature->style = style;
feature->x1 = start ;
feature->x2 = end ;
feature->strand = strand ;
@@ -1037,7 +1038,9 @@ void zMapFeatureSetStyle(ZMapFeatureSet feature_set, ZMapFeatureTypeStyle style)
{
zMapAssert(feature_set && style) ;
- //feature_set->style = style ;
+ // MH17: was for the column (historically)
+ // new put back to be used for each feature
+ feature_set->style = style ;
return ;
}
@@ -2591,7 +2594,7 @@ static ZMapFeatureContextExecuteStatus addModeCB(GQuark key_id,
-/* A GDataForeachFunc() to add a mode to the styles for all features in a set, note that
+/* A GHashTableForeachFunc() to add a mode to the styles for all features in a set, note that
* this is not efficient as we go through all features but we would need more information
* stored in the feature set to avoid this as there may be several different types of
* feature stored in a feature set.
diff --git a/src/zmapFeature/zmapFeatureContext.c b/src/zmapFeature/zmapFeatureContext.c
index b07b1fcc0..12f8edef7 100755
--- a/src/zmapFeature/zmapFeatureContext.c
+++ b/src/zmapFeature/zmapFeatureContext.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Nov 30 16:23 2009 (edgrif)
* Created: Tue Jan 17 16:13:12 2006 (edgrif)
- * CVS info: $Id: zmapFeatureContext.c,v 1.53 2010-05-17 14:41:15 mh17 Exp $
+ * CVS info: $Id: zmapFeatureContext.c,v 1.54 2010-06-08 08:31:23 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -123,7 +123,7 @@ static gboolean catch_hash_abuse_G = TRUE;
* mappings etc.....needs some thought and effort....
*
*/
-void zMapFeatureReverseComplement(ZMapFeatureContext context, GData *styles)
+void zMapFeatureReverseComplement(ZMapFeatureContext context, GHashTable *styles)
{
RevCompDataStruct cb_data ;
diff --git a/src/zmapFeature/zmapFeatureOutput.c b/src/zmapFeature/zmapFeatureOutput.c
index ba10746f5..880dec91f 100755
--- a/src/zmapFeature/zmapFeatureOutput.c
+++ b/src/zmapFeature/zmapFeatureOutput.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Mar 29 09:16 2010 (edgrif)
* Created: Tue Oct 28 16:20:33 2008 (rds)
- * CVS info: $Id: zmapFeatureOutput.c,v 1.11 2010-03-29 15:32:39 mh17 Exp $
+ * CVS info: $Id: zmapFeatureOutput.c,v 1.12 2010-06-08 08:31:23 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -58,7 +58,7 @@ typedef struct
{
gboolean status ;
GIOChannel *channel ;
- GData *styles ;
+ GHashTable *styles ;
GString *dump_string;
GError **dump_error ;
DumpAny dump_data; /* will contain the user's data in dump_data->user_data */
@@ -80,7 +80,7 @@ static ZMapFeatureContextExecuteStatus dump_features_cb(GQuark key,
char **err_out);
static void invoke_dump_features_cb(gpointer list_data, gpointer user_data);
static gboolean simple_context_print_cb(ZMapFeatureAny feature_any,
- GData *styles,
+ GHashTable *styles,
GString *dump_string_in_out,
GError **error,
gpointer user_data);
@@ -98,7 +98,7 @@ static ZMapFeatureContextExecuteStatus range_invoke_dump_features_cb(GQuark ke
/*!
* \brief Dump the Feature Context in a zmap speific context format. Useful for debugging.
*/
-gboolean zMapFeatureContextDump(ZMapFeatureContext feature_context, GData *styles,
+gboolean zMapFeatureContextDump(ZMapFeatureContext feature_context, GHashTable *styles,
GIOChannel *file, GError **error_out)
{
gboolean result = FALSE;
@@ -111,7 +111,7 @@ gboolean zMapFeatureContextDump(ZMapFeatureContext feature_context, GData *style
}
/* N.B. call only returns TRUE if the dump _and_ the io channel close succeed. */
-gboolean zMapFeatureDumpStdOutFeatures(ZMapFeatureContext feature_context, GData *styles, GError **error_out)
+gboolean zMapFeatureDumpStdOutFeatures(ZMapFeatureContext feature_context, GHashTable *styles, GError **error_out)
{
gboolean result = FALSE ;
GIOChannel *file ;
@@ -139,7 +139,7 @@ gboolean zMapFeatureDumpStdOutFeatures(ZMapFeatureContext feature_context, GData
}
-gboolean zMapFeatureDumpToFileName(ZMapFeatureContext feature_context,char *filename, char *header, GData *styles, GError **error_out)
+gboolean zMapFeatureDumpToFileName(ZMapFeatureContext feature_context,char *filename, char *header, GHashTable *styles, GError **error_out)
{
gboolean result = FALSE ;
GIOChannel *file ;
@@ -170,7 +170,7 @@ gboolean zMapFeatureDumpToFileName(ZMapFeatureContext feature_context,char *file
* The GFunc expects (ZMapFeatureAny feature, gpointer dumper_data_out)
*/
gboolean zMapFeatureListForeachDumperCreate(ZMapFeatureDumpFeatureFunc dump_func,
- GData *styles,
+ GHashTable *styles,
gpointer dump_user_data,
GDestroyNotify dump_user_free,
GIOChannel *dump_file,
@@ -248,7 +248,7 @@ gboolean zMapFeatureListForeachDumperDestroy(gpointer dumper_data)
}
gboolean zMapFeatureListDumpToFile(GList *feature_list,
- GData *styles,
+ GHashTable *styles,
ZMapFeatureDumpFeatureFunc dump_func,
gpointer dump_user_data,
GIOChannel *dump_file,
@@ -293,7 +293,7 @@ gboolean zMapFeatureListDumpToFile(GList *feature_list,
* and this code calls the callback to do the output of the feature in the appropriate
* form. */
gboolean zMapFeatureContextDumpToFile(ZMapFeatureAny dump_set,
- GData *styles,
+ GHashTable *styles,
ZMapFeatureDumpFeatureFunc dump_func,
gpointer dump_user_data,
GIOChannel *dump_file,
@@ -342,7 +342,7 @@ gboolean zMapFeatureContextDumpToFile(ZMapFeatureAny dump_set,
}
gboolean zMapFeatureContextRangeDumpToFile(ZMapFeatureAny dump_set,
- GData *styles,
+ GHashTable *styles,
ZMapSpan span_data,
ZMapFeatureDumpFeatureFunc dump_func,
gpointer dump_user_data,
@@ -524,7 +524,7 @@ static void invoke_dump_features_cb(gpointer list_data, gpointer user_data)
}
static gboolean simple_context_print_cb(ZMapFeatureAny feature_any,
- GData *styles,
+ GHashTable *styles,
GString *dump_string_in_out,
GError **error,
gpointer user_data)
diff --git a/src/zmapFeature/zmapFeatureTypes.c b/src/zmapFeature/zmapFeatureTypes.c
index ba3f62b06..e4414bd18 100755
--- a/src/zmapFeature/zmapFeatureTypes.c
+++ b/src/zmapFeature/zmapFeatureTypes.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Jan 26 12:02 2010 (edgrif)
* Created: Tue Dec 14 13:15:11 2004 (edgrif)
- * CVS info: $Id: zmapFeatureTypes.c,v 1.97 2010-05-26 12:02:50 mh17 Exp $
+ * CVS info: $Id: zmapFeatureTypes.c,v 1.98 2010-06-08 08:31:23 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -63,17 +63,18 @@ typedef struct
{
ZMapStyleMergeMode merge_mode ;
- GData *curr_styles ;
+ GHashTable *curr_styles ;
} MergeStyleCBStruct, *MergeStyleCB ;
typedef struct
{
gboolean *error ;
- GData *copy_set ;
+ GHashTable *copy_set ;
} CopyStyleCBStruct, *CopyStyleCB ;
+/*
typedef struct
{
gboolean error ;
@@ -84,22 +85,21 @@ typedef struct
typedef struct
{
gboolean errors ;
- GData *style_set ;
- GData *inherited_styles ;
+ GhashTable *style_set ;
+ GhashTable *inherited_styles ;
ZMapFeatureTypeStyle prev_style ;
} InheritAllCBStruct, *InheritAllCB ;
+*/
-static void doTypeSets(GQuark key_id, gpointer data, gpointer user_data) ;
-
static void checkListName(gpointer data, gpointer user_data) ;
static gint compareNameToStyle(gconstpointer glist_data, gconstpointer user_data) ;
-static void mergeStyle(GQuark style_id, gpointer data, gpointer user_data_unused) ;
-static void destroyStyle(GQuark style_id, gpointer data, gpointer user_data_unused) ;
+static void mergeStyle(gpointer style_id, gpointer data, gpointer user_data_unused) ;
+static gboolean destroyStyle(gpointer style_id, gpointer data, gpointer user_data_unused) ;
-static void copySetCB(GQuark key_id, gpointer data, gpointer user_data) ;
+static void copySetCB(gpointer key_id, gpointer data, gpointer user_data) ;
static void setStrandFrameAttrs(ZMapFeatureTypeStyle type,
@@ -124,7 +124,7 @@ static void mergeColours(ZMapStyleFullColour curr, ZMapStyleFullColour new) ;
/* Add a style to a set of styles, if the style is already there no action is taken
* and FALSE is returned. */
-gboolean zMapStyleSetAdd(GData **style_set, ZMapFeatureTypeStyle style)
+gboolean zMapStyleSetAdd(GHashTable *style_set, ZMapFeatureTypeStyle style)
{
gboolean result = FALSE ;
GQuark style_id ;
@@ -133,9 +133,9 @@ gboolean zMapStyleSetAdd(GData **style_set, ZMapFeatureTypeStyle style)
style_id = zMapStyleGetUniqueID(style) ;
- if (!(zMapFindStyle(*style_set, style_id)))
+ if (!g_hash_table_lookup(style_set, GUINT_TO_POINTER(style_id)))
{
- g_datalist_id_set_data(style_set, style_id, style) ;
+ g_hash_table_insert(style_set, GUINT_TO_POINTER(style_id), style) ;
result = TRUE ;
}
@@ -156,7 +156,6 @@ gboolean zMapStyleSetAdd(GData **style_set, ZMapFeatureTypeStyle style)
* the errors.
*
* re-written by mh17 May 2010 to use a more efficient way of finding parent styles and inheriting then
- * Still uses GData as input and output as changing that would involve a lot of code
* (previous version performed badly on sorted data...erm got an infinite list due to self-parenting styles)
* ..anyway this version runs as fast as a single datalist or hash table function
* & does strictly less inherit operations than the number of styles
@@ -167,7 +166,7 @@ gboolean zMapStyleSetAdd(GData **style_set, ZMapFeatureTypeStyle style)
// inherit the parent style, recursively inheriting its ancestors first
// replaces and frees the old style with the new one and returns the new
// or NULL on failure
-static ZMapFeatureTypeStyle inherit_parent(ZMapFeatureTypeStyle style, GHashTable *root_styles, int depth, GData **style_set)
+static ZMapFeatureTypeStyle inherit_parent(ZMapFeatureTypeStyle style, GHashTable *root_styles, int depth)
{
ZMapFeatureTypeStyle parent,tmp_style = NULL;
@@ -197,7 +196,7 @@ static ZMapFeatureTypeStyle inherit_parent(ZMapFeatureTypeStyle style, GHashTabl
}
if(!parent->inherited)
- parent = inherit_parent(parent,root_styles,depth+1,style_set);
+ parent = inherit_parent(parent,root_styles,depth+1);
if(parent)
{
@@ -209,7 +208,6 @@ static ZMapFeatureTypeStyle inherit_parent(ZMapFeatureTypeStyle style, GHashTabl
// keep this up to date
g_hash_table_replace(root_styles,GUINT_TO_POINTER(style->unique_id),tmp_style);
- g_datalist_id_set_data(style_set,tmp_style->unique_id,tmp_style);
zMapStyleDestroy(style);
}
@@ -235,59 +233,48 @@ static ZMapFeatureTypeStyle inherit_parent(ZMapFeatureTypeStyle style, GHashTabl
}
+
// add a style to a hash table
-static void set_root_style(GQuark key, gpointer item, gpointer user)
+static void clear_inherited(gpointer key, gpointer item, gpointer user)
{
- GHashTable *roots = (GHashTable *) user;
ZMapFeatureTypeStyle style = (ZMapFeatureTypeStyle) item;
style->inherited = FALSE;
-
- g_hash_table_insert(roots,GUINT_TO_POINTER(style->unique_id),style);
}
-// really we want to replace GData with GHashTable all through the styles code
-// but there's a lot of it
-// first we fix this function, then the server code that creates the Gdata style_set
-// then we can hit the application layer at leisure
-// after that we can remove all these copying to/from Gdata stuff
-
-gboolean zMapStyleInheritAllStyles(GData **style_set)
+gboolean zMapStyleInheritAllStyles(GHashTable *style_set)
{
gboolean result = TRUE ;
- GHashTable *root_styles;
+// GHashTable *root_styles;
GList *iter;
ZMapFeatureTypeStyle old,new;
- // make a hash table of all styles that are inherited
- root_styles = g_hash_table_new(NULL,NULL);
- g_datalist_foreach(style_set,set_root_style,root_styles);
+
+ g_hash_table_foreach(style_set,clear_inherited,style_set);
// we need to process the hash table and alter the data pointers
- // probably not safe to assume GLib's opaque functions can cope
// get a list of keys
- zMap_g_hash_table_get_keys(&iter,root_styles);
+ zMap_g_hash_table_get_keys(&iter,style_set);
// lookup each one and replace in turn, update the output datalist
for(;iter;iter = iter->next)
{
// lookup the style: must do this for each as
// these may be changed by inheritance of previous styles
- old = (ZMapFeatureTypeStyle) g_hash_table_lookup(root_styles,iter->data);
+ old = (ZMapFeatureTypeStyle) g_hash_table_lookup(style_set,iter->data);
zMapAssert(old);
// recursively inherit parent while not already done
- new = inherit_parent(old,root_styles,0,style_set);
+ new = inherit_parent(old,style_set,0);
if(!new)
result = FALSE;
}
// tidy up
g_list_free(iter);
- g_hash_table_destroy(root_styles);
return result ;
}
@@ -296,20 +283,20 @@ gboolean zMapStyleInheritAllStyles(GData **style_set)
/* Copies a set of styles.
*
* If there are errors in trying to copy styles then this function returns FALSE
- * and a GData set containing as many styles as it could copy, there will be
+ * and a GHashTable containing as many styles as it could copy, there will be
* log messages identifying the errors. It returns TRUE if there were no errors
* at all.
*
* */
-gboolean zMapStyleCopyAllStyles(GData **style_set, GData **copy_style_set_out)
+gboolean zMapStyleCopyAllStyles(GHashTable *style_set, GHashTable **copy_style_set_out)
{
gboolean result = TRUE ;
CopyStyleCBStruct cb_data = {NULL} ;
cb_data.error = &result ;
- g_datalist_init(&(cb_data.copy_set)) ;
+ cb_data.copy_set = g_hash_table_new(NULL,NULL) ;
- g_datalist_foreach(style_set, copySetCB, &cb_data) ;
+ g_hash_table_foreach(style_set, copySetCB, &cb_data) ;
*copy_style_set_out = cb_data.copy_set ;
@@ -438,58 +425,51 @@ static void mergeColours(ZMapStyleFullColour curr, ZMapStyleFullColour new)
}
+//---------------------------------
+// previous style access functions replaced with macros
+// they provided default value by we can make the opbject do that
+// external modules have read-only access.
+//---------------------------------
-GQuark zMapStyleGetID(ZMapFeatureTypeStyle style)
-{
- return style->original_id ; // is always set
-}
-
-GQuark zMapStyleGetUniqueID(ZMapFeatureTypeStyle style)
+// too complicated for macros
+GQuark zMapStyleGetSubFeature(ZMapFeatureTypeStyle style,ZMapStyleSubFeature i)
{
- return style->unique_id ; // is always set
-}
+ GQuark x = 0;
-const gchar *zMapStyleGetName(ZMapFeatureTypeStyle style)
-{
- // this is the original name, stored internally as a squark
- return g_quark_to_string(style->original_id) ; // is always set
+ if(i > 0 && i < ZMAPSTYLE_SUB_FEATURE_MAX)
+ x = style->sub_features[i];
+ return(x);
}
-gchar *zMapStyleGetDescription(ZMapFeatureTypeStyle style)
-{
- return style->description ; // is always set
-}
-ZMapStyleBumpMode zMapStyleGetBumpMode(ZMapFeatureTypeStyle style)
+ZMapStyleGlyphShape zMapStyleGlyphShape5(ZMapFeatureTypeStyle style)
{
- ZMapStyleBumpMode mode = ZMAPBUMP_INVALID;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_BUMP_MODE))
- mode = style->curr_bump_mode;
+ ZMapStyleGlyphShape shape = NULL;
- return mode;
+ if(zMapStyleIsPropertySetId(style,STYLE_PROP_GLYPH_SHAPE_5))
+ shape = &style->mode_data.glyph.glyph5;
+ else
+ shape = &style->mode_data.glyph.glyph;
+ return(shape);
}
-ZMapStyleBumpMode zMapStyleGetDefaultBumpMode(ZMapFeatureTypeStyle style)
+
+ZMapStyleGlyphShape zMapStyleGlyphShape3(ZMapFeatureTypeStyle style)
{
- ZMapStyleBumpMode mode = ZMAPBUMP_INVALID;
+ ZMapStyleGlyphShape shape = NULL;
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_BUMP_DEFAULT))
- mode = style->default_bump_mode;
+ if(zMapStyleIsPropertySetId(style,STYLE_PROP_GLYPH_SHAPE_3))
+ shape = &style->mode_data.glyph.glyph3;
+ else
+ shape = &style->mode_data.glyph.glyph;
+ return(shape);
+}
- return mode;
+//---------------------------------
-}
-gboolean zMapStyleGetUnmarked(ZMapFeatureTypeStyle style)
-{
- gboolean x = TRUE; // spec says default to true
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_ALIGNMENT_UNMARKED_COLINEAR))
- x = style->mode_data.alignment.unmarked_colinear;
- return(x);
-}
void zMapStyleSetParent(ZMapFeatureTypeStyle style, char *parent_name)
@@ -519,15 +499,6 @@ void zMapStyleSetWidth(ZMapFeatureTypeStyle style, double width)
return ;
}
-double zMapStyleGetBumpWidth(ZMapFeatureTypeStyle style)
-{
- double bump_spacing = 0.0 ;
-
- if (zMapStyleIsPropertySetId(style,STYLE_PROP_BUMP_SPACING))
- bump_spacing = style->bump_spacing ;
-
- return bump_spacing ;
-}
@@ -553,7 +524,7 @@ void zMapStyleSetMag(ZMapFeatureTypeStyle style, double min_mag, double max_mag)
}
-
+// these next two functions are not called
gboolean zMapStyleIsMinMag(ZMapFeatureTypeStyle style, double *min_mag)
{
gboolean mag_set = FALSE ;
@@ -605,16 +576,6 @@ gboolean zMapStyleHasMode(ZMapFeatureTypeStyle style)
}
-ZMapStyleMode zMapStyleGetMode(ZMapFeatureTypeStyle style)
-{
- ZMapStyleMode mode = ZMAPSTYLE_MODE_INVALID ;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_MODE))
- mode = style->mode;
-
- return mode;
-}
-
@@ -630,68 +591,6 @@ void zMapStyleSetPfetch(ZMapFeatureTypeStyle style, gboolean pfetchable)
-const gchar *zMapStyleGetGFFSource(ZMapFeatureTypeStyle style)
-{
- const gchar *gff_source = NULL;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_GFF_SOURCE))
- gff_source = g_quark_to_string(style->gff_source);
-
- return gff_source ;
-}
-
-const gchar *zMapStyleGetGFFFeature(ZMapFeatureTypeStyle style)
-{
- const gchar *gff_feature = NULL ;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_GFF_FEATURE))
- gff_feature = g_quark_to_string(style->gff_feature);
-
- return gff_feature ;
-}
-
-
-gboolean zMapStyleIsDirectionalEnd(ZMapFeatureTypeStyle style)
-{
- gboolean ends = FALSE ;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_DIRECTIONAL_ENDS))
- ends = style->directional_end;
-
- return ends ;
-}
-
-
-unsigned int zmapStyleGetWithinAlignError(ZMapFeatureTypeStyle style)
-{
- unsigned int error = 0;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_ALIGNMENT_BETWEEN_ERROR))
- error = style->mode_data.alignment.between_align_error;
-
- return error ;
-}
-
-
-gboolean zMapStyleIsParseGaps(ZMapFeatureTypeStyle style)
-{
- gboolean parse_gaps = FALSE;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_ALIGNMENT_PARSE_GAPS))
- parse_gaps = style->mode_data.alignment.parse_gaps;
-
- return parse_gaps ;
-}
-
-gboolean zMapStyleIsShowGaps(ZMapFeatureTypeStyle style)
-{
- gboolean show_gaps =FALSE ;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_ALIGNMENT_SHOW_GAPS))
- show_gaps = style->mode_data.alignment.show_gaps;
-
- return show_gaps ;
-}
void zMapStyleSetShowGaps(ZMapFeatureTypeStyle style, gboolean show_gaps)
{
@@ -721,17 +620,6 @@ void zMapStyleSetGappedAligns(ZMapFeatureTypeStyle style, gboolean parse_gaps, g
}
-void zMapStyleGetGappedAligns(ZMapFeatureTypeStyle style, gboolean *parse_gaps, gboolean *show_gaps)
-{
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_ALIGNMENT_PARSE_GAPS))
- *parse_gaps = style->mode_data.alignment.parse_gaps;
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_ALIGNMENT_SHOW_GAPS))
- *show_gaps = style->mode_data.alignment.show_gaps;
-
- return ;
-}
-
-
void zMapStyleSetJoinAligns(ZMapFeatureTypeStyle style, unsigned int between_align_error)
{
@@ -745,22 +633,6 @@ void zMapStyleSetJoinAligns(ZMapFeatureTypeStyle style, unsigned int between_ali
}
-/* Returns TRUE and returns the between_align_error if join_aligns is TRUE for the style,
- * otherwise returns FALSE. */
-gboolean zMapStyleGetJoinAligns(ZMapFeatureTypeStyle style, unsigned int *between_align_error)
-{
- gboolean result = FALSE ;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_ALIGNMENT_PARSE_GAPS))
- {
- *between_align_error = style->mode_data.alignment.between_align_error;
- result = TRUE ;
- }
-
- return result ;
-}
-
-
void zMapStyleSetDisplayable(ZMapFeatureTypeStyle style, gboolean displayable)
{
style->displayable = displayable ;
@@ -769,17 +641,6 @@ void zMapStyleSetDisplayable(ZMapFeatureTypeStyle style, gboolean displayable)
return ;
}
-gboolean zMapStyleIsDisplayable(ZMapFeatureTypeStyle style)
-{
- gboolean result = FALSE ;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_DISPLAYABLE))
- result = style->displayable;
-
- return result ;
-}
-
-
void zMapStyleSetDeferred(ZMapFeatureTypeStyle style, gboolean deferred)
{
style->deferred = deferred;
@@ -787,16 +648,6 @@ void zMapStyleSetDeferred(ZMapFeatureTypeStyle style, gboolean deferred)
return ;
}
-gboolean zMapStyleIsDeferred(ZMapFeatureTypeStyle style)
-{
- gboolean result = FALSE;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_DEFERRED))
- result = style->deferred;
-
- return result ;
-}
-
void zMapStyleSetLoaded(ZMapFeatureTypeStyle style, gboolean loaded)
{
style->loaded = loaded;
@@ -805,16 +656,6 @@ void zMapStyleSetLoaded(ZMapFeatureTypeStyle style, gboolean loaded)
return ;
}
-gboolean zMapStyleIsLoaded(ZMapFeatureTypeStyle style)
-{
- gboolean result = FALSE;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_LOADED))
- result = style->loaded;
-
- return result ;
-}
-
/* Controls whether the feature set is displayed. */
void zMapStyleSetDisplay(ZMapFeatureTypeStyle style, ZMapStyleColumnDisplayState col_show)
@@ -828,31 +669,6 @@ void zMapStyleSetDisplay(ZMapFeatureTypeStyle style, ZMapStyleColumnDisplayState
return ;
}
-ZMapStyleColumnDisplayState zMapStyleGetDisplay(ZMapFeatureTypeStyle style)
-{
- ZMapStyleColumnDisplayState mode = ZMAPSTYLE_COLDISPLAY_INVALID;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_COLUMN_DISPLAY_MODE))
- mode = style->col_display_state;
-
- return mode ;
-}
-
-
-gboolean zMapStyleIsHidden(ZMapFeatureTypeStyle style)
-{
- gboolean result = FALSE ;
- ZMapStyleColumnDisplayState mode = ZMAPSTYLE_COLDISPLAY_INVALID;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_COLUMN_DISPLAY_MODE))
- mode = style->col_display_state;
-
- if (mode == ZMAPSTYLE_COLDISPLAY_HIDE)
- result = TRUE ;
-
- return result ;
-}
-
/* Controls whether the feature set is displayed initially. */
void zMapStyleSetShowWhenEmpty(ZMapFeatureTypeStyle style, gboolean show_when_empty)
@@ -865,169 +681,6 @@ void zMapStyleSetShowWhenEmpty(ZMapFeatureTypeStyle style, gboolean show_when_em
return ;
}
-gboolean zMapStyleGetShowWhenEmpty(ZMapFeatureTypeStyle style)
-{
- gboolean show = FALSE;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_COLUMN_DISPLAY_MODE))
- show = style->show_when_empty;
-
- return show ;
-}
-
-
-
-double zMapStyleGetWidth(ZMapFeatureTypeStyle style)
-{
- double width = 0.0 ;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_WIDTH))
- width = style->width;
-
- return width ;
-}
-
-double zMapStyleGetMaxScore(ZMapFeatureTypeStyle style)
-{
- double max_score = 0.0 ;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_MAX_SCORE))
- max_score = style->max_score;
-
- return max_score ;
-}
-
-double zMapStyleGetMinScore(ZMapFeatureTypeStyle style)
-{
- double min_score = 0.0 ;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_MIN_SCORE))
- min_score = style->min_score;
-
- return min_score ;
-}
-
-ZMapStyleGlyphAlign zMapStyleGetAlign(ZMapFeatureTypeStyle style)
-{
- ZMapStyleGlyphAlign z = ZMAPSTYLE_GLYPH_ALIGN_INVALID;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_GLYPH_ALIGN))
- z = style->mode_data.glyph.glyph_align;
- return(z);
-}
-
-ZMapStyleScoreMode zMapStyleGetScoreMode(ZMapFeatureTypeStyle style)
-{
- ZMapStyleScoreMode z = ZMAPSCORE_INVALID;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_SCORE_MODE))
- z = style->score_mode;
- return(z);
-}
-
-double zMapStyleGetMinMag(ZMapFeatureTypeStyle style)
-{
- double min_mag = 0.0 ;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_MIN_MAG))
- min_mag = style->min_mag;
-
- return min_mag ;
-}
-
-
-double zMapStyleGetMaxMag(ZMapFeatureTypeStyle style)
-{
- double max_mag = 0.0 ;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_MAX_MAG))
- max_mag = style->max_mag;
-
- return max_mag ;
-}
-
-
-double zMapStyleBaseline(ZMapFeatureTypeStyle style)
-{
- double baseline = 0.0 ;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_GRAPH_BASELINE))
- baseline = style->mode_data.graph.baseline;
-
- return baseline ;
-}
-
-
-ZMapStyleGlyphStrand zMapStyleGlyphStrand(ZMapFeatureTypeStyle style)
-{
- int glyph_strand = ZMAPSTYLE_GLYPH_STRAND_INVALID;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_GLYPH_STRAND))
- glyph_strand = style->mode_data.glyph.glyph_strand;
-
- return glyph_strand ;
-}
-
-
-int zMapStyleGlyphThreshold(ZMapFeatureTypeStyle style)
-{
- return(style->mode_data.glyph.glyph_threshold);
-}
-
-GQuark zMapStyleGetSubFeature(ZMapFeatureTypeStyle style,ZMapStyleSubFeature i)
-{
- GQuark x = 0;
-
- if(i > 0 && i < ZMAPSTYLE_SUB_FEATURE_MAX)
- x = style->sub_features[i];
- return(x);
-}
-
-ZMapStyleGlyphShape zMapStyleGlyphShape(ZMapFeatureTypeStyle style)
-{
- ZMapStyleGlyphShape shape = NULL;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_GLYPH_SHAPE))
- shape = &style->mode_data.glyph.glyph;
- return(shape);
-}
-
-ZMapStyleGlyphShape zMapStyleGlyphShape5(ZMapFeatureTypeStyle style)
-{
- ZMapStyleGlyphShape shape = NULL;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_GLYPH_SHAPE_5))
- shape = &style->mode_data.glyph.glyph5;
- else
- shape = zMapStyleGlyphShape(style);
- return(shape);
-}
-
-
-ZMapStyleGlyphShape zMapStyleGlyphShape3(ZMapFeatureTypeStyle style)
-{
- ZMapStyleGlyphShape shape = NULL;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_GLYPH_SHAPE_3))
- shape = &style->mode_data.glyph.glyph3;
- else
- shape = zMapStyleGlyphShape(style);
- return(shape);
-}
-
-
-
-/* Returns TRUE if bumping has been fixed to one type, FALSE otherwise. */
-gboolean zmapStyleBumpIsFixed(ZMapFeatureTypeStyle style)
-{
- gboolean is_fixed = FALSE ;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_BUMP_FIXED))
- is_fixed = style->bump_fixed;
-
- return is_fixed ;
-}
-
@@ -1258,46 +911,7 @@ gboolean zMapStyleIsFrameSpecific(ZMapFeatureTypeStyle style)
return frame_specific ;
}
-gboolean zMapStyleIsFrameOneColumn(ZMapFeatureTypeStyle style)
-{
- gboolean one_column = FALSE ;
-
- if (zMapStyleIsPropertySetId(style,STYLE_PROP_FRAME_MODE) && style->frame_mode == ZMAPSTYLE_3_FRAME_ONLY_1)
- one_column = TRUE ;
-
- return one_column ;
-}
-
-gboolean zMapStyleIsStrandSpecific(ZMapFeatureTypeStyle style)
-{
- gboolean strand_specific = FALSE ;
-
- if (zMapStyleIsPropertySetId(style,STYLE_PROP_STRAND_SPECIFIC))
- strand_specific = style->strand_specific ;
-
- return strand_specific ;
-}
-
-gboolean zMapStyleIsShowReverseStrand(ZMapFeatureTypeStyle style)
-{
- gboolean show_rev_strand = FALSE ;
-
- if (zMapStyleIsPropertySetId(style,STYLE_PROP_SHOW_REV_STRAND))
- show_rev_strand = style->show_rev_strand ;
-
- return show_rev_strand ;
-}
-
-gboolean zMapStyleIsHideForwardStrand(ZMapFeatureTypeStyle style)
-{
- gboolean hide_fwd_strand = FALSE ;
-
- if (zMapStyleIsPropertySetId(style,STYLE_PROP_HIDE_FWD_STRAND))
- hide_fwd_strand = style->hide_fwd_strand ;
-
- return hide_fwd_strand ;
-}
void zMapStyleSetGFF(ZMapFeatureTypeStyle style, char *gff_source, char *gff_feature)
{
@@ -1325,7 +939,7 @@ void zMapStyleSetBumpMode(ZMapFeatureTypeStyle style, ZMapStyleBumpMode bump_mod
if(!(bump_mode >= ZMAPBUMP_START && bump_mode <= ZMAPBUMP_END))
bump_mode = ZMAPBUMP_UNBUMP; // better than going Assert
- if (!zmapStyleBumpIsFixed(style))
+ if (!style->bump_fixed)
{
// MH17: this looked wrong, refer to old version
if(!zMapStyleIsPropertySetId(style,STYLE_PROP_BUMP_DEFAULT))
@@ -1350,25 +964,13 @@ void zMapStyleSetBumpSpace(ZMapFeatureTypeStyle style, double bump_spacing)
}
-double zMapStyleGetBumpSpace(ZMapFeatureTypeStyle style)
-{
- double spacing = 0.0 ;
-
-
- if (zMapStyleIsPropertySetId(style,STYLE_PROP_BUMP_SPACING))
- spacing = style->bump_spacing ;
-
- return spacing ;
-}
-
-
/* Reset bump mode to default and returns the default mode. */
ZMapStyleBumpMode zMapStyleResetBumpMode(ZMapFeatureTypeStyle style)
{
ZMapStyleBumpMode default_mode = ZMAPBUMP_INVALID ;
- if (!zmapStyleBumpIsFixed(style))
+ if (!style->bump_fixed)
{
default_mode = style->curr_bump_mode = style->default_bump_mode ;
}
@@ -1387,7 +989,7 @@ void zMapStyleInitBumpMode(ZMapFeatureTypeStyle style,
&& (curr_bump_mode == ZMAPBUMP_INVALID
|| (curr_bump_mode >= ZMAPBUMP_START && curr_bump_mode <= ZMAPBUMP_END))) ;
- if (!zmapStyleBumpIsFixed(style))
+ if (!style->bump_fixed)
{
if (curr_bump_mode != ZMAPBUMP_INVALID)
{
@@ -1443,35 +1045,6 @@ GQuark zMapStyleCreateID(char *style)
}
-gboolean zMapStyleDisplayInSeparator(ZMapFeatureTypeStyle style)
-{
- gboolean separator_style = FALSE;
-
- if(zMapStyleIsPropertySetId(style,STYLE_PROP_SHOW_ONLY_IN_SEPARATOR))
- separator_style = style->show_only_in_separator;
-
- return separator_style;
-}
-
-
-
-
-gboolean zMapFeatureTypeSetAugment(GData **current, GData **new)
-{
- gboolean result = FALSE ;
-
- zMapAssert(new && *new) ;
-
- if (!current || !*current)
- g_datalist_init(current) ;
-
- g_datalist_foreach(new, doTypeSets, (void *)current) ;
-
- result = TRUE ; /* currently shouldn't fail.... */
-
- return result ;
-}
-
/* Check that every name has a style, if the style can't be found, remove the name from the list. */
gboolean zMapSetListEqualStyles(GList **feature_set_names, GList **styles)
@@ -1498,15 +1071,15 @@ gboolean zMapSetListEqualStyles(GList **feature_set_names, GList **styles)
* overloads curr_style.
*
* */
-GData *zMapStyleMergeStyles(GData *curr_styles, GData *new_styles, ZMapStyleMergeMode merge_mode)
+GHashTable *zMapStyleMergeStyles(GHashTable *curr_styles, GHashTable *new_styles, ZMapStyleMergeMode merge_mode)
{
- GData *merged_styles = NULL ;
+ GHashTable *merged_styles = NULL ;
MergeStyleCBStruct merge_data = {FALSE} ;
merge_data.merge_mode = merge_mode ;
merge_data.curr_styles = curr_styles ;
- g_datalist_foreach(&new_styles, mergeStyle, &merge_data) ;
+ g_hash_table_foreach(new_styles, mergeStyle, &merge_data) ;
merged_styles = merge_data.curr_styles ;
@@ -1514,11 +1087,11 @@ GData *zMapStyleMergeStyles(GData *curr_styles, GData *new_styles, ZMapStyleMerg
}
-/* Returns a GData of all predefined styles, the user should free the list AND the styles when
+/* Returns a GhashTable of all predefined styles, the user should free the list AND the styles when
* they have finished with them. */
-GData *zMapStyleGetAllPredefined(void)
+GHashTable *zMapStyleGetAllPredefined(void)
{
- GData *style_list = NULL ;
+ GHashTable *style_list = NULL ;
ZMapFeatureTypeStyle curr = NULL ;
@@ -1526,6 +1099,7 @@ GData *zMapStyleGetAllPredefined(void)
* we should (e.g. DNA), this is because what we really want is to only show the forward
* version of the column. This points to a flaw or lack of a column type. */
+ style_list = g_hash_table_new(NULL,NULL);
/* 3 Frame - meta mode controlling whether we do 3 frame display or not. */
curr = zMapStyleCreate(ZMAP_FIXED_STYLE_3FRAME, ZMAP_FIXED_STYLE_3FRAME_TEXT) ;
@@ -1535,7 +1109,7 @@ GData *zMapStyleGetAllPredefined(void)
ZMAPSTYLE_PROPERTY_DEFAULT_BUMP_MODE, ZMAPBUMP_UNBUMP,
ZMAPSTYLE_PROPERTY_DISPLAYABLE, FALSE,
NULL) ;
- g_datalist_id_set_data(&style_list, curr->unique_id, curr) ;
+ g_hash_table_insert(style_list, GUINT_TO_POINTER(curr->unique_id), curr) ;
/* 3 Frame Translation */
@@ -1575,7 +1149,7 @@ GData *zMapStyleGetAllPredefined(void)
ZMAPSTYLE_PROPERTY_COLOURS, colours,
NULL);
}
- g_datalist_id_set_data(&style_list, curr->unique_id, curr);
+ g_hash_table_insert(style_list, GUINT_TO_POINTER(curr->unique_id), curr);
/* DNA */
@@ -1601,7 +1175,7 @@ GData *zMapStyleGetAllPredefined(void)
ZMAPSTYLE_PROPERTY_COLOURS, colours,
NULL);
}
- g_datalist_id_set_data(&style_list, curr->unique_id, curr);
+ g_hash_table_insert(style_list, GUINT_TO_POINTER(curr->unique_id), curr);
/* Locus */
@@ -1619,7 +1193,7 @@ GData *zMapStyleGetAllPredefined(void)
ZMAPSTYLE_PROPERTY_STRAND_SPECIFIC, TRUE,
ZMAPSTYLE_PROPERTY_COLOURS, colours,
NULL);
- g_datalist_id_set_data(&style_list, curr->unique_id, curr);
+ g_hash_table_insert(style_list, GUINT_TO_POINTER(curr->unique_id), curr);
}
@@ -1634,7 +1208,7 @@ GData *zMapStyleGetAllPredefined(void)
ZMAPSTYLE_PROPERTY_DEFAULT_BUMP_MODE, ZMAPBUMP_UNBUMP,
ZMAPSTYLE_PROPERTY_BUMP_FIXED, TRUE,
NULL);
- g_datalist_id_set_data(&style_list, curr->unique_id, curr);
+ g_hash_table_insert(style_list, GUINT_TO_POINTER(curr->unique_id), curr);
/* Scale Bar */
@@ -1648,7 +1222,7 @@ GData *zMapStyleGetAllPredefined(void)
ZMAPSTYLE_PROPERTY_DEFAULT_BUMP_MODE, ZMAPBUMP_UNBUMP,
ZMAPSTYLE_PROPERTY_BUMP_FIXED, TRUE,
NULL);
- g_datalist_id_set_data(&style_list, curr->unique_id, curr);
+ g_hash_table_insert(style_list, GUINT_TO_POINTER(curr->unique_id), curr);
/* NEED TO CHECK THAT THIS ACTUALLY WORKS...DOESN'T SEEM TO JUST NOW...... */
@@ -1669,7 +1243,7 @@ GData *zMapStyleGetAllPredefined(void)
ZMAPSTYLE_PROPERTY_COLOURS, colours,
NULL);
}
- g_datalist_id_set_data(&style_list, curr->unique_id, curr);
+ g_hash_table_insert(style_list, GUINT_TO_POINTER(curr->unique_id), curr);
/* strand separator */
@@ -1683,7 +1257,7 @@ GData *zMapStyleGetAllPredefined(void)
ZMAPSTYLE_PROPERTY_DEFAULT_BUMP_MODE, ZMAPBUMP_UNBUMP,
ZMAPSTYLE_PROPERTY_BUMP_FIXED, TRUE,
NULL);
- g_datalist_id_set_data(&style_list, curr->unique_id, curr);
+ g_hash_table_insert(style_list, GUINT_TO_POINTER(curr->unique_id), curr);
/* Search results hits */
@@ -1707,7 +1281,7 @@ GData *zMapStyleGetAllPredefined(void)
ZMAPSTYLE_PROPERTY_REV_COLOURS, strand_colours,
NULL);
}
- g_datalist_id_set_data(&style_list, curr->unique_id, curr);
+ g_hash_table_insert(style_list, GUINT_TO_POINTER(curr->unique_id), curr);
/* Assembly path */
@@ -1729,7 +1303,7 @@ GData *zMapStyleGetAllPredefined(void)
ZMAPSTYLE_PROPERTY_ASSEMBLY_PATH_NON_COLOURS, non_path_colours,
NULL);
}
- g_datalist_id_set_data(&style_list, curr->unique_id, curr);
+ g_hash_table_insert(style_list, GUINT_TO_POINTER(curr->unique_id), curr);
return style_list ;
@@ -1738,11 +1312,9 @@ GData *zMapStyleGetAllPredefined(void)
/* need a func to free a styles list here..... */
-void zMapStyleDestroyStyles(GData **styles)
+void zMapStyleDestroyStyles(GHashTable *styles)
{
- g_datalist_foreach(styles, destroyStyle, NULL) ;
-
- g_datalist_clear(styles) ;
+ g_hash_table_foreach_remove(styles, destroyStyle, NULL) ;
return ;
}
@@ -1763,27 +1335,6 @@ void zMapStyleDestroyStyles(GData **styles)
-static void doTypeSets(GQuark key_id, gpointer data, gpointer user_data)
-{
- ZMapFeatureTypeStyle new_type = (ZMapFeatureTypeStyle)data ;
- GData **current_out = (GData **)user_data ;
- GData *current = *current_out ;
-
- if (!g_datalist_id_get_data(¤t, key_id))
- {
- /* copy the struct and then add it to the current set. */
- ZMapFeatureTypeStyle type ;
-
- type = zMapFeatureStyleCopy(new_type) ;
-
- g_datalist_id_set_data(¤t, key_id, type) ;
- }
-
- *current_out = current ;
-
- return ;
-}
-
/* A GFunc() called from zMapSetListEqualStyles() to check that a given feature_set name
* has a corresponding style. */
@@ -1822,16 +1373,16 @@ static gint compareNameToStyle(gconstpointer glist_data, gconstpointer user_data
/* Either merges a new style or adds it to current list. */
-static void mergeStyle(GQuark style_id, gpointer data, gpointer user_data)
+static void mergeStyle(gpointer style_id, gpointer data, gpointer user_data)
{
ZMapFeatureTypeStyle new_style = (ZMapFeatureTypeStyle)data ;
MergeStyleCB merge_data = (MergeStyleCB)user_data ;
- GData *curr_styles = merge_data->curr_styles ;
+ GHashTable *curr_styles = merge_data->curr_styles ;
ZMapFeatureTypeStyle curr_style = NULL ;
/* If we find the style then process according to merge_mode, if not then add a copy to the curr_styles. */
- if ((curr_style = zMapFindStyle(curr_styles, new_style->unique_id)))
+ if ((curr_style = g_hash_table_lookup(curr_styles, GUINT_TO_POINTER(new_style->unique_id))))
{
switch (merge_data->merge_mode)
{
@@ -1845,11 +1396,10 @@ static void mergeStyle(GQuark style_id, gpointer data, gpointer user_data)
/* Remove the existing style and put the new one in its place. */
ZMapFeatureTypeStyle copied_style = NULL ;
- g_datalist_id_remove_data(&curr_styles, curr_style->unique_id) ;
- zMapStyleDestroy(curr_style) ;
+ copied_style = zMapFeatureStyleCopy(new_style);
+ g_hash_table_replace(curr_styles,GUINT_TO_POINTER(new_style->unique_id),copied_style);
- copied_style = zMapFeatureStyleCopy(new_style);
- g_datalist_id_set_data(&curr_styles, new_style->unique_id, copied_style) ;
+ zMapStyleDestroy(curr_style) ;
merge_data->curr_styles = curr_styles ;
@@ -1876,7 +1426,7 @@ static void mergeStyle(GQuark style_id, gpointer data, gpointer user_data)
ZMapFeatureTypeStyle copied_style = NULL ;
copied_style = zMapFeatureStyleCopy(new_style);
- g_datalist_id_set_data(&curr_styles, new_style->unique_id, copied_style) ;
+ g_hash_table_insert(curr_styles, GUINT_TO_POINTER(new_style->unique_id), copied_style) ;
merge_data->curr_styles = curr_styles ;
}
@@ -1886,35 +1436,29 @@ static void mergeStyle(GQuark style_id, gpointer data, gpointer user_data)
/* Destroy the given style. */
-static void destroyStyle(GQuark style_id, gpointer data, gpointer user_data_unused)
+static gboolean destroyStyle(gpointer style_id, gpointer data, gpointer user_data_unused)
{
ZMapFeatureTypeStyle style = (ZMapFeatureTypeStyle)data ;
zMapStyleDestroy(style);
- return ;
+ return TRUE;
}
-/* A GDataForeachFunc() to copy styles into a GDatalist */
-static void copySetCB(GQuark key_id, gpointer data, gpointer user_data)
+/* A GHashTableForeachFunc() to copy styles into a GHashTable */
+static void copySetCB(gpointer key_id, gpointer data, gpointer user_data)
{
ZMapFeatureTypeStyle curr_style = (ZMapFeatureTypeStyle)data ;
CopyStyleCB cb_data = (CopyStyleCB)user_data ;
ZMapFeatureTypeStyle copy_style ;
- GData *style_set = cb_data->copy_set ;
-
-
-if(key_id != curr_style->unique_id)
-{
- printf("copySetCB: %s != %s\n",g_quark_to_string(key_id), g_quark_to_string(curr_style->unique_id));
-}
+ GHashTable *style_set = cb_data->copy_set ;
- zMapAssert(key_id == curr_style->unique_id) ;
+ zMapAssert(GPOINTER_TO_UINT(key_id) == curr_style->unique_id) ;
if ((copy_style = zMapFeatureStyleCopy(curr_style)))
- g_datalist_id_set_data(&style_set, key_id, copy_style) ;
+ g_hash_table_insert(style_set, key_id, copy_style) ;
else
*(cb_data->error) = TRUE ;
diff --git a/src/zmapFeature/zmapFeatureUtils.c b/src/zmapFeature/zmapFeatureUtils.c
index 49d1b5552..6fe2172a6 100755
--- a/src/zmapFeature/zmapFeatureUtils.c
+++ b/src/zmapFeature/zmapFeatureUtils.c
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: Sep 2 09:42 2009 (edgrif)
* Created: Tue Nov 2 2004 (rnc)
- * CVS info: $Id: zmapFeatureUtils.c,v 1.69 2010-03-29 15:32:39 mh17 Exp $
+ * CVS info: $Id: zmapFeatureUtils.c,v 1.70 2010-06-08 08:31:24 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -55,7 +55,7 @@ static int feature_block_frame_offset(ZMapFeature feature);
static void get_feature_list_extent(gpointer list_data, gpointer span_data);
static gint findStyleName(gconstpointer list_data, gconstpointer user_data) ;
-static void addTypeQuark(GQuark style_id, gpointer data, gpointer user_data) ;
+static void addTypeQuark(gpointer style_id, gpointer data, gpointer user_data) ;
static void map_parent2child(gpointer exon_data, gpointer user_data);
static int sortGapsByTarget(gconstpointer a, gconstpointer b) ;
@@ -626,11 +626,11 @@ char *zMapFeatureSetGetName(ZMapFeatureSet feature_set)
/* Retrieve a style struct for the given style id. */
-ZMapFeatureTypeStyle zMapFindStyle(GData *styles, GQuark style_id)
+ZMapFeatureTypeStyle zMapFindStyle(GHashTable *styles, GQuark style_id)
{
ZMapFeatureTypeStyle style = NULL ;
- style = (ZMapFeatureTypeStyle)g_datalist_id_get_data(&styles, style_id) ;
+ style = (ZMapFeatureTypeStyle) g_hash_table_lookup(styles, GUINT_TO_POINTER(style_id));
return style ;
}
@@ -654,20 +654,20 @@ gboolean zMapStyleNameExists(GList *style_name_list, char *style_name)
/* Retrieve a Glist of the names of all the styles... */
-GList *zMapStylesGetNames(GData *styles)
+GList *zMapStylesGetNames(GHashTable *styles)
{
GList *quark_list = NULL ;
zMapAssert(styles) ;
- g_datalist_foreach(&styles, addTypeQuark, (void *)&quark_list) ;
+ g_hash_table_foreach(styles, addTypeQuark, (void *)&quark_list) ;
return quark_list ;
}
/* GFunc() callback function, appends style names to a string, its called for lists
* of either style name GQuarks or lists of style structs. */
-static void addTypeQuark(GQuark style_id, gpointer data, gpointer user_data)
+static void addTypeQuark(gpointer key, gpointer data, gpointer user_data)
{
ZMapFeatureTypeStyle style = (ZMapFeatureTypeStyle)data ;
GList **quarks_out = (GList **)user_data ;
diff --git a/src/zmapFeature/zmapFeature_P.h b/src/zmapFeature/zmapFeature_P.h
index ccc186c76..5b1b81fd4 100755
--- a/src/zmapFeature/zmapFeature_P.h
+++ b/src/zmapFeature/zmapFeature_P.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -27,7 +27,7 @@
* HISTORY:
* Last edited: May 10 08:06 2007 (edgrif)
* Created: Wed Nov 24 11:01:24 2004 (edgrif)
- * CVS info: $Id: zmapFeature_P.h,v 1.7 2010-03-04 15:10:30 mh17 Exp $
+ * CVS info: $Id: zmapFeature_P.h,v 1.8 2010-06-08 08:31:24 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_FEATURE_P_H
@@ -49,7 +49,7 @@ typedef struct
// mh17: needed in zmapFeature3Frame.c as well as FeatureContext.c
typedef struct
{
- GData *styles ;
+ GHashTable *styles ;
int start;
int end ;
} RevCompDataStruct, *RevCompData ;
diff --git a/src/zmapFeature/zmapStyle.c b/src/zmapFeature/zmapStyle.c
index a25f357a1..366a7baaf 100755
--- a/src/zmapFeature/zmapStyle.c
+++ b/src/zmapFeature/zmapStyle.c
@@ -28,7 +28,7 @@
*
* Exported functions: See ZMap/zmapStyle.h
*
- * CVS info: $Id: zmapStyle.c,v 1.53 2010-05-26 12:02:50 mh17 Exp $
+ * CVS info: $Id: zmapStyle.c,v 1.54 2010-06-08 08:31:24 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -396,7 +396,7 @@ GType zMapFeatureTypeStyleGetType(void)
(GClassInitFunc) zmap_feature_type_style_class_init,
(GClassFinalizeFunc) NULL,
NULL /* class_data */,
- sizeof (zmapFeatureTypeStyle),
+ sizeof (zmapFeatureTypeStyleStruct),
0 /* n_preallocs */,
(GInstanceInitFunc) zmap_feature_type_style_init,
NULL
@@ -1478,7 +1478,7 @@ ZMapFeatureTypeStyle zMapStyleLegacyStyle(char *name)
ZMAPSTYLE_PROPERTY_SCORE_MODE, ZMAPSCORE_WIDTH,
ZMAPSTYLE_PROPERTY_SHOW_REVERSE_STRAND,FALSE,
- ZMAPSTYLE_PROPERTY_STRAND_SPECIFIC,TRUE,
+ ZMAPSTYLE_PROPERTY_HIDE_FORWARD_STRAND,TRUE, ZMAPSTYLE_PROPERTY_STRAND_SPECIFIC,TRUE,
ZMAPSTYLE_PROPERTY_WIDTH,30.0,
ZMAPSTYLE_PROPERTY_MIN_SCORE,-2.0,
@@ -1688,6 +1688,12 @@ static void zmap_feature_type_style_init(ZMapFeatureTypeStyle style)
{
zmapStyleSetIsSet(style,STYLE_PROP_IS_SET);
+ // default values, they don't count as being set for inheritance
+ // but will be returned if a paramter is not set
+ // ** only need to set if non zero **
+
+// style->curr_bump_mode = ZMAPBUMP_INVALID; // why not umbump?
+
return ;
}
@@ -1939,6 +1945,14 @@ static void zmap_feature_type_style_set_property_full(ZMapFeatureTypeStyle style
break;
#endif
+
+ case STYLE_PROP_MODE:
+ // set non zero default vaues for mode data
+ if(style->mode == ZMAPSTYLE_MODE_ALIGNMENT)
+ {
+ style->mode_data.alignment.unmarked_colinear = TRUE;
+ }
+ break;
default:
break;
}
diff --git a/src/zmapFeature/zmapStyleUtils.c b/src/zmapFeature/zmapStyleUtils.c
index f52516485..2a1457476 100755
--- a/src/zmapFeature/zmapStyleUtils.c
+++ b/src/zmapFeature/zmapStyleUtils.c
@@ -30,7 +30,7 @@
* HISTORY:
* Last edited: Jul 29 09:53 2009 (edgrif)
* Created: Thu Oct 30 10:24:35 2008 (edgrif)
- * CVS info: $Id: zmapStyleUtils.c,v 1.17 2010-04-20 12:00:37 mh17 Exp $
+ * CVS info: $Id: zmapStyleUtils.c,v 1.18 2010-06-08 08:31:24 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -91,7 +91,7 @@ typedef struct
-static void setPrintFunc(GQuark key_id, gpointer data, gpointer user_data) ;
+static void setPrintFunc(gpointer key_id, gpointer data, gpointer user_data) ;
static void listPrintFunc(gpointer data, gpointer user_data) ;
@@ -171,7 +171,7 @@ ZMAP_ENUM_TO_SHORT_TEXT_FUNC(zmapStyleBumpMode2ShortText, ZMapStyleBu
-void zMapStyleSetPrintAll(ZMapIOOut dest, GData *type_set, char *user_string, gboolean full)
+void zMapStyleSetPrintAll(ZMapIOOut dest, GHashTable *type_set, char *user_string, gboolean full)
{
StylePrintStruct print_data ;
@@ -180,12 +180,12 @@ void zMapStyleSetPrintAll(ZMapIOOut dest, GData *type_set, char *user_string, gb
zMapOutWriteFormat(dest, "\nTypes at %s\n", user_string) ;
- g_datalist_foreach(&type_set, setPrintFunc, &print_data) ;
+ g_hash_table_foreach(type_set, setPrintFunc, &print_data) ;
return ;
}
-void zMapStyleSetPrintAllStdOut(GData *type_set, char *user_string, gboolean full)
+void zMapStyleSetPrintAllStdOut(GHashTable *type_set, char *user_string, gboolean full)
{
ZMapIOOut output ;
@@ -380,7 +380,7 @@ void zMapStylePrint(ZMapIOOut dest, ZMapFeatureTypeStyle style, char *prefix, gb
-static void setPrintFunc(GQuark key_id, gpointer data, gpointer user_data)
+static void setPrintFunc(gpointer key_id, gpointer data, gpointer user_data)
{
ZMapFeatureTypeStyle style = (ZMapFeatureTypeStyle)data ;
StylePrint print_data = (StylePrint)user_data ;
diff --git a/src/zmapFeature/zmapStyle_I.h b/src/zmapFeature/zmapStyle_I.h
index c6f6bf4ba..99f8644f1 100755
--- a/src/zmapFeature/zmapStyle_I.h
+++ b/src/zmapFeature/zmapStyle_I.h
@@ -28,13 +28,14 @@
* HISTORY:
* Last edited: May 14 13:46 2010 (edgrif)
* Created: Mon Feb 26 09:13:30 2007 (edgrif)
- * CVS info: $Id: zmapStyle_I.h,v 1.25 2010-05-26 12:02:50 mh17 Exp $
+ * CVS info: $Id: zmapStyle_I.h,v 1.26 2010-06-08 08:31:24 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef __ZMAP_STYLE_I_H__
#define __ZMAP_STYLE_I_H__
+#define ZMAPSTYLE_INTERNAL 1
#include <ZMap/zmapStyle.h>
#include <ZMap/zmapBase.h>
@@ -136,299 +137,6 @@ typedef struct _zmapFeatureTypeStyleClassStruct
-/*! @addtogroup zmapstyles
- * @{
- * */
-
-
-/*! @struct ZMapStyleColour zmapStyle_P.h
- * @brief ZMap object colours
- *
- * All ZMap objects can potentially have a border colour, a fill colour and a draw colour
- * which can be used to "draw" over the fill colour. */
-
-typedef struct
-{
- struct
- {
- unsigned int draw : 1 ;
- unsigned int fill : 1 ;
- unsigned int border : 1 ;
- } fields_set ;
-
- GdkColor draw ; /* Overlaid on fill colour. */
- GdkColor fill ; /* Fill/background colour. */
- GdkColor border ; /* Surround/line colour. */
-} ZMapStyleColourStruct, *ZMapStyleColour ;
-
-
-/*! @struct ZMapStyleFullColour zmapStyle_P.h
- * @brief ZMap feature colours
- *
- * All features in ZMap can be selected and hence must have both "normal" and "selected"
- * colours. */
-typedef struct
-{
- ZMapStyleColourStruct normal ;
- ZMapStyleColourStruct selected ;
-} ZMapStyleFullColourStruct, *ZMapStyleFullColour ;
-
-/* At most 6 colour specs can be given for any one field (i.e. all the combinations of selected,
- * normal and draw, fill, border. */
-enum {ZMAPSTYLE_MAX_COLOUR_SPECS = 6} ;
-
-
-
-/*! Styles have different modes, e.g. graph, alignment etc, information specific to a particular
- * style is held in its own struct. */
-
-
-/*! @struct ZMapBasicGraph zmapStyle_P.h
- * @brief Basic feature
- *
- * < currently this is empty > */
-typedef struct
-{
- char *dummy ;
-
-} ZMapStyleBasicStruct, *ZMapStyleBasic ;
-
-/*! @struct ZMapSequenceGraph zmapStyle_P.h
- * @brief Sequence feature
- *
- * (currently this is empty) */
-typedef struct
-{
- char *dummy ;
-
-} ZMapStyleSequenceStruct, *ZMapStyleSequence ;
-
-/*! @struct ZMapTextGraph zmapStyle_P.h
- * @brief Text feature
- *
- * (currently this is empty) */
-typedef struct
-{
- char *font;
-
-} ZMapStyleTextStruct, *ZMapStyleText ;
-
-
-
-/*! @struct ZMapStyleGraph zmapStyle_P.h
- * @brief Graph feature
- *
- * Draws a feature as a graph, the feature must contain graph points. */
-typedef struct
-{
- ZMapStyleGraphMode mode ; /*!< Graph style. */
-
- double baseline ; /*!< zero level for graph. */
-
-} ZMapStyleGraphStruct, *ZMapStyleGraph ;
-
-
-
-
-
-/*! @struct ZMapStyleGlyph zmapStyle_P.h
- * @brief Glyph feature
- *
- * Draws shapes of various kinds, e.g. splice site indicators etc. */
-typedef struct
-{
- // sub feature glyphs or glyphs for glyph mode
- GQuark glyph_name,glyph_name_5,glyph_name_3;
- ZMapStyleGlyphShapeStruct glyph; // single glyph or unspecified 5' or 3' end
- ZMapStyleGlyphShapeStruct glyph5; // shape for 5' end
- ZMapStyleGlyphShapeStruct glyph3; // shape for 3' end
- ZMapStyleFullColourStruct glyph_alt_colours;
- ZMapStyleGlyphStrand glyph_strand;
- ZMapStyleGlyphAlign glyph_align;
- guint glyph_threshold;
-
-} ZMapStyleGlyphStruct, *ZMapStyleGlyph ;
-
-
-
-/*! @struct ZMapStyleAlignment zmapStyle_P.h
- * @brief Alignment feature
- *
- * Draws an alignment as a series of blocks joined by straight lines. The lines can be coloured
- * to indicate colinearity between adjacent blocks. */
-typedef struct
- {
- /* If set then blixem will be run with nucleotide or peptide sequences for the features. */
- ZMapStyleBlixemType blixem_type ;
-
- gboolean pfetchable ; /* TRUE => alignments have pfetch entries. */
-
- gboolean allow_misalign; /* TRUE => ref and match sequences
- don't have to be exactly same
- length, ref coords dominate. */
-
- /*! Allowable align errors, used to decide whether a match should be classified as "perfect".
- * between_align_error is used to assess several alignments (e.g. for exon matches) if join_homols = TRUE
- *
- * Number is allowable number of missing bases between blocks/alignments, default is 0. */
- unsigned int between_align_error ;
-
- /*! Colours for bars joining up intra/inter alignment gaps. */
- ZMapStyleFullColourStruct perfect ;
- ZMapStyleFullColourStruct colinear ;
- ZMapStyleFullColourStruct noncolinear ;
- ZMapStyleColumnDisplayState unmarked_colinear; /* paint colinear lines even if not marked */
-
- /* Options for processing gapped aligns. */
- gboolean parse_gaps ; /* TRUE means parse gaps from input data, */
- gboolean show_gaps ; /* TRUE means gaps within alignment are displayed,
- otherwise alignment is displayed as a single block. */
-
-} ZMapStyleAlignmentStruct, *ZMapStyleAlignment ;
-
-
-/*! @struct ZMapStyleTranscript zmapStyle_P.h
- * @brief Transcript feature
- *
- * Draws a transcript as a series of boxes joined by angled lines. */
-typedef struct
-{
- ZMapStyleFullColourStruct CDS_colours ; /*!< Colour for CDS part of feature. */
-
-} ZMapStyleTranscriptStruct, *ZMapStyleTranscript ;
-
-
-/*! @struct ZMapStyleAssemblyPath zmapStyle_P.h
- * @brief AssemblyPath feature
- *
- * Draws an assembly path as a series of boxes placed alternately to form a tiling path. */
-typedef struct
-{
- ZMapStyleFullColourStruct non_path_colours ; /*!< Colour for non-assembly part of feature. */
-
-} ZMapStyleAssemblyPathStruct, *ZMapStyleAssemblyPath ;
-
-
-/* THIS STRUCT NEEDS A MAGIC PTR, ONCE IT HAS ONE THEN ADD A TEST TO zmapStyleIsValid() FOR IT.... */
-
-/*! @struct ZMapFeatureTypeStyle zmapStyle_P.h
- * @brief ZMap Style
- *
- * ZMap Style definition, the style must have a mode which specifies what sort of
- * of feature the style represents. */
-typedef struct _zmapFeatureTypeStyleStruct
-{
- GObject __parent__;
-
-#define STYLE_IS_SET_SIZE ((_STYLE_PROP_N_ITEMS + 7) / 8)
- guchar is_set[STYLE_IS_SET_SIZE]; // flags to say whether fields are set
- // includes mode dependant fields
- // but colours have thier own flags
-
- /*! _All_ styles must have these fields set, no other fields are compulsory. */
- GQuark original_id ; /*!< Original name. */
- GQuark unique_id ; /*!< Name normalised to be unique. */
-
-
- /*! Data fields for the style. */
-
-
- GQuark parent_id ; /*!< Styles can inherit from other
- styles, the parent style _must_ be
- identified by its unique id. */
-
- char *description ; /*!< Description of what this style
- represents. */
-
- ZMapStyleMode mode ; /*!< Specifies how features that
- reference this style will be processed. */
- // must be set before setting mode dependant fields
- // and may not be unset/changed afterwards
-
- GQuark sub_features[ZMAPSTYLE_SUB_FEATURE_MAX]; // style ID quarks indexed by SUBFEATURE ENUM
-
- ZMapStyleFullColourStruct colours ; /*!< Main feature colours. */
-
- /*! Colours for when feature is shown in frames. */
- ZMapStyleFullColourStruct frame0_colours ;
- ZMapStyleFullColourStruct frame1_colours ;
- ZMapStyleFullColourStruct frame2_colours ;
-
- /*! Colours for when feature is shown stranded by colour */
- ZMapStyleFullColourStruct strand_rev_colours;
-
-
- ZMapStyleColumnDisplayState col_display_state ; /* Controls how/when col is displayed. */
-
- ZMapStyleBumpMode default_bump_mode ; /*!< Allows return to original bump mode. */
- ZMapStyleBumpMode curr_bump_mode ; /*!< Controls how features are grouped
- into sub columns within a column. */
- double bump_spacing ; /*!< gap between bumped features. */
-
- ZMapStyle3FrameMode frame_mode ; /*!< Controls how frame sensitive
- features are displayed. */
-
- double min_mag ; /*!< Don't display if fewer bases/line */
- double max_mag ; /*!< Don't display if more bases/line */
-
- double width ; /*!< column width */
-
- ZMapStyleScoreMode score_mode ; /*!< Controls width of features that
- have scores. */
- double min_score, max_score ; /*!< Min/max for score width calc. */
-
-
- /*! GFF feature dumping, allows specifying of source/feature types independently of feature
- * attributes. */
- GQuark gff_source ;
- GQuark gff_feature ;
-
-
- /*! State information for the style. */
- gboolean displayable; /* FALSE means never, ever display,
- for TRUE see col_display_state. */
-
-
- gboolean show_when_empty; /*!< If FALSE, features' column is
- displayed even if there are no features. */
- gboolean bump_fixed; /*!< If TRUE then bump mode cannot be changed. */
-
- gboolean showText; /*!< Should feature text be displayed. */
-
- /*! Strand, show reverse and frame are all linked: something that is frame specific must be
- * strand specific as well.... */
- gboolean strand_specific; /*!< Feature that is on one strand of the dna. */
- gboolean show_rev_strand; /*!< Only display the feature on the
- reverse strand if this is set. */
- gboolean hide_fwd_strand; /* don't show the fwd strand when revcomp'd */
- gboolean show_only_in_separator;
-
- gboolean directional_end; /*!< Display pointy ends on exons etc. */
-
- gboolean deferred; /* flag for to say if this style is deferred loaded */
-
- gboolean loaded; /* flag to say if we're loaded */
-
- gboolean inherited; // style has inherited it's parents
-
- /*! Mode specific fields, see docs for individual structs. */
- union
- {
- ZMapStyleBasicStruct basic ;
- ZMapStyleSequenceStruct sequence ;
- ZMapStyleTextStruct text ;
- ZMapStyleTranscriptStruct transcript ;
- ZMapStyleAssemblyPathStruct assembly_path ;
- ZMapStyleAlignmentStruct alignment ;
- ZMapStyleGraphStruct graph ;
- ZMapStyleGlyphStruct glyph ;
- } mode_data ;
-
-
-} zmapFeatureTypeStyleStruct ;
-
-
-
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
diff --git a/src/zmapGFF/gffparser.c b/src/zmapGFF/gffparser.c
index 1627ff9dd..93763f48a 100755
--- a/src/zmapGFF/gffparser.c
+++ b/src/zmapGFF/gffparser.c
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk,
* Rob Clack (Sanger Institute, UK) rnc@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Nov 19 15:23 2009 (edgrif)
* Created: Wed Jan 11 11:30:39 2006 (rds)
- * CVS info: $Id: gffparser.c,v 1.10 2010-03-04 15:10:35 mh17 Exp $
+ * CVS info: $Id: gffparser.c,v 1.11 2010-06-08 08:31:24 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -50,7 +50,7 @@ typedef struct
-static int parseFile(char *filename, GData *styles) ;
+static int parseFile(char *filename, GHashTable *styles) ;
static GIOChannel *openFileOrDie(char *filename) ;
static int readHeader(parserFile data) ;
static gboolean readFeatures(parserFile data) ;
@@ -59,7 +59,7 @@ static gboolean readFeatures(parserFile data) ;
int main(int argc, char *argv[])
{
int main_rc ;
- GData *styles = NULL;
+ GHashTable *styles = NULL;
#if !defined G_THREADS_ENABLED || defined G_THREADS_IMPL_NONE || !defined G_THREADS_IMPL_POSIX
#error "Cannot compile, threads not properly enabled."
@@ -70,7 +70,7 @@ int main(int argc, char *argv[])
g_thread_init(NULL);
zMapConfigDirCreate(NULL, NULL) ;
-
+
zMapLogCreate(NULL) ;
zMapConfigIniGetStylesFromFile(argv[2],argv[3],&styles); // styles = zMapFeatureTypeGetFromFile(argv[2], argv[3]) ;
@@ -85,12 +85,12 @@ int main(int argc, char *argv[])
-/*
- * Internal routines.
+/*
+ * Internal routines.
*/
-static int parseFile(char *filename, GData *styles)
+static int parseFile(char *filename, GHashTable *styles)
{
parserFileStruct data = {NULL};
@@ -101,7 +101,7 @@ static int parseFile(char *filename, GData *styles)
if(!(readHeader(&data)))
readFeatures(&data);
-
+
zMapGFFDestroyParser(data.parser) ;
g_string_free(data.gff_line, TRUE) ;
@@ -143,13 +143,13 @@ static int readHeader(parserFile data)
if (!zMapGFFParseHeader(data->parser, data->gff_line->str, &done_header))
{
GError *error = zMapGFFGetError(data->parser) ;
-
+
if (!error && (header = zMapGFFGetHeader(data->parser)))
{
/* Header finished..ugh poor interface.... */
break ;
}
-
+
if (!error)
{
printf("error %d\n", __LINE__);
@@ -170,7 +170,7 @@ static int readHeader(parserFile data)
error_occurred = 1;
}
}
-
+
break ;
}
data->gff_line = g_string_truncate(data->gff_line, 0) ;
@@ -197,7 +197,7 @@ static gboolean readFeatures(parserFile data)
parser = data->parser;
gff_file = data->file;
gff_line = data->gff_line;
-
+
while ((status = g_io_channel_read_line_string(gff_file, gff_line, &terminator_pos,
&gff_file_err)) == G_IO_STATUS_NORMAL)
{
@@ -224,7 +224,7 @@ static gboolean readFeatures(parserFile data)
}
else
{
- /* Ignore these for this debugging.
+ /* Ignore these for this debugging.
printf("%s", error->message) ;
*/
}
diff --git a/src/zmapGFF/zmapGFF2Dumper.c b/src/zmapGFF/zmapGFF2Dumper.c
index 1698c7304..1ff5187af 100755
--- a/src/zmapGFF/zmapGFF2Dumper.c
+++ b/src/zmapGFF/zmapGFF2Dumper.c
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: Apr 22 14:46 2010 (edgrif)
* Created: Mon Nov 14 13:21:14 2005 (edgrif)
- * CVS info: $Id: zmapGFF2Dumper.c,v 1.19 2010-04-22 13:49:41 edgrif Exp $
+ * CVS info: $Id: zmapGFF2Dumper.c,v 1.20 2010-06-08 08:31:24 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -65,8 +65,8 @@ GFF_END
#define GFF_SEP_NOSCORE GFF_SEPARATOR "%c"
#define GFF_STRAND_FRAME GFF_SEPARATOR GFF_STRAND GFF_SEPARATOR GFF_FRAME
#define GFF_SEP_ATTRIBUTES GFF_SEPARATOR GFF_ATTRIBUTES
-#define GFF_OBLIGATORY GFF_SEQ_SOURCE_FEAT_START_END GFF_SEP_SCORE GFF_STRAND_FRAME
-#define GFF_OBLIGATORY_NOSCORE GFF_SEQ_SOURCE_FEAT_START_END GFF_SEP_NOSCORE GFF_STRAND_FRAME
+#define GFF_OBLIGATORY GFF_SEQ_SOURCE_FEAT_START_END GFF_SEP_SCORE GFF_STRAND_FRAME
+#define GFF_OBLIGATORY_NOSCORE GFF_SEQ_SOURCE_FEAT_START_END GFF_SEP_NOSCORE GFF_STRAND_FRAME
#define GFF_FULL_LINE GFF_SEQ_SOURCE_FEAT_START_END GFF_SEP_SCORE GFF_STRAND_FRAME GFF_SEP_ATTRIBUTES
typedef struct _GFFDumpDataStruct *GFFDumpData;
@@ -87,7 +87,7 @@ typedef struct
/* Fields are: <sequence> <source> <feature> <start> <end> <score> <strand> <frame> <attributes> */
typedef struct _GFFDumpDataStruct
{
- GData *styles ;
+ GHashTable *styles ;
const char *gff_sequence; /* The sequence name. e.g. 16.12345-23456 */
char *gff_source; /* The source e.g. augustus, TrEMBL, trf, polya_site */
@@ -106,8 +106,8 @@ typedef struct _GFFDumpDataStruct
/* Functions to dump the header section of gff files */
static gboolean dump_full_header(ZMapFeatureAny feature_any, GIOChannel *file, GError **error_out,
const char **sequence_in_out) ;
-static ZMapFeatureContextExecuteStatus get_type_seq_header_cb(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus get_type_seq_header_cb(GQuark key,
+ gpointer data,
gpointer user_data,
char **err_out) ;
@@ -115,7 +115,7 @@ static ZMapFeatureContextExecuteStatus get_type_seq_header_cb(GQuark key,
/* ZMapFeatureDumpFeatureFunc to dump gff. writes lines into gstring buffer... */
static gboolean dump_gff_cb(ZMapFeatureAny feature_any,
- GData *styles,
+ GHashTable *styles,
GString *gff_string,
GError **error,
gpointer user_data);
@@ -156,7 +156,7 @@ static gboolean dump_transcript_subpart_lines(ZMapFeature feature,
static gboolean dump_transcript_foreach_subpart(ZMapFeature feature,
GString *buffer,
GError **error_out,
- GArray *subparts,
+ GArray *subparts,
GFFDumpData gff_data);
@@ -202,18 +202,18 @@ static DumpGFFAttrFunc text_funcs_G[] = {
dump_text_note,
dump_transcript_locus,
NULL
-};
+};
/* NOTE: if we want this to dump a context it will have to cope with lots of different
* sequences for the different alignments...I think the from alignment down is ok but the title
* for the file is not if we have different alignments....and neither are the coords....?????
- *
+ *
* I think we would need multiple Type and sequence-region comment lines for the different
* sequences.
- *
+ *
* */
-gboolean zMapGFFDump(ZMapFeatureAny dump_set, GData *styles, GIOChannel *file, GError **error_out)
+gboolean zMapGFFDump(ZMapFeatureAny dump_set, GHashTable *styles, GIOChannel *file, GError **error_out)
{
gboolean result = TRUE;
@@ -222,7 +222,7 @@ gboolean zMapGFFDump(ZMapFeatureAny dump_set, GData *styles, GIOChannel *file, G
return result;
}
-gboolean zMapGFFDumpRegion(ZMapFeatureAny dump_set, GData *styles,
+gboolean zMapGFFDumpRegion(ZMapFeatureAny dump_set, GHashTable *styles,
ZMapSpan region_span, GIOChannel *file, GError **error_out)
{
const char *sequence = NULL;
@@ -249,22 +249,22 @@ gboolean zMapGFFDumpRegion(ZMapFeatureAny dump_set, GData *styles,
/* This might get overwritten later, but as DumpToFile uses
* Subset, there's a chance it wouldn't get set at all */
- gff_data.gff_sequence = sequence;
+ gff_data.gff_sequence = sequence;
if(region_span)
- result = zMapFeatureContextRangeDumpToFile((ZMapFeatureAny)dump_set, styles, region_span,
+ result = zMapFeatureContextRangeDumpToFile((ZMapFeatureAny)dump_set, styles, region_span,
dump_gff_cb, &gff_data, file, error_out) ;
else
- result = zMapFeatureContextDumpToFile((ZMapFeatureAny)dump_set, styles, dump_gff_cb,
+ result = zMapFeatureContextDumpToFile((ZMapFeatureAny)dump_set, styles, dump_gff_cb,
&gff_data, file, error_out) ;
}
- return result ;
+ return result ;
}
/*!
* \brief Dump a list of ZMapFeatureAny. sequence can be NULL
*/
-gboolean zMapGFFDumpList(GList *dump_list, GData *styles, char *sequence, GIOChannel *file, GError **error_out)
+gboolean zMapGFFDumpList(GList *dump_list, GHashTable *styles, char *sequence, GIOChannel *file, GError **error_out)
{
const char *int_sequence = NULL;
gboolean result = FALSE ;
@@ -290,16 +290,16 @@ gboolean zMapGFFDumpList(GList *dump_list, GData *styles, char *sequence, GIOCha
/* This might get overwritten later, but as DumpToFile uses
* Subset, there's a chance it wouldn't get set at all */
- gff_data.gff_sequence = int_sequence;
+ gff_data.gff_sequence = int_sequence;
- result = zMapFeatureListDumpToFile(dump_list, styles, dump_gff_cb, &gff_data,
+ result = zMapFeatureListDumpToFile(dump_list, styles, dump_gff_cb, &gff_data,
file, error_out) ;
}
return result ;
}
-gboolean zMapGFFDumpForeachList(ZMapFeatureAny first_feature, GData *styles,
+gboolean zMapGFFDumpForeachList(ZMapFeatureAny first_feature, GHashTable *styles,
GIOChannel *file, GError **error_out,
char *sequence,
GFunc *list_func_out, gpointer *list_data_out)
@@ -325,10 +325,10 @@ gboolean zMapGFFDumpForeachList(ZMapFeatureAny first_feature, GData *styles,
/* This might get overwritten later, but as DumpToFile uses
* Subset, there's a chance it wouldn't get set at all */
- gff_data->gff_sequence = int_sequence;
+ gff_data->gff_sequence = int_sequence;
result = zMapFeatureListForeachDumperCreate(dump_gff_cb, styles, gff_data, g_free,
- file, error_out,
+ file, error_out,
list_func_out, list_data_out) ;
}
}
@@ -355,7 +355,7 @@ static gboolean dump_full_header(ZMapFeatureAny feature_any, GIOChannel *file, G
header_data.gff_sequence = *sequence_in_out;
/* gff-version, source-version, date */
- g_string_append_printf(header_data.header_string,
+ g_string_append_printf(header_data.header_string,
"##gff-version %d\n"
"##source-version %s %s\n"
"##date %s\n",
@@ -367,15 +367,15 @@ static gboolean dump_full_header(ZMapFeatureAny feature_any, GIOChannel *file, G
zMapFeatureContextExecute(feature_any, ZMAPFEATURE_STRUCT_BLOCK,
get_type_seq_header_cb, &header_data);
-
+
if(header_data.status)
{
GIOStatus write_status ;
gsize bytes_written ;
- if ((write_status = g_io_channel_write_chars(file,
- header_data.header_string->str,
- header_data.header_string->len,
+ if ((write_status = g_io_channel_write_chars(file,
+ header_data.header_string->str,
+ header_data.header_string->len,
&bytes_written, error_out)) != G_IO_STATUS_NORMAL)
{
header_data.status = FALSE;
@@ -390,8 +390,8 @@ static gboolean dump_full_header(ZMapFeatureAny feature_any, GIOChannel *file, G
return header_data.status;
}
-static ZMapFeatureContextExecuteStatus get_type_seq_header_cb(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus get_type_seq_header_cb(GQuark key,
+ gpointer data,
gpointer user_data,
char **err_out)
{
@@ -402,7 +402,7 @@ static ZMapFeatureContextExecuteStatus get_type_seq_header_cb(GQuark key,
switch(feature_any->struct_type)
{
case ZMAPFEATURE_STRUCT_CONTEXT:
-
+
break;
case ZMAPFEATURE_STRUCT_ALIGN:
if(header_data->status && header_data->cont)
@@ -426,17 +426,17 @@ static ZMapFeatureContextExecuteStatus get_type_seq_header_cb(GQuark key,
ZMapFeatureBlock feature_block = (ZMapFeatureBlock)feature_any;
gboolean reversed = FALSE;
int start, end;
-
+
start = feature_block->block_to_sequence.q1;
end = feature_block->block_to_sequence.q2;
-
+
/* I'm a little unsure about the strand stuff...think more about this... */
if (feature_block->block_to_sequence.q_strand == ZMAPSTRAND_REVERSE)
reversed = TRUE ;
-
+
g_string_append_printf(header_data->header_string,
"##sequence-region %s %d %d %s\n",
- g_quark_to_string(feature_any->original_id),
+ g_quark_to_string(feature_any->original_id),
start, end, (reversed ? "(reversed)" : "")) ;
header_data->status = TRUE;
header_data->cont = FALSE;
@@ -452,15 +452,15 @@ static ZMapFeatureContextExecuteStatus get_type_seq_header_cb(GQuark key,
return status;
}
-static gboolean dump_gff_cb(ZMapFeatureAny feature_any,
- GData *styles,
+static gboolean dump_gff_cb(ZMapFeatureAny feature_any,
+ GHashTable *styles,
GString *gff_string,
GError **error,
gpointer user_data)
{
GFFDumpData gff_data = (GFFDumpData)user_data;
gboolean result = TRUE;
-
+
switch(feature_any->struct_type)
{
case ZMAPFEATURE_STRUCT_ALIGN:
@@ -487,7 +487,7 @@ static gboolean dump_gff_cb(ZMapFeatureAny feature_any,
gff_data->gff_source = (char *)zMapStyleGetName(style);
if(!(gff_data->gff_feature = (char *)zMapStyleGetGFFFeature(style)))
gff_data->gff_feature = (char *)g_quark_to_string(feature->ontology);
-
+
/* Obligatory fields. */
g_string_append_printf(gff_string,
GFF_SEQ_SOURCE_FEAT_START_END,
@@ -501,7 +501,7 @@ static gboolean dump_gff_cb(ZMapFeatureAny feature_any,
g_string_append_printf(gff_string, GFF_SEP_SCORE, feature->score) ;
else
g_string_append_printf(gff_string, GFF_SEP_NOSCORE, '.') ;
-
+
g_string_append_printf(gff_string, GFF_STRAND_FRAME,
strand2Char(feature->strand),
phase2Char(feature->phase)) ;
@@ -511,8 +511,8 @@ static gboolean dump_gff_cb(ZMapFeatureAny feature_any,
switch(feature->type)
{
case ZMAPSTYLE_MODE_BASIC:
- {
- result = dump_attributes(gff_data->basic, feature,
+ {
+ result = dump_attributes(gff_data->basic, feature,
&(feature->feature.basic),
gff_string, error, gff_data);
}
@@ -524,15 +524,15 @@ static gboolean dump_gff_cb(ZMapFeatureAny feature_any,
gff_data->link_term = "Sequence";
gff_data->link_term = gff_data->gff_feature;
- result = dump_attributes(gff_data->transcript, feature,
+ result = dump_attributes(gff_data->transcript, feature,
&(feature->feature.transcript),
gff_string, error, gff_data);
-
+
}
break;
case ZMAPSTYLE_MODE_ALIGNMENT:
{
- result = dump_attributes(gff_data->homol, feature,
+ result = dump_attributes(gff_data->homol, feature,
&(feature->feature.homol),
gff_string, error, gff_data);
}
@@ -585,10 +585,10 @@ static gboolean dump_attributes(DumpGFFAttrFunc func_array[],
if((*funcs_ptr)(feature, feature_data, gff_string, error, gff_data))
need_separator = TRUE;
-
+
funcs_ptr++;
}
-
+
return result;
}
@@ -602,7 +602,7 @@ static gboolean dump_text_note(ZMapFeature feature,
if(feature->description)
{
- g_string_append_printf(gff_string,
+ g_string_append_printf(gff_string,
GFF_ATTRIBUTE_TAB_BEGIN GFF_QUOTED_ATTRIBUTE GFF_ATTRIBUTE_TAB_END,
"Note", feature->description);
result = TRUE;
@@ -624,11 +624,11 @@ static gboolean dump_transcript_identifier(ZMapFeature feature,
gboolean result = TRUE;
/* To make Sequence "AC12345.1" */
- g_string_append_printf(gff_string,
+ g_string_append_printf(gff_string,
GFF_ATTRIBUTE_TAB_BEGIN GFF_QUOTED_ATTRIBUTE GFF_ATTRIBUTE_TAB_END,
gff_data->link_term,
gff_data->feature_name);
-
+
return result;
}
@@ -644,13 +644,13 @@ static gboolean dump_transcript_locus(ZMapFeature feature,
if(feature->locus_id)
{
/* To make Locus "AC12345.1" */
- g_string_append_printf(gff_string,
+ g_string_append_printf(gff_string,
GFF_ATTRIBUTE_TAB_BEGIN GFF_QUOTED_ATTRIBUTE GFF_ATTRIBUTE_TAB_END,
"Locus",
(char *)g_quark_to_string(feature->locus_id));
result = TRUE;
}
-
+
return result;
}
@@ -668,7 +668,7 @@ static gboolean dump_transcript_subpart_lines(ZMapFeature feature,
if(result && transcript->exons)
{
gff_data->gff_feature = "exon";
- result = dump_transcript_foreach_subpart(feature, gff_string, error,
+ result = dump_transcript_foreach_subpart(feature, gff_string, error,
transcript->exons, gff_data);
}
@@ -682,19 +682,19 @@ static gboolean dump_transcript_subpart_lines(ZMapFeature feature,
if(result && transcript->flags.cds)
{
gff_data->gff_feature = "CDS";
- g_string_append_printf(gff_string,
+ g_string_append_printf(gff_string,
"\n" GFF_OBLIGATORY_NOSCORE,
gff_data->gff_sequence,
gff_data->gff_source,
gff_data->gff_feature,
- transcript->cds_start,
+ transcript->cds_start,
transcript->cds_end,
'.',
strand2Char(feature->strand),
phase2Char(feature->phase)) ;
-
+
result = dump_transcript_identifier(feature, transcript,
- gff_string, error,
+ gff_string, error,
gff_data);
}
@@ -704,7 +704,7 @@ static gboolean dump_transcript_subpart_lines(ZMapFeature feature,
static gboolean dump_transcript_foreach_subpart(ZMapFeature feature,
GString *buffer,
GError **error_out,
- GArray *subparts,
+ GArray *subparts,
GFFDumpData gff_data)
{
gboolean result = TRUE ;
@@ -731,7 +731,7 @@ static gboolean dump_transcript_foreach_subpart(ZMapFeature feature,
result = dump_transcript_identifier(feature, &(feature->feature.transcript),
buffer, error_out, gff_data);
}
-
+
return result ;
}
@@ -747,7 +747,7 @@ static gboolean dump_alignment_target(ZMapFeature feature, gpointer homol_data,
if(feature->original_id)
{
- g_string_append_printf(gff_string,
+ g_string_append_printf(gff_string,
GFF_ATTRIBUTE_TAB_BEGIN GFF_QUOTED_ATTRIBUTE " %d %d" GFF_ATTRIBUTE_TAB_END,
"Target", g_quark_to_string(feature->original_id),
homol->y1, homol->y2);
@@ -770,28 +770,28 @@ static gboolean dump_alignment_gaps(ZMapFeature feature, gpointer homol_data,
has_gaps = TRUE;
g_string_append_printf(gff_string, GFF_ATTRIBUTE_TAB_BEGIN "%s ", "Gaps");
-
+
g_string_append_c(gff_string, '"');
for(i = 0; i < gaps_array->len; i++)
{
ZMapAlignBlock block = NULL;
-
+
block = &(g_array_index(gaps_array, ZMapAlignBlockStruct, i));
-
- g_string_append_printf(gff_string, "%d %d %d %d,",
- block->q1, block->q2,
+
+ g_string_append_printf(gff_string, "%d %d %d %d,",
+ block->q1, block->q2,
block->t1, block->t2);
}
-
+
/* remove the last comma! */
g_string_truncate(gff_string, gff_string->len - 1);
/* and add a quote and a tab?*/
- g_string_append_printf(gff_string,
+ g_string_append_printf(gff_string,
"%c" GFF_ATTRIBUTE_TAB_END,
'"');
}
-
+
return has_gaps;
}
@@ -804,7 +804,7 @@ static gboolean dump_alignment_clone(ZMapFeature feature, gpointer homol_data,
if(homol->flags.has_clone_id)
{
- g_string_append_printf(gff_string,
+ g_string_append_printf(gff_string,
GFF_ATTRIBUTE_TAB_BEGIN GFF_QUOTED_ATTRIBUTE GFF_ATTRIBUTE_TAB_END,
"Clone", g_quark_to_string(homol->clone_id));
has_clone = TRUE;
@@ -821,8 +821,8 @@ static gboolean dump_alignment_length(ZMapFeature feature, gpointer homol_data,
gboolean has_length = FALSE;
if(homol->length)
- {
- g_string_append_printf(gff_string,
+ {
+ g_string_append_printf(gff_string,
GFF_ATTRIBUTE_TAB_BEGIN "Length %d" GFF_ATTRIBUTE_TAB_END,
homol->length);
has_length = TRUE;
diff --git a/src/zmapGFF/zmapGFF2parser.c b/src/zmapGFF/zmapGFF2parser.c
index 68beae32e..1cdca5bdf 100755
--- a/src/zmapGFF/zmapGFF2parser.c
+++ b/src/zmapGFF/zmapGFF2parser.c
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: Apr 28 09:11 2010 (edgrif)
* Created: Fri May 28 14:25:12 2004 (edgrif)
- * CVS info: $Id: zmapGFF2parser.c,v 1.110 2010-05-19 13:15:31 mh17 Exp $
+ * CVS info: $Id: zmapGFF2parser.c,v 1.111 2010-06-08 08:31:24 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -143,7 +143,7 @@ ZMapGFFParser zMapGFFCreateParser(void)
/* We should do this internally with a var in the parser struct.... */
/* This function must be called prior to parsing feature lines, it is not required
* for either the header lines or sequences. */
-gboolean zMapGFFParserInitForFeatures(ZMapGFFParser parser, GData *sources, gboolean parse_only)
+gboolean zMapGFFParserInitForFeatures(ZMapGFFParser parser, GHashTable *sources, gboolean parse_only)
{
gboolean result = FALSE ;
GQuark locus_id ;
@@ -1158,7 +1158,7 @@ static gboolean makeNewFeature(ZMapGFFParser parser, NameFindType name_find,
char *feature_name_id = NULL, *feature_name = NULL ;
GQuark feature_style_id ;
ZMapFeatureSet feature_set = NULL ;
- ZMapFeatureTypeStyle feature_set_style, feature_style ;
+ ZMapFeatureTypeStyle feature_set_style = NULL, feature_style = NULL;
ZMapFeature feature = NULL ;
ZMapGFFParserFeatureSet parser_feature_set = NULL ;
char *feature_set_name = NULL ;
@@ -1232,11 +1232,18 @@ static gboolean makeNewFeature(ZMapGFFParser parser, NameFindType name_find,
feature_set_name = source ;
}
+ // get the feature set so that we can find the style for the feature;
+ parser_feature_set = (ZMapGFFParserFeatureSet)g_datalist_get_data(&(parser->feature_sets),
+ feature_set_name);
+ // we know featureset is set (see below) but this costs little
+ if(parser_feature_set && parser_feature_set->feature_set)
+ feature_set_style = parser_feature_set->feature_set->style;
/* If a feature set style or a feature style is missing then we can't carry on.
* NOTE the feature sets style has the same name as the feature set. */
- if (!(feature_set_style = zMapFindStyle(parser->sources, feature_style_id)))
+
+ if (!feature_set_style && !(feature_set_style = zMapFindStyle(parser->sources, feature_style_id)))
{
*err_text = g_strdup_printf("feature ignored, could not find style \"%s\" for feature set \"%s\".",
g_quark_to_string(feature_style_id), feature_set_name) ;
@@ -1244,8 +1251,10 @@ static gboolean makeNewFeature(ZMapGFFParser parser, NameFindType name_find,
return result ;
}
+ feature_style = feature_set_style;
- if (!(feature_style = zMapFindStyle(parser->sources, feature_style_id)))
+#if MH17_NOT_NEEDED
+ if (!feature_style && !(feature_style = zMapFindStyle(parser->sources, feature_style_id)))
{
*err_text = g_strdup_printf("feature ignored, could not find its style \"%s\".",
g_quark_to_string(feature_style_id)) ;
@@ -1253,7 +1262,7 @@ static gboolean makeNewFeature(ZMapGFFParser parser, NameFindType name_find,
return result ;
}
-
+#endif
/* I'M NOT HAPPY WITH THIS, IT DOESN'T WORK AS A CONCEPT....NEED TYPES IN FEATURE STRUCT
* AND IN STYLE...BUT THEY HAVE DIFFERENT PURPOSE.... */
@@ -1308,9 +1317,9 @@ static gboolean makeNewFeature(ZMapGFFParser parser, NameFindType name_find,
/* Check if the feature_set_name for this feature is already known, if it is then check if there
* is already a multiline feature with the same name as we will need to augment it with this data. */
- if (!parser->parse_only &&
- (parser_feature_set = (ZMapGFFParserFeatureSet)g_datalist_get_data(&(parser->feature_sets),
- feature_set_name)))
+ if (!parser->parse_only && parser_feature_set)
+// (parser_feature_set = (ZMapGFFParserFeatureSet)g_datalist_get_data(&(parser->feature_sets),
+// feature_set_name)))
{
feature_set = parser_feature_set->feature_set ;
@@ -1348,7 +1357,14 @@ static gboolean makeNewFeature(ZMapGFFParser parser, NameFindType name_find,
feature_set = parser_feature_set->feature_set = zMapFeatureSetCreate(feature_set_name, NULL) ;
- zMapFeatureSetStyle(feature_set, feature_set_style) ; /* Set the style for the set. */
+ // thse are both the same, feature_set_style no longer used
+ // but ZMap now has a column style in addition
+ // zMapFeatureSetStyle(feature_set, feature_set_style) ; /* Set the style for the set. */
+
+ // we need a copy as these may be re-used.
+ // styles have already been inherited by this point by zmapView code and passed back to us
+ feature_style = zMapFeatureStyleCopy(feature_style);
+ zMapFeatureSetStyle(feature_set, feature_style) ; /* Set the style for the set. */
parser_feature_set->multiline_features = NULL ;
g_datalist_init(&(parser_feature_set->multiline_features)) ;
@@ -1462,7 +1478,7 @@ static gboolean makeNewFeature(ZMapGFFParser parser, NameFindType name_find,
result = zMapFeatureAddAlignmentData(feature, clone_id,
query_start, query_end,
homol_type, query_length, query_strand, ZMAPPHASE_0,
- gaps, zmapStyleGetWithinAlignError(feature_style),
+ gaps, zMapStyleGetWithinAlignError(feature_style),
local_sequence) ;
}
else if (feature_type == ZMAPSTYLE_MODE_ASSEMBLY_PATH)
@@ -2463,6 +2479,9 @@ static void destroyFeatureArray(gpointer data)
/* No data to free in this list, just clear it. */
g_datalist_clear(&(parser_feature_set->multiline_features)) ;
+ if(parser_feature_set->feature_set && parser_feature_set->feature_set->style)
+ zMapStyleDestroy(parser_feature_set->feature_set->style);
+
g_free(parser_feature_set) ;
diff --git a/src/zmapGFF/zmapGFF_P.h b/src/zmapGFF/zmapGFF_P.h
index bf468fd90..6eb6fa2ba 100755
--- a/src/zmapGFF/zmapGFF_P.h
+++ b/src/zmapGFF/zmapGFF_P.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -27,7 +27,7 @@
* HISTORY:
* Last edited: Apr 22 14:26 2010 (edgrif)
* Created: Sat May 29 13:18:32 2004 (edgrif)
- * CVS info: $Id: zmapGFF_P.h,v 1.22 2010-04-22 13:51:48 edgrif Exp $
+ * CVS info: $Id: zmapGFF_P.h,v 1.23 2010-06-08 08:31:24 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_GFF_P_H
@@ -69,7 +69,7 @@ typedef enum
{
GFF_BUF_SEQUENCE, GFF_BUF_SOURCE, GFF_BUF_FEATURE_TYPE,
GFF_BUF_SCORE, GFF_BUF_STRAND, GFF_BUF_PHASE,
- GFF_BUF_ATTRIBUTES, GFF_BUF_COMMENTS,
+ GFF_BUF_ATTRIBUTES, GFF_BUF_COMMENTS,
GFF_BUF_NUM
} GFFStringFieldsType ;
@@ -151,7 +151,8 @@ typedef struct ZMapGFFParserStruct_
GQuark locus_set_id ; /* If not zero then make a locus set from
locus tags in sequence objects. */
- GData *sources ; /* If present, only make features from
+ // NB for sources read styles
+ GHashTable *sources ; /* If present, only make features from
GFF records with a source from this
list. */
@@ -165,7 +166,7 @@ typedef struct ZMapGFFParserStruct_
* known line length and construct a format string for the scanf using this length. */
gsize buffer_length ;
char **buffers[GFF_BUF_NUM] ;
- char *format_str ;
+ char *format_str ;
/* Parsing DNA sequence data, used when DNA sequence is embedded in the file. */
struct
diff --git a/src/zmapServer/acedb/acedbServer.c b/src/zmapServer/acedb/acedbServer.c
index 8680a037f..cfc890055 100755
--- a/src/zmapServer/acedb/acedbServer.c
+++ b/src/zmapServer/acedb/acedbServer.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Apr 21 17:20 2010 (edgrif)
* Created: Wed Aug 6 15:46:38 2003 (edgrif)
- * CVS info: $Id: acedbServer.c,v 1.156 2010-05-19 13:15:31 mh17 Exp $
+ * CVS info: $Id: acedbServer.c,v 1.157 2010-06-08 08:31:24 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -62,7 +62,7 @@ typedef struct
{
GList *methods ;
GHashTable *method_2_data ;
- GData *styles ;
+ GHashTable *styles ;
} LoadableStruct, *Loadable ;
@@ -96,7 +96,7 @@ typedef struct
{
ZMapServerResponseType result ;
AcedbServer server ;
- GData *styles ;
+ GHashTable *styles ;
GHFunc eachBlock ;
} DoAllAlignBlocksStruct, *DoAllAlignBlocks ;
@@ -111,7 +111,7 @@ typedef struct
typedef struct
{
GHashTable *method_2_data ;
- GData *styles;
+ GHashTable *styles;
GList *fetch_methods ;
} MethodFetchStruct, *MethodFetch ;
@@ -162,12 +162,12 @@ static ZMapServerResponseType getFeatureSetNames(void *server,
GHashTable **featureset_2_stylelist_inout,
GHashTable **featureset_2_column_inout,
GHashTable **source_2_sourcedata_inout) ;
-static ZMapServerResponseType getStyles(void *server, GData **styles_out) ;
+static ZMapServerResponseType getStyles(void *server, GHashTable **styles_out) ;
static ZMapServerResponseType haveModes(void *server, gboolean *have_mode) ;
static ZMapServerResponseType getSequences(void *server_in, GList *sequences_inout) ;
static ZMapServerResponseType setContext(void *server, ZMapFeatureContext feature_context) ;
-static ZMapServerResponseType getFeatures(void *server_in, GData *styles, ZMapFeatureContext feature_context_out) ;
-static ZMapServerResponseType getContextSequence(void *server_in, GData *styles, ZMapFeatureContext feature_context_out) ;
+static ZMapServerResponseType getFeatures(void *server_in, GHashTable *styles, ZMapFeatureContext feature_context_out) ;
+static ZMapServerResponseType getContextSequence(void *server_in, GHashTable *styles, ZMapFeatureContext feature_context_out) ;
static char *lastErrorMsg(void *server) ;
static ZMapServerResponseType closeConnection(void *server_in) ;
static ZMapServerResponseType destroyConnection(void *server) ;
@@ -179,13 +179,13 @@ static ZMapServerResponseType findColStyleTags(AcedbServer server,
GList **feature_methods_out,
GList **required_styles_out,
GHashTable **featureset_2_stylelist_inout) ;
-static GList *getMethodsLoadable(GList *all_methods, GHashTable *method_2_data, GData *styles) ;
+static GList *getMethodsLoadable(GList *all_methods, GHashTable *method_2_data, GHashTable *styles) ;
static void loadableCB(gpointer data, gpointer user_data) ;
static char *getMethodString(GList *styles_or_style_names,
gboolean style_name_list, gboolean find_string, gboolean find_methods) ;
static void addTypeName(gpointer data, gpointer user_data) ;
-static gboolean sequenceRequest(AcedbServer server, GData *styles, ZMapFeatureBlock feature_block) ;
-static gboolean blockDNARequest(AcedbServer server, GData *styles, ZMapFeatureBlock feature_block) ;
+static gboolean sequenceRequest(AcedbServer server, GHashTable *styles, ZMapFeatureBlock feature_block) ;
+static gboolean blockDNARequest(AcedbServer server, GHashTable *styles, ZMapFeatureBlock feature_block) ;
static gboolean getDNARequest(AcedbServer server, char *sequence_name, int start, int end,
int *dna_length_out, char **dna_sequence_out) ;
static gboolean getSequenceMapping(AcedbServer server, ZMapFeatureContext feature_context) ;
@@ -199,7 +199,7 @@ static gboolean checkServerVersion(AcedbServer server) ;
static gboolean findSequence(AcedbServer server, char *sequence_name) ;
static gboolean setQuietMode(AcedbServer server) ;
-static gboolean parseTypes(AcedbServer server, GData **styles_out,
+static gboolean parseTypes(AcedbServer server, GHashTable **styles_out,
ParseMethodNamesFunc parse_func_in, gpointer user_data) ;
static ZMapServerResponseType findMethods(AcedbServer server, char *search_str, int *num_found) ;
static ZMapServerResponseType getObjNames(AcedbServer server, GList **style_names_out) ;
@@ -626,7 +626,7 @@ static ZMapServerResponseType getFeatureSetNames(void *server_in,
-static ZMapServerResponseType getStyles(void *server_in, GData **styles_out)
+static ZMapServerResponseType getStyles(void *server_in, GHashTable **styles_out)
{
ZMapServerResponseType result = ZMAP_SERVERRESPONSE_REQFAIL ;
AcedbServer server = (AcedbServer)server_in ;
@@ -748,7 +748,7 @@ static ZMapServerResponseType setContext(void *server_in, ZMapFeatureContext fea
/* Get features sequence. */
-static ZMapServerResponseType getFeatures(void *server_in, GData *styles, ZMapFeatureContext feature_context)
+static ZMapServerResponseType getFeatures(void *server_in, GHashTable *styles, ZMapFeatureContext feature_context)
{
AcedbServer server = (AcedbServer)server_in ;
DoAllAlignBlocksStruct get_features ;
@@ -788,7 +788,7 @@ static ZMapServerResponseType getFeatures(void *server_in, GData *styles, ZMapFe
/* Get features and/or sequence. */
-static ZMapServerResponseType getContextSequence(void *server_in, GData *styles, ZMapFeatureContext feature_context)
+static ZMapServerResponseType getContextSequence(void *server_in, GHashTable *styles, ZMapFeatureContext feature_context)
{
AcedbServer server = (AcedbServer)server_in ;
DoAllAlignBlocksStruct get_sequence ;
@@ -1060,7 +1060,7 @@ static ZMapServerResponseType findColStyleTags(AcedbServer server,
-static GList *getMethodsLoadable(GList *all_methods, GHashTable *method_2_data, GData *styles)
+static GList *getMethodsLoadable(GList *all_methods, GHashTable *method_2_data, GHashTable *styles)
{
GList *loadable_methods = NULL ;
LoadableStruct loadable_data ;
@@ -1096,7 +1096,7 @@ static void loadableCB(gpointer data, gpointer user_data)
{
gboolean deferred = FALSE ;
- g_object_get(style, ZMAPSTYLE_PROPERTY_DEFERRED, &deferred, NULL) ;
+ g_object_get(G_OBJECT(style), ZMAPSTYLE_PROPERTY_DEFERRED, &deferred, NULL) ;
if (!deferred)
loadable_data->methods = g_list_append(loadable_data->methods, GUINT_TO_POINTER(data)) ;
@@ -1216,7 +1216,7 @@ static void addTypeName(gpointer data, gpointer user_data)
* I guess the best thing is to shove the errors out to the log and look for the gff start...
*
*/
-static gboolean sequenceRequest(AcedbServer server, GData *styles, ZMapFeatureBlock feature_block)
+static gboolean sequenceRequest(AcedbServer server, GHashTable *styles, ZMapFeatureBlock feature_block)
{
gboolean result = FALSE ;
char *gene_finder_cmds = "seqactions -gf_features no_draw ;" ;
@@ -1529,7 +1529,7 @@ static void eachBlockDNARequest(gpointer key, gpointer data, gpointer user_data)
*
*
*/
-static gboolean blockDNARequest(AcedbServer server, GData *styles, ZMapFeatureBlock feature_block)
+static gboolean blockDNARequest(AcedbServer server, GHashTable *styles, ZMapFeatureBlock feature_block)
{
gboolean result = FALSE ;
ZMapFeatureContext context = NULL ;
@@ -2211,7 +2211,7 @@ static gboolean getServerInfo(AcedbServer server, ZMapServerInfo info)
*
*
* */
-static gboolean parseTypes(AcedbServer server, GData **types_out,
+static gboolean parseTypes(AcedbServer server, GHashTable **types_out,
ParseMethodNamesFunc parse_func_in, gpointer user_data)
{
gboolean result = FALSE ;
@@ -2219,7 +2219,7 @@ static gboolean parseTypes(AcedbServer server, GData **types_out,
char *acedb_request = NULL ;
void *reply = NULL ;
int reply_len = 0 ;
- GData *types = NULL ;
+ GHashTable *types = NULL ;
/* Get all the methods and then filter them if there are requested types. */
command = "show -a" ;
@@ -2264,7 +2264,7 @@ static gboolean parseTypes(AcedbServer server, GData **types_out,
}
else if ((style = (parse_func)(next_line, &curr_pos, &col_group)))
{
- g_datalist_id_set_data(&types, zMapStyleGetUniqueID(style), style) ;
+ g_hash_table_insert(types, GUINT_TO_POINTER(zMapStyleGetUniqueID(style)), style) ;
num_types++ ;
}
diff --git a/src/zmapServer/das/dasServer.c b/src/zmapServer/das/dasServer.c
index f1312abdf..64e3cab58 100755
--- a/src/zmapServer/das/dasServer.c
+++ b/src/zmapServer/das/dasServer.c
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: Jan 14 10:10 2010 (edgrif)
* Created: Wed Aug 6 15:46:38 2003 (edgrif)
- * CVS info: $Id: dasServer.c,v 1.46 2010-05-17 14:41:15 mh17 Exp $
+ * CVS info: $Id: dasServer.c,v 1.47 2010-06-08 08:31:24 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -42,14 +42,14 @@ typedef struct
{
ZMapServerResponseType result ;
DasServer server ;
- GData *styles ;
+ GHashTable *styles ;
} GetFeaturesStruct, *GetFeatures ;
typedef struct
{
ZMapFeatureBlock block;
DasServer server;
- GData *styles ;
+ GHashTable *styles ;
} BlockServerStruct, *BlockServer;
typedef struct
@@ -62,7 +62,7 @@ typedef struct
{
ZMapServerResponseType result ;
DasServer server;
- GData *output;
+ GHashTable *output;
}DasServerTypesStruct, *DasServerTypes;
typedef struct
@@ -88,7 +88,7 @@ static gboolean createConnection(void **server_out,
char *version_str, int timeout) ;
static ZMapServerResponseType openConnection(void *server,gboolean sequence_server) ;
static ZMapServerResponseType getInfo(void *server, ZMapServerInfo info) ;
-static ZMapServerResponseType getStyles(void *server, GData **styles_out) ;
+static ZMapServerResponseType getStyles(void *server, GHashTable **styles_out) ;
static ZMapServerResponseType haveModes(void *server, gboolean *have_mode) ;
static ZMapServerResponseType getSequences(void *server_in, GList *sequences_inout) ;
static ZMapServerResponseType getFeatureSets(void *server,
@@ -99,8 +99,8 @@ static ZMapServerResponseType getFeatureSets(void *server,
GHashTable **featureset_2_column_inout,
GHashTable **source_2_sourcedata_inout) ;
static ZMapServerResponseType setContext(void *server, ZMapFeatureContext feature_context);
-static ZMapServerResponseType getFeatures(void *server_in, GData *styles, ZMapFeatureContext feature_context) ;
-static ZMapServerResponseType getContextSequence(void *server_in, GData *styles, ZMapFeatureContext feature_context) ;
+static ZMapServerResponseType getFeatures(void *server_in, GHashTable *styles, ZMapFeatureContext feature_context) ;
+static ZMapServerResponseType getContextSequence(void *server_in, GHashTable *styles, ZMapFeatureContext feature_context) ;
static char *lastErrorMsg(void *server) ;
static ZMapServerResponseType closeConnection(void *server) ;
static ZMapServerResponseType destroyConnection(void *server) ;
@@ -120,7 +120,7 @@ static void initialiseXMLParser(DasServer server);
static void getFeatures4Aligns(gpointer key, gpointer data, gpointer userData);
static void getFeatures4Blocks(gpointer key, gpointer data, gpointer userData) ;
-static gboolean fetchFeatures(DasServer server, GData *styles, ZMapFeatureBlock block);
+static gboolean fetchFeatures(DasServer server, GHashTable *styles, ZMapFeatureBlock block);
/* curl required */
@@ -137,7 +137,7 @@ static void typesFilter (ZMapDAS1Type type, gpointer user_data
static void featureFilter (ZMapDAS1Feature feature, gpointer user_data);
static void stylesheetFilter (ZMapDAS1Stylesheet style, gpointer user_data);
-static void applyGlyphToEachType(GQuark style_id, gpointer data, gpointer user_data) ;
+static void applyGlyphToEachType(gpointer style_id, gpointer data, gpointer user_data) ;
static gboolean getRequestedDSN(DasServer das, ZMapDAS1DSN *dsn_out);
@@ -384,7 +384,7 @@ static ZMapServerResponseType getInfo(void *server_in, ZMapServerInfo info)
-static ZMapServerResponseType getStyles(void *server_in, GData **types)
+static ZMapServerResponseType getStyles(void *server_in, GHashTable **types)
{
ZMapServerResponseType result = ZMAP_SERVERRESPONSE_OK;
DasServer server = (DasServer)server_in;
@@ -487,7 +487,7 @@ static ZMapServerResponseType setContext(void *server, ZMapFeatureContext featur
}
-static ZMapServerResponseType getFeatures(void *server_in, GData *styles, ZMapFeatureContext feature_context)
+static ZMapServerResponseType getFeatures(void *server_in, GHashTable *styles, ZMapFeatureContext feature_context)
{
ZMapServerResponseType result = ZMAP_SERVERRESPONSE_OK;
DasServer server = (DasServer)server_in;
@@ -503,7 +503,7 @@ static ZMapServerResponseType getFeatures(void *server_in, GData *styles, ZMapFe
}
-static ZMapServerResponseType getContextSequence(void *server_in, GData *styles, ZMapFeatureContext feature_context)
+static ZMapServerResponseType getContextSequence(void *server_in, GHashTable *styles, ZMapFeatureContext feature_context)
{
ZMapServerResponseType result = ZMAP_SERVERRESPONSE_OK ;
@@ -995,7 +995,7 @@ static void getFeatures4Blocks(gpointer key, gpointer data, gpointer userData)
return ;
}
-static gboolean fetchFeatures(DasServer server, GData *styles, ZMapFeatureBlock block)
+static gboolean fetchFeatures(DasServer server, GHashTable *styles, ZMapFeatureBlock block)
{
char *segStr = NULL, *query = NULL, *url = NULL;
requestParseDetailStruct detail = {0};
@@ -1308,7 +1308,7 @@ static void typesFilter (ZMapDAS1Type type, gpointer user_data
zMapStyleSetWidth(style, width) ;
- g_datalist_id_set_data(&(server_types->output), zMapStyleGetID(style), style) ;
+ g_hash_table_insert(server_types->output, GUINT_TO_POINTER(zMapStyleGetID(style)), (gpointer) style) ;
return ;
}
@@ -1332,7 +1332,7 @@ static void featureFilter (ZMapDAS1Feature feature, gpointer user_data
/* gdouble feature_score = 0.0; */
gboolean has_score = TRUE;
- GData *all_styles = NULL;
+ GHashTable *all_styles = NULL;
char *feature_name = NULL,
*short_ft_name = NULL,
*type_name = NULL,
@@ -1409,7 +1409,7 @@ static void featureFilter (ZMapDAS1Feature feature, gpointer user_data
return ;
}
-static void applyGlyphToEachType(GQuark style_id, gpointer data, gpointer user_data)
+static void applyGlyphToEachType(gpointer style_id, gpointer data, gpointer user_data)
{
ZMapFeatureTypeStyle style = (ZMapFeatureTypeStyle)data;
ZMapDAS1Glyph glyph = (ZMapDAS1Glyph)user_data;
@@ -1441,7 +1441,7 @@ static void stylesheetFilter (ZMapDAS1Stylesheet style, gpointer user_data)
if(category->id == default_id) /* apply to all categories */
{
if(type->id == default_id) /* apply to all types in all categories*/
- g_datalist_foreach(&(server_types->output), applyGlyphToEachType, (gpointer)glyph);
+ g_hash_table_foreach(server_types->output, applyGlyphToEachType, (gpointer)glyph);
else /* apply to just the specific type in all categories */
printf("[dasServer] Applying type '%s' to like types in all categories\n",
(char *)g_quark_to_string(type->id));
diff --git a/src/zmapServer/das/dasServer_P.h b/src/zmapServer/das/dasServer_P.h
index 81f894dc4..57d747f5b 100755
--- a/src/zmapServer/das/dasServer_P.h
+++ b/src/zmapServer/das/dasServer_P.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -22,11 +22,11 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Rob Clack (Sanger Institute, UK) rnc@sanger.ac.uk
*
- * Description:
+ * Description:
* HISTORY:
* Last edited: Feb 4 15:02 2009 (edgrif)
* Created: Thu Mar 18 12:02:52 2004 (edgrif)
- * CVS info: $Id: dasServer_P.h,v 1.13 2010-03-04 14:41:01 mh17 Exp $
+ * CVS info: $Id: dasServer_P.h,v 1.14 2010-06-08 08:31:24 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef DAS_SERVER_P_H
@@ -95,8 +95,7 @@ typedef struct _DasServerStruct
ZMapFeatureContext req_context ;
ZMapFeatureContext cur_context ;
- GData *curr_styles ; /* ROY you will probably want to chang
- this ! */
+ GHashTable *curr_styles ;
} DasServerStruct, *DasServer ;
diff --git a/src/zmapServer/pipe/pipeServer.c b/src/zmapServer/pipe/pipeServer.c
index 82af5c69b..975f7c29f 100755
--- a/src/zmapServer/pipe/pipeServer.c
+++ b/src/zmapServer/pipe/pipeServer.c
@@ -34,7 +34,7 @@
* HISTORY:
* Last edited: Jan 14 10:10 2010 (edgrif)
* Created: 2009-11-26 12:02:40 (mh17)
- * CVS info: $Id: pipeServer.c,v 1.23 2010-05-17 14:41:15 mh17 Exp $
+ * CVS info: $Id: pipeServer.c,v 1.24 2010-06-08 08:31:24 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -82,12 +82,12 @@ static ZMapServerResponseType getFeatureSetNames(void *server,
GHashTable **featureset_2_stylelist_inout,
GHashTable **featureset_2_column_out,
GHashTable **source_2_sourcedata_out) ;
-static ZMapServerResponseType getStyles(void *server, GData **styles_out) ;
+static ZMapServerResponseType getStyles(void *server, GHashTable **styles_out) ;
static ZMapServerResponseType haveModes(void *server, gboolean *have_mode) ;
static ZMapServerResponseType getSequences(void *server_in, GList *sequences_inout) ;
static ZMapServerResponseType setContext(void *server, ZMapFeatureContext feature_context) ;
-static ZMapServerResponseType getFeatures(void *server_in, GData *styles, ZMapFeatureContext feature_context_out) ;
-static ZMapServerResponseType getContextSequence(void *server_in, GData *styles, ZMapFeatureContext feature_context_out) ;
+static ZMapServerResponseType getFeatures(void *server_in, GHashTable *styles, ZMapFeatureContext feature_context_out) ;
+static ZMapServerResponseType getContextSequence(void *server_in, GHashTable *styles, ZMapFeatureContext feature_context_out) ;
static char *lastErrorMsg(void *server) ;
static ZMapServerResponseType closeConnection(void *server_in) ;
static ZMapServerResponseType destroyConnection(void *server) ;
@@ -462,7 +462,7 @@ static ZMapServerResponseType getFeatureSetNames(void *server_in,
* something has gone wrong.
*
* */
-static ZMapServerResponseType getStyles(void *server_in, GData **styles_out)
+static ZMapServerResponseType getStyles(void *server_in, GHashTable **styles_out)
{
ZMapServerResponseType result = ZMAP_SERVERRESPONSE_REQFAIL ;
PipeServer server = (PipeServer)server_in ;
@@ -653,7 +653,7 @@ static ZMapServerResponseType pipeGetSequence(PipeServer server)
/* Get features sequence. */
-static ZMapServerResponseType getFeatures(void *server_in, GData *styles, ZMapFeatureContext feature_context)
+static ZMapServerResponseType getFeatures(void *server_in, GHashTable *styles, ZMapFeatureContext feature_context)
{
PipeServer server = (PipeServer)server_in ;
@@ -808,7 +808,7 @@ static void eachAlignmentSequence(gpointer key, gpointer data, gpointer user_dat
/*
* we have pre-read the sequence and simple copy/move the data over if it's there
*/
-static ZMapServerResponseType getContextSequence(void *server_in, GData *styles, ZMapFeatureContext feature_context_out)
+static ZMapServerResponseType getContextSequence(void *server_in, GHashTable *styles, ZMapFeatureContext feature_context_out)
{
PipeServer server = (PipeServer)server_in ;
diff --git a/src/zmapServer/zmapServer.c b/src/zmapServer/zmapServer.c
index 1fc7e1f69..847011fb1 100755
--- a/src/zmapServer/zmapServer.c
+++ b/src/zmapServer/zmapServer.c
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: Jan 14 10:10 2010 (edgrif)
* Created: Wed Aug 6 15:46:38 2003 (edgrif)
- * CVS info: $Id: zmapServer.c,v 1.46 2010-05-17 14:41:15 mh17 Exp $
+ * CVS info: $Id: zmapServer.c,v 1.47 2010-06-08 08:31:24 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -211,7 +211,7 @@ ZMapServerResponseType zMapServerFeatureSetNames(ZMapServer server,
}
-ZMapServerResponseType zMapServerGetStyles(ZMapServer server, GData **styles_out)
+ZMapServerResponseType zMapServerGetStyles(ZMapServer server, GHashTable **styles_out)
{
ZMapServerResponseType result = ZMAP_SERVERRESPONSE_REQFAIL ;
@@ -294,7 +294,7 @@ ZMapServerResponseType zMapServerSetContext(ZMapServer server, ZMapFeatureContex
}
-ZMapServerResponseType zMapServerGetFeatures(ZMapServer server, GData *styles, ZMapFeatureContext feature_context)
+ZMapServerResponseType zMapServerGetFeatures(ZMapServer server, GHashTable *styles, ZMapFeatureContext feature_context)
{
ZMapServerResponseType result = ZMAP_SERVERRESPONSE_REQFAIL ;
@@ -315,7 +315,7 @@ ZMapServerResponseType zMapServerGetFeatures(ZMapServer server, GData *styles, Z
}
-ZMapServerResponseType zMapServerGetContextSequences(ZMapServer server, GData *styles,
+ZMapServerResponseType zMapServerGetContextSequences(ZMapServer server, GHashTable *styles,
ZMapFeatureContext feature_context)
{
ZMapServerResponseType result = ZMAP_SERVERRESPONSE_REQFAIL ;
diff --git a/src/zmapServer/zmapServer.h b/src/zmapServer/zmapServer.h
index 90e0e3e3a..9f357df4e 100755
--- a/src/zmapServer/zmapServer.h
+++ b/src/zmapServer/zmapServer.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: Jan 14 10:20 2010 (edgrif)
* Created: Wed Aug 6 15:48:47 2003 (edgrif)
- * CVS info: $Id: zmapServer.h,v 1.19 2010-03-04 14:40:58 mh17 Exp $
+ * CVS info: $Id: zmapServer.h,v 1.20 2010-06-08 08:31:24 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_SERVER_H
@@ -68,14 +68,14 @@ ZMapServerResponseType zMapServerFeatureSetNames(ZMapServer server,
GHashTable **featureset_2_stylelist_out,
GHashTable **source_2_featureset_out,
GHashTable **source_2_sourcedata_out) ;
-ZMapServerResponseType zMapServerGetStyles(ZMapServer server, GData **types_out) ;
+ZMapServerResponseType zMapServerGetStyles(ZMapServer server, GHashTable **types_out) ;
ZMapServerResponseType zMapServerStylesHaveMode(ZMapServer server, gboolean *have_mode) ;
ZMapServerResponseType zMapServerGetSequence(ZMapServer server, GList *sequences_inout) ;
ZMapServerResponseType zMapServerSetContext(ZMapServer server, ZMapFeatureContext feature_context) ;
ZMapFeatureContext zMapServerCopyContext(ZMapServer server) ;
-ZMapServerResponseType zMapServerGetFeatures(ZMapServer server, GData *styles, ZMapFeatureContext feature_context) ;
+ZMapServerResponseType zMapServerGetFeatures(ZMapServer server, GHashTable *styles, ZMapFeatureContext feature_context) ;
ZMapServerResponseType zMapServerGetContextSequences(ZMapServer server,
- GData *styles, ZMapFeatureContext feature_context) ;
+ GHashTable *styles, ZMapFeatureContext feature_context) ;
char *zMapServerLastErrorMsg(ZMapServer server) ;
ZMapServerResponseType zMapServerCloseConnection(ZMapServer server) ;
ZMapServerResponseType zMapServerFreeConnection(ZMapServer server) ;
diff --git a/src/zmapServer/zmapServerProtocolHandler.c b/src/zmapServer/zmapServerProtocolHandler.c
index 8693509ee..f289cf124 100755
--- a/src/zmapServer/zmapServerProtocolHandler.c
+++ b/src/zmapServer/zmapServerProtocolHandler.c
@@ -27,7 +27,7 @@
* HISTORY:
* Last edited: Jan 14 10:26 2010 (edgrif)
* Created: Thu Jan 27 13:17:43 2005 (edgrif)
- * CVS info: $Id: zmapServerProtocolHandler.c,v 1.60 2010-05-17 14:41:15 mh17 Exp $
+ * CVS info: $Id: zmapServerProtocolHandler.c,v 1.61 2010-06-08 08:31:24 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -70,7 +70,7 @@ typedef struct
typedef struct
{
- GData *all_styles ;
+ GHashTable *all_styles ;
gboolean found_style ;
GString *missing_styles ;
} FindStylesStruct, *FindStyles ;
@@ -92,10 +92,10 @@ static int findProtocol(gconstpointer list_protocol, gconstpointer protocol) ;
static ZMapThreadReturnCode getSequence(ZMapServer server, ZMapServerReqGetSequence request, char **err_msg_out) ;
static ZMapThreadReturnCode terminateServer(ZMapServer *server, char **err_msg_out) ;
static ZMapThreadReturnCode destroyServer(ZMapServer *server) ;
-static gboolean haveRequiredStyles(GData *all_styles, GList *required_styles, char **missing_styles_out) ;
+static gboolean haveRequiredStyles(GHashTable *all_styles, GList *required_styles, char **missing_styles_out) ;
static void findStyleCB(gpointer data, gpointer user_data) ;
#if OLD_STYLES_CODE
-static gboolean getStylesFromFile(char *styles_list, char *styles_file, GData **styles_out) ;
+static gboolean getStylesFromFile(char *styles_list, char *styles_file, GHashTable **styles_out) ;
#endif
ZMapThreadReturnCode getStyles(ZMapServer server, ZMapServerReqStyles styles, char **err_msg_out) ;
@@ -747,7 +747,7 @@ static ZMapThreadReturnCode destroyServer(ZMapServer *server)
// returns whether we have any of the needed styles and lists the ones we don't
-static gboolean haveRequiredStyles(GData *all_styles, GList *required_styles, char **missing_styles_out)
+static gboolean haveRequiredStyles(GHashTable *all_styles, GList *required_styles, char **missing_styles_out)
{
gboolean result = FALSE ;
FindStylesStruct find_data = {NULL} ;
@@ -798,7 +798,7 @@ static void findStyleCB(gpointer data, gpointer user_data)
ZMapThreadReturnCode getStyles(ZMapServer server, ZMapServerReqStyles styles, char **err_msg_out)
{
ZMapThreadReturnCode thread_rc = ZMAPTHREAD_RETURNCODE_OK ;
- GData *tmp_styles = NULL ;
+ GHashTable *tmp_styles = NULL ;
char *missing_styles = NULL ;
@@ -859,7 +859,7 @@ ZMapThreadReturnCode getStyles(ZMapServer server, ZMapServerReqStyles styles, ch
tmp_styles = zMapStyleMergeStyles(tmp_styles, styles->styles_out, ZMAPSTYLE_MERGE_MERGE) ;
- zMapStyleDestroyStyles(&(styles->styles_out)) ;
+ zMapStyleDestroyStyles(styles->styles_out) ;
if(styles_debug)
@@ -876,7 +876,7 @@ ZMapThreadReturnCode getStyles(ZMapServer server, ZMapServerReqStyles styles, ch
}
/* Now we have all the styles do the inheritance for them all. */
- if (!zMapStyleInheritAllStyles(&(tmp_styles)))
+ if (!zMapStyleInheritAllStyles(tmp_styles))
zMapLogWarning("%s", "There were errors in inheriting styles.") ;
diff --git a/src/zmapServer/zmapServerPrototype.h b/src/zmapServer/zmapServerPrototype.h
index 49126fb80..1f13a4558 100755
--- a/src/zmapServer/zmapServerPrototype.h
+++ b/src/zmapServer/zmapServerPrototype.h
@@ -30,7 +30,7 @@
* HISTORY:
* Last edited: Jan 14 09:51 2010 (edgrif)
* Created: Wed Aug 6 15:48:47 2003 (edgrif)
- * CVS info: $Id: zmapServerPrototype.h,v 1.35 2010-05-17 14:41:15 mh17 Exp $
+ * CVS info: $Id: zmapServerPrototype.h,v 1.36 2010-06-08 08:31:24 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_SERVER_PROTOTYPEP_H
@@ -74,7 +74,7 @@ typedef ZMapServerResponseType (*ZMapServerGetFeatureSets)(void *server_in,
GHashTable **source_2_sourcedata_out) ;
typedef ZMapServerResponseType (*ZMapServerGetStyles)(void *server_in,
- GData **styles_out) ;
+ GHashTable **styles_out) ;
typedef ZMapServerResponseType (*ZMapServerStylesHaveModes)(void *server_in, gboolean *have_modes_out) ;
@@ -87,10 +87,10 @@ typedef ZMapFeatureContext
(*ZMapServerCopyContextFunc)(void *server_conn) ;
typedef ZMapServerResponseType
- (*ZMapServerGetFeatures)(void *server_conn, GData *styles, ZMapFeatureContext feature_context) ;
+ (*ZMapServerGetFeatures)(void *server_conn, GHashTable *styles, ZMapFeatureContext feature_context) ;
typedef ZMapServerResponseType
- (*ZMapServerGetContextSequences)(void *server_conn, GData *styles, ZMapFeatureContext feature_context) ;
+ (*ZMapServerGetContextSequences)(void *server_conn, GHashTable *styles, ZMapFeatureContext feature_context) ;
typedef char * (*ZMapServerGetErrorMsgFunc)(void *server_conn) ;
diff --git a/src/zmapUtils/zmapGLibUtils.c b/src/zmapUtils/zmapGLibUtils.c
index 9d06f2788..302c63f35 100755
--- a/src/zmapUtils/zmapGLibUtils.c
+++ b/src/zmapUtils/zmapGLibUtils.c
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: Jun 12 08:44 2009 (edgrif)
* Created: Thu Oct 13 15:22:35 2005 (edgrif)
- * CVS info: $Id: zmapGLibUtils.c,v 1.33 2010-05-25 14:17:01 mh17 Exp $
+ * CVS info: $Id: zmapGLibUtils.c,v 1.34 2010-06-08 08:31:25 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -78,8 +78,7 @@ typedef struct
static inline GQuark g_quark_new(ZMapQuarkSet quark_set, gchar *string) ;
static void printCB(gpointer data, gpointer user_data) ;
static gint caseCompareFunc(gconstpointer a, gconstpointer b) ;
-static void get_datalist_length(GQuark key, gpointer data, gpointer user_data);
-static void get_first_datalist_key(GQuark id, gpointer data, gpointer user_data);
+
static gboolean getNthHashElement(gpointer key, gpointer value, gpointer user_data) ;
static void hashCopyListCB(gpointer key, gpointer value, gpointer user_data) ;
@@ -699,9 +698,29 @@ gboolean zMap_g_hash_table_iter_next(GList **iter,gpointer *key, gpointer *value
* Additions to GDatalist
*/
-
+#if MH17_NOT_USED
G_LOCK_DEFINE_STATIC(datalist_first);
+static void get_datalist_length(GQuark key, gpointer data, gpointer user_data)
+{
+ gint *length = (gint *)user_data;
+
+ (*length)++;
+
+ return ;
+}
+
+static void get_first_datalist_key(GQuark id, gpointer data, gpointer user_data)
+{
+ DatalistFirstID key = (DatalistFirstID)user_data;
+
+ if(!key->id)
+ key->id = id;
+
+ return ;
+}
+
+
gpointer zMap_g_datalist_first(GData **datalist)
{
DatalistFirstIDStruct key = {0};
@@ -723,6 +742,7 @@ gint zMap_g_datalist_length(GData **datalist)
return length;
}
+#endif
/*
* Additions to GArray
@@ -993,25 +1013,6 @@ static gint caseCompareFunc(gconstpointer a, gconstpointer b)
return result ;
}
-static void get_datalist_length(GQuark key, gpointer data, gpointer user_data)
-{
- gint *length = (gint *)user_data;
-
- (*length)++;
-
- return ;
-}
-
-static void get_first_datalist_key(GQuark id, gpointer data, gpointer user_data)
-{
- DatalistFirstID key = (DatalistFirstID)user_data;
-
- if(!key->id)
- key->id = id;
-
- return ;
-}
-
diff --git a/src/zmapUtils/zmapUtils.c b/src/zmapUtils/zmapUtils.c
index 6df1b7535..5f54188ac 100755
--- a/src/zmapUtils/zmapUtils.c
+++ b/src/zmapUtils/zmapUtils.c
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,12 +23,12 @@
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
* Description: Utility functions for the ZMap code.
- *
+ *
* Exported functions: See ZMap/zmapUtils.h
* HISTORY:
* Last edited: Jun 5 17:55 2009 (edgrif)
* Created: Fri Mar 12 08:16:24 2004 (edgrif)
- * CVS info: $Id: zmapUtils.c,v 1.33 2010-03-04 15:11:27 mh17 Exp $
+ * CVS info: $Id: zmapUtils.c,v 1.34 2010-06-08 08:31:25 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -51,9 +51,9 @@ static gboolean getVersionNumbers(char *version_str,
/*! @defgroup zmaputils zMapUtils: utilities for ZMap
* @{
- *
+ *
* \brief Utilities for ZMap.
- *
+ *
* zMapUtils routines provide services such as debugging, testing and logging,
* string handling, file utilities and GUI functions. They are general routines
* used by all of ZMap.
@@ -62,13 +62,13 @@ static gboolean getVersionNumbers(char *version_str,
/*! Can be set on/off to turn on/off debugging output via the zMapDebug() macro. */
-gboolean zmap_debug_G = FALSE ;
+gboolean zmap_debug_G = FALSE ;
/*! A global timer used for giving overall timings for zmap operations.
* See the timer macros in zmapUtilsDebug.h */
GTimer *zmap_global_timer_G = NULL ;
-
+gboolean zmap_timing_G = FALSE; // ouput timing info?
@@ -283,7 +283,7 @@ char *zMapGetTimeString(ZMapTimeFormat format, char *format_str_in)
/* Given an int between 0 and 9 returns the corresponding char representation,
* (surely this must exist somewhere ??).
- *
+ *
* Returns '.' if number not in [0-9]
* */
char zMapInt2Char(int num)
@@ -302,7 +302,7 @@ char zMapInt2Char(int num)
/* There follow a series of conversion routines. These are provided either
* because there are no existing ones or because the existing ones have
* arcane usage.
- *
+ *
* All of them can just be used to test for validity without needing a
* return variable.
* */
@@ -423,7 +423,7 @@ gboolean zMapStr2Float(char *str, float *float_out)
if (str && *str)
{
errno = 0 ;
-
+
ret_val = strtof(str, &end_ptr) ;
if (ret_val == 0 && end_ptr == str)
@@ -469,7 +469,7 @@ gboolean zMapStr2Double(char *str, double *double_out)
if (str && *str)
{
errno = 0 ;
-
+
ret_val = strtod(str, &end_ptr) ;
if (ret_val == 0 && end_ptr == str)
@@ -514,7 +514,7 @@ gboolean zMapStr2Double(char *str, double *double_out)
* If the call failed and err_msg_out is non-NULL then an error message is returned
* explaining the failure. The caller should free error message using g_free() when
* no longer required.
- *
+ *
* It is not straight forward to interpret the return value of the system call so this
* function attempts to interpret the value correctly.
*
@@ -564,7 +564,7 @@ gboolean zMapUtilsSysCall(char *cmd_str, char **err_msg_out)
result = FALSE ;
if (err_msg_out)
*err_msg_out = g_strdup("Child process did not exit normally.") ;
-
+
}
else
{
@@ -572,7 +572,7 @@ gboolean zMapUtilsSysCall(char *cmd_str, char **err_msg_out)
int true_rc ;
true_rc = WEXITSTATUS(sys_rc) ;
-
+
if (true_rc == EXIT_SUCCESS)
result = TRUE ;
else
@@ -594,7 +594,7 @@ gboolean zMapUtilsSysCall(char *cmd_str, char **err_msg_out)
void zMapPrintQuark(GQuark quark)
{
printf("GQuark (%d) = '%s'\n", quark, g_quark_to_string(quark));
- return ;
+ return ;
}
/* make logging from totalview evaluations a lot easier... */
@@ -659,7 +659,7 @@ gboolean zMapLogQuarkHasStr(GQuark quark, char *sub_str)
-/*
+/*
* Internal routines.
*/
@@ -685,7 +685,7 @@ static gboolean getVersionNumbers(char *version_str,
*release_out = release ;
*update_out = update ;
}
-
+
return result ;
}
diff --git a/src/zmapUtils/zmapUtilsConfig.c b/src/zmapUtils/zmapUtilsConfig.c
index 1bdab4914..85a82bf48 100755
--- a/src/zmapUtils/zmapUtilsConfig.c
+++ b/src/zmapUtils/zmapUtilsConfig.c
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -22,12 +22,12 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Rob Clack (Sanger Institute, UK) rnc@sanger.ac.uk
*
- * Description:
+ * Description:
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Oct 1 16:07 2008 (rds)
* Created: Mon Oct 18 09:05:27 2004 (edgrif)
- * CVS info: $Id: zmapUtilsConfig.c,v 1.7 2010-03-04 15:11:28 mh17 Exp $
+ * CVS info: $Id: zmapUtilsConfig.c,v 1.8 2010-06-08 08:31:25 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -38,6 +38,7 @@
// headers for globals
#include <ZMap/zmapThreads.h>
#include <ZMap/zmapServerProtocol.h>
+#include <ZMap/zmapUtilsDebug.h>
/* SHOULD MAKE THIS INTO A COVER FUNCTION FOR A MORE GENERALISED FUNCTION THAT GIVEN
@@ -55,20 +56,25 @@ gboolean zMapUtilsConfigDebug(void)
{
result = TRUE;
- zMapConfigIniContextGetBoolean(context,
- ZMAPSTANZA_DEBUG_CONFIG,
+ zMapConfigIniContextGetBoolean(context,
+ ZMAPSTANZA_DEBUG_CONFIG,
ZMAPSTANZA_DEBUG_CONFIG,
ZMAPSTANZA_DEBUG_APP_THREADS, &zmap_thread_debug_G);
- zMapConfigIniContextGetBoolean(context,
- ZMAPSTANZA_DEBUG_CONFIG,
+ zMapConfigIniContextGetBoolean(context,
+ ZMAPSTANZA_DEBUG_CONFIG,
ZMAPSTANZA_DEBUG_CONFIG,
ZMAPSTANZA_DEBUG_APP_FEATURE2STYLE, &zmap_server_feature2style_debug_G);
- zMapConfigIniContextGetBoolean(context,
- ZMAPSTANZA_DEBUG_CONFIG,
+ zMapConfigIniContextGetBoolean(context,
+ ZMAPSTANZA_DEBUG_CONFIG,
ZMAPSTANZA_DEBUG_CONFIG,
ZMAPSTANZA_DEBUG_APP_STYLES, &zmap_server_styles_debug_G);
+ zMapConfigIniContextGetBoolean(context,
+ ZMAPSTANZA_DEBUG_CONFIG,
+ ZMAPSTANZA_DEBUG_CONFIG,
+ ZMAPSTANZA_DEBUG_APP_TIMING, &zmap_timing_G);
+
zMapConfigIniContextDestroy(context);
}
diff --git a/src/zmapView/zmapView.c b/src/zmapView/zmapView.c
index 9230b5962..a123d5cc4 100755
--- a/src/zmapView/zmapView.c
+++ b/src/zmapView/zmapView.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: May 5 17:39 2010 (edgrif)
* Created: Thu May 13 15:28:26 2004 (edgrif)
- * CVS info: $Id: zmapView.c,v 1.200 2010-06-03 12:21:41 mh17 Exp $
+ * CVS info: $Id: zmapView.c,v 1.201 2010-06-08 08:31:25 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -44,6 +44,7 @@
#include <ZMap/zmapUtilsXRemote.h>
#include <ZMap/zmapXRemote.h>
#include <ZMap/zmapCmdLineArgs.h>
+#include <ZMap/zmapConfigDir.h>
#include <ZMap/zmapConfigIni.h>
#include <ZMap/zmapConfigStrings.h>
#include <ZMap/zmapConfigStanzaStructs.h>
@@ -78,7 +79,7 @@ typedef struct
GHashTable *featureset_2_column; // needed by pipeServers
GHashTable *source_2_sourcedata;
- GData *curr_styles ; /* Styles for this context. */
+ GHashTable *curr_styles ; /* Styles for this context. */
ZMapFeatureContext curr_context ;
ZMapServerReqType display_after ;
@@ -94,7 +95,7 @@ typedef struct
typedef struct
{
- GData *styles ;
+ GHashTable *styles ;
gboolean error ;
} UnsetDeferredLoadStylesStruct, *UnsetDeferredLoadStyles ;
@@ -120,7 +121,7 @@ static void viewSplitToPatternCB(ZMapWindow window, void *caller_data, void *win
static void setZoomStatus(gpointer data, gpointer user_data);
static void splitMagic(gpointer data, gpointer user_data);
-static void unsetDeferredLoadStylesCB(GQuark key_id, gpointer data, gpointer user_data) ;
+static void unsetDeferredLoadStylesCB(gpointer key_id, gpointer data, gpointer user_data) ;
static void startStateConnectionChecking(ZMapView zmap_view) ;
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
@@ -150,14 +151,14 @@ static void killConnections(ZMapView zmap_view) ;
static void resetWindows(ZMapView zmap_view) ;
static void displayDataWindows(ZMapView zmap_view,
ZMapFeatureContext all_features,
- ZMapFeatureContext new_features, GData *new_styles,
+ ZMapFeatureContext new_features, GHashTable *new_styles,
gboolean undisplay) ;
static void killAllWindows(ZMapView zmap_view) ;
static ZMapViewWindow createWindow(ZMapView zmap_view, ZMapWindow window) ;
static void destroyWindow(ZMapView zmap_view, ZMapViewWindow view_window) ;
-static void getFeatures(ZMapView zmap_view, ZMapServerReqGetFeatures feature_req, GData *styles) ;
+static void getFeatures(ZMapView zmap_view, ZMapServerReqGetFeatures feature_req, GHashTable *styles) ;
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
@@ -165,8 +166,8 @@ static GList *string2StyleQuarks(char *feature_sets) ;
static gboolean nextIsQuoted(char **text) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-static gboolean justMergeContext(ZMapView view, ZMapFeatureContext *context_inout, GData *styles);
-static void justDrawContext(ZMapView view, ZMapFeatureContext diff_context, GData *styles);
+static gboolean justMergeContext(ZMapView view, ZMapFeatureContext *context_inout, GHashTable *styles);
+static void justDrawContext(ZMapView view, ZMapFeatureContext diff_context, GHashTable *styles);
static ZMapFeatureContext createContext(char *sequence, int start, int end, GList *feature_set_names) ;
@@ -174,7 +175,7 @@ static ZMapViewWindow addWindow(ZMapView zmap_view, GtkWidget *parent_widget) ;
static void addAlignments(ZMapFeatureContext context) ;
-static gboolean mergeAndDrawContext(ZMapView view, ZMapFeatureContext context_inout, GData *styles);
+static gboolean mergeAndDrawContext(ZMapView view, ZMapFeatureContext context_inout, GHashTable *styles);
static void eraseAndUndrawContext(ZMapView view, ZMapFeatureContext context_inout);
#ifdef NOT_REQUIRED_ATM
@@ -193,11 +194,11 @@ static void killAllSpawned(ZMapView zmap_view);
static gboolean checkContinue(ZMapView zmap_view) ;
-static gboolean makeStylesDrawable(GData *styles, char **missing_styles_out) ;
-static void drawableCB(GQuark key_id, gpointer data, gpointer user_data) ;
+static gboolean makeStylesDrawable(GHashTable *styles, char **missing_styles_out) ;
+static void drawableCB(gpointer key_id, gpointer data, gpointer user_data) ;
-static void addPredefined(GData **styles_inout, GHashTable **featureset_2_stylelist_inout) ;
-static void styleCB(GQuark key_id, gpointer data, gpointer user_data) ;
+static void addPredefined(GHashTable **styles_inout, GHashTable **featureset_2_stylelist_inout) ;
+static void styleCB(gpointer key_id, gpointer data, gpointer user_data) ;
static void invoke_merge_in_names(gpointer list_data, gpointer user_data);
@@ -327,6 +328,7 @@ ZMapViewWindow zMapViewCreate(GtkWidget *xremote_widget, GtkWidget *view_contain
* in config file and next time they create a view the debugging will go on/off. */
zMapUtilsConfigDebug();
+ zMapInitTimer() ; // operates as a reset if already defined
/* Set up sequence to be fetched, in this case server defaults to whatever is set in config. file. */
sequence_fetch = g_new0(ZMapViewSequenceMapStruct, 1) ;
@@ -701,7 +703,7 @@ gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
{
GList *settings_list = NULL, *free_this_list = NULL;
- zMapStartTimer(ZMAP_GLOBAL_TIMER) ;
+
zMapPrintTimer(NULL, "Open connection") ;
zmapViewBusy(zmap_view, TRUE) ;
@@ -910,7 +912,7 @@ ZMapViewWindow zMapViewCopyWindow(ZMapView zmap_view, GtkWidget *parent_widget,
if (zmap_view->state != ZMAPVIEW_DYING)
{
- GData *copy_styles ;
+ GHashTable *copy_styles ;
/* the view _must_ already have a window _and_ data. */
@@ -1178,29 +1180,36 @@ gboolean zMapViewReverseComplement(ZMapView zmap_view)
zmapViewBusy(zmap_view, TRUE) ;
+ zMapStartTimer("RevComp","");
+
/* Call the feature code that will do the revcomp. */
zMapFeatureReverseComplement(zmap_view->features, zmap_view->orig_styles) ;
+ zMapStopTimer("RevComp","Feature");
+
/* Set our record of reverse complementing. */
zmap_view->revcomped_features = !(zmap_view->revcomped_features) ;
zMapWindowNavigatorReset(zmap_view->navigator_window);
zMapWindowNavigatorSetStrand(zmap_view->navigator_window, zmap_view->revcomped_features);
zMapWindowNavigatorDrawFeatures(zmap_view->navigator_window, zmap_view->features, zmap_view->orig_styles);
+ zMapStopTimer("RevComp","Navigator");
if((list_item = g_list_first(zmap_view->window_list)))
{
do
{
ZMapViewWindow view_window ;
- GData *copy_styles = NULL;
+ GHashTable *copy_styles = NULL;
view_window = list_item->data ;
copy_styles = zmap_view->orig_styles ;
+ zMapStartTimer("RevComp","Window");
zMapWindowFeatureRedraw(view_window->window, zmap_view->features,
zmap_view->orig_styles, copy_styles, TRUE) ;
+ zMapStopTimer("RevComp","Window");
}
while ((list_item = g_list_next(list_item))) ;
}
@@ -1209,6 +1218,7 @@ gboolean zMapViewReverseComplement(ZMapView zmap_view)
/* signal our caller that we have data. */
(*(view_cbs_G->load_data))(zmap_view, zmap_view->app_data, NULL) ;
+ zMapStopTimer("RevComp","");
zmapViewBusy(zmap_view, FALSE);
result = TRUE ;
@@ -1356,9 +1366,9 @@ ZMapFeatureContext zMapViewGetFeatures(ZMapView zmap_view)
return features ;
}
-GData *zMapViewGetStyles(ZMapViewWindow view_window)
+GHashTable *zMapViewGetStyles(ZMapViewWindow view_window)
{
- GData *styles = NULL ;
+ GHashTable *styles = NULL ;
ZMapView view = zMapViewGetView(view_window);
if (view->state != ZMAPVIEW_DYING)
@@ -2871,9 +2881,9 @@ printf("\nview styles lists after merge:\n");
ZMapServerReqStyles get_styles = (ZMapServerReqStyles)req_any ;
//printf("\nmerging...old\n");
- //g_datalist_foreach(&(zmap_view->orig_styles), printStyle, "got styles") ;
+ //g_hash_table_foreach(&(zmap_view->orig_styles), printStyle, "got styles") ;
//printf("\nmerging...new\n");
- //g_datalist_foreach(&(get_styles->styles_out), printStyle, "got styles") ;
+ //g_hash_table_foreach(&(get_styles->styles_out), printStyle, "got styles") ;
/* Merge the retrieved styles into the views canonical style list. */
zmap_view->orig_styles = zMapStyleMergeStyles(zmap_view->orig_styles, get_styles->styles_out,
@@ -2884,9 +2894,9 @@ printf("\nview styles lists after merge:\n");
gboolean is_complete_sequence = FALSE;
if (is_complete_sequence)
- g_datalist_foreach(&(zmap_view->orig_styles), unsetDeferredLoadStylesCB, NULL) ;
+ g_hash_table_foreach(zmap_view->orig_styles, unsetDeferredLoadStylesCB, NULL) ;
- g_datalist_foreach(&(get_styles->styles_out), unsetDeferredLoadStylesCB, NULL) ;
+ g_hash_table_foreach(get_styles->styles_out, unsetDeferredLoadStylesCB, NULL) ;
}
@@ -3287,7 +3297,7 @@ static void resetWindows(ZMapView zmap_view)
/* Signal all windows there is data to draw. */
static void displayDataWindows(ZMapView zmap_view,
ZMapFeatureContext all_features,
- ZMapFeatureContext new_features, GData *new_styles,
+ ZMapFeatureContext new_features, GHashTable *new_styles,
gboolean undisplay)
{
GList *list_item, *window_list = NULL;
@@ -3405,7 +3415,7 @@ static void destroyWindow(ZMapView zmap_view, ZMapViewWindow view_window)
/* We have far too many function calls here...it's all confusing..... */
-static void getFeatures(ZMapView zmap_view, ZMapServerReqGetFeatures feature_req, GData *styles)
+static void getFeatures(ZMapView zmap_view, ZMapServerReqGetFeatures feature_req, GHashTable *styles)
{
ZMapFeatureContext new_features = NULL ;
@@ -3434,7 +3444,7 @@ static void getFeatures(ZMapView zmap_view, ZMapServerReqGetFeatures feature_req
* We should free the context_inout context here....actually better
* would to have a "free" flag............
* */
-static gboolean mergeAndDrawContext(ZMapView view, ZMapFeatureContext context_in, GData *styles)
+static gboolean mergeAndDrawContext(ZMapView view, ZMapFeatureContext context_in, GHashTable *styles)
{
gboolean merge_results = FALSE ;
ZMapFeatureContext diff_context = NULL ;
@@ -3449,7 +3459,7 @@ static gboolean mergeAndDrawContext(ZMapView view, ZMapFeatureContext context_in
return merge_results ;
}
-static gboolean justMergeContext(ZMapView view, ZMapFeatureContext *context_inout, GData *styles)
+static gboolean justMergeContext(ZMapView view, ZMapFeatureContext *context_inout, GHashTable *styles)
{
gboolean merge_result = FALSE ;
ZMapFeatureContext new_features, diff_context = NULL ;
@@ -3459,15 +3469,15 @@ static gboolean justMergeContext(ZMapView view, ZMapFeatureContext *context_inou
// printf("just Merge new = %s\n",zMapFeatureContextGetDNAStatus(new_features) ? "yes" : "non");
- zMapPrintTimer(NULL, "Merge Context starting...") ;
+ zMapStartTimer("Merge Context","") ;
if (view->revcomped_features)
{
- zMapPrintTimer(NULL, "Merge Context has to rev comp first, starting") ;
+ zMapStartTimer("MergeRevComp","") ;
zMapFeatureReverseComplement(new_features, view->orig_styles);
- zMapPrintTimer(NULL, "Merge Context has to rev comp first, finished") ;
+ zMapStopTimer("MergeRevComp","") ;
}
merge = zMapFeatureContextMerge(&(view->features), &new_features, &diff_context) ;
@@ -3496,7 +3506,7 @@ static gboolean justMergeContext(ZMapView view, ZMapFeatureContext *context_inou
zMapLogCritical("%s", "Context merge failed, serious error.") ;
- zMapPrintTimer(NULL, "Merge Context Finished.") ;
+ zMapStopTimer("Merge Context","") ;
/* Return the diff_context which is the just the new features (NULL if merge fails). */
*context_inout = diff_context ;
@@ -3504,7 +3514,7 @@ static gboolean justMergeContext(ZMapView view, ZMapFeatureContext *context_inou
return merge_result ;
}
-static void justDrawContext(ZMapView view, ZMapFeatureContext diff_context, GData *new_styles)
+static void justDrawContext(ZMapView view, ZMapFeatureContext diff_context, GHashTable *new_styles)
{
/* Signal the ZMap that there is work to be done. */
displayDataWindows(view, view->features, diff_context, new_styles, FALSE) ;
@@ -4157,12 +4167,12 @@ static gboolean checkContinue(ZMapView zmap_view)
-static gboolean makeStylesDrawable(GData *styles, char **missing_styles_out)
+static gboolean makeStylesDrawable(GHashTable *styles, char **missing_styles_out)
{
gboolean result = FALSE ;
DrawableDataStruct drawable_data = {FALSE} ;
- g_datalist_foreach(&styles, drawableCB, &drawable_data) ;
+ g_hash_table_foreach(styles, drawableCB, &drawable_data) ;
if (drawable_data.missing_styles)
*missing_styles_out = g_string_free(drawable_data.missing_styles, FALSE) ;
@@ -4174,9 +4184,10 @@ static gboolean makeStylesDrawable(GData *styles, char **missing_styles_out)
-/* A GDataForeachFunc() to make the given style drawable. */
-static void drawableCB(GQuark key_id, gpointer data, gpointer user_data)
+/* A GHashListForeachFunc() to make the given style drawable. */
+static void drawableCB(gpointer key, gpointer data, gpointer user_data)
{
+ GQuark key_id = GPOINTER_TO_UINT(key);
ZMapFeatureTypeStyle style = (ZMapFeatureTypeStyle)data ;
DrawableData drawable_data = (DrawableData)user_data ;
@@ -4200,8 +4211,8 @@ static void drawableCB(GQuark key_id, gpointer data, gpointer user_data)
-/* A GDataForeachFunc() func that unsets DeferredLoads for styles in the target. */
-static void unsetDeferredLoadStylesCB(GQuark key_id, gpointer data, gpointer user_data_unused)
+/* A GhashListForeachFunc() func that unsets DeferredLoads for styles in the target. */
+static void unsetDeferredLoadStylesCB(gpointer key, gpointer data, gpointer user_data_unused)
{
ZMapFeatureTypeStyle orig_style = (ZMapFeatureTypeStyle)data ;
@@ -4214,14 +4225,14 @@ static void unsetDeferredLoadStylesCB(GQuark key_id, gpointer data, gpointer use
-static void addPredefined(GData **styles_out, GHashTable **featureset_2_stylelist_inout)
+static void addPredefined(GHashTable **styles_out, GHashTable **featureset_2_stylelist_inout)
{
- GData *styles ;
+ GHashTable *styles ;
GHashTable *f2s = *featureset_2_stylelist_inout ;
styles = zMapStyleGetAllPredefined() ;
- g_datalist_foreach(&styles, styleCB, f2s) ;
+ g_hash_table_foreach(styles, styleCB, f2s) ;
*styles_out = styles ;
*featureset_2_stylelist_inout = f2s ;
@@ -4229,9 +4240,10 @@ static void addPredefined(GData **styles_out, GHashTable **featureset_2_stylelis
return ;
}
-/* GDataForeachFunc() to set up a feature_set/style hash. */
-static void styleCB(GQuark key_id, gpointer data, gpointer user_data)
+/* GHashListForeachFunc() to set up a feature_set/style hash. */
+static void styleCB(gpointer key, gpointer data, gpointer user_data)
{
+ GQuark key_id = GPOINTER_TO_UINT(key);
GHashTable *hash = (GHashTable *)user_data ;
GQuark feature_set_id, feature_set_name_id;
diff --git a/src/zmapView/zmapViewRemoteReceive.c b/src/zmapView/zmapViewRemoteReceive.c
index 5e1291da6..11a2fbc70 100755
--- a/src/zmapView/zmapViewRemoteReceive.c
+++ b/src/zmapView/zmapViewRemoteReceive.c
@@ -31,7 +31,7 @@
* HISTORY:
* Last edited: Apr 30 13:15 2010 (edgrif)
* Created: Tue Jul 10 21:02:42 2007 (rds)
- * CVS info: $Id: zmapViewRemoteReceive.c,v 1.47 2010-06-03 12:21:42 mh17 Exp $
+ * CVS info: $Id: zmapViewRemoteReceive.c,v 1.48 2010-06-08 08:31:25 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -121,8 +121,8 @@ typedef struct
GQuark style_id ;
ZMapFeatureTypeStyle style ;
- GList *feature_list;
- GData *styles;
+ GList *feature_list;
+ GHashTable *styles;
GList *locations ;
diff --git a/src/zmapView/zmapView_P.h b/src/zmapView/zmapView_P.h
index 9dc079981..4f6a15a7e 100755
--- a/src/zmapView/zmapView_P.h
+++ b/src/zmapView/zmapView_P.h
@@ -26,7 +26,7 @@
* HISTORY:
* Last edited: Apr 7 13:48 2010 (edgrif)
* Created: Thu May 13 15:06:21 2004 (edgrif)
- * CVS info: $Id: zmapView_P.h,v 1.61 2010-05-17 14:41:16 mh17 Exp $
+ * CVS info: $Id: zmapView_P.h,v 1.62 2010-06-08 08:31:25 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_VIEW_P_H
@@ -253,7 +253,7 @@ typedef struct _ZMapViewStruct
/* Original styles, these are all the styles as they were loaded from the server(s).
* N.B. the list may be updated during the lifetime of the view and hence is always
* passed into window for all update operations. */
- GData *orig_styles ;
+ GHashTable *orig_styles ;
GHashTable *featureset_2_stylelist ; /* Mapping of each feature_set to all the styles
* the styles it requires. using a GHashTable of
diff --git a/src/zmapWindow/items/zmapWindowAlignmentFeature.c b/src/zmapWindow/items/zmapWindowAlignmentFeature.c
index 6e613a62b..99691fc01 100755
--- a/src/zmapWindow/items/zmapWindowAlignmentFeature.c
+++ b/src/zmapWindow/items/zmapWindowAlignmentFeature.c
@@ -30,7 +30,7 @@
* HISTORY:
* Last edited: May 26 12:53 2010 (edgrif)
* Created: Wed Dec 3 10:02:22 2008 (rds)
- * CVS info: $Id: zmapWindowAlignmentFeature.c,v 1.10 2010-05-26 12:44:34 edgrif Exp $
+ * CVS info: $Id: zmapWindowAlignmentFeature.c,v 1.11 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -132,7 +132,9 @@ void zmap_window_alignment_feature_clear(ZMapWindowCanvasItem canvas_item)
style = (ZMAP_CANVAS_ITEM_GET_CLASS(canvas_item)->get_style)(canvas_item);
- zMapStyleGetGappedAligns(style, &parse_gaps, &show_gaps) ;
+// zMapStyleGetGappedAligns(style, &parse_gaps, &show_gaps) ;
+ parse_gaps = zMapStyleIsParseGaps(style);
+ show_gaps = zMapStyleIsShowGaps(style);
if(alignment->flags.no_gaps_hidden == 0 &&
alignment->flags.no_gaps_display == 1 &&
diff --git a/src/zmapWindow/items/zmapWindowAlignmentFeature.h b/src/zmapWindow/items/zmapWindowAlignmentFeature.h
index 9f3eccf03..86fe1226c 100755
--- a/src/zmapWindow/items/zmapWindowAlignmentFeature.h
+++ b/src/zmapWindow/items/zmapWindowAlignmentFeature.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Feb 16 10:14 2010 (edgrif)
* Created: Wed Dec 3 08:44:06 2008 (rds)
- * CVS info: $Id: zmapWindowAlignmentFeature.h,v 1.4 2010-03-04 15:11:41 mh17 Exp $
+ * CVS info: $Id: zmapWindowAlignmentFeature.h,v 1.5 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -42,8 +42,15 @@
#define ZMAP_WINDOW_ALIGNMENT_FEATURE_NAME "ZMapWindowAlignmentFeature"
#define ZMAP_TYPE_WINDOW_ALIGNMENT_FEATURE (zMapWindowAlignmentFeatureGetType())
+
+#if GOBJ_CAST
+#define ZMAP_WINDOW_ALIGNMENT_FEATURE(obj) ((ZMapWindowAlignmentFeature) obj)
+#define ZMAP_WINDOW_ALIGNMENT_FEATURE_CONST(obj) ((ZMapWindowAlignmentFeature const) obj)
+#else
#define ZMAP_WINDOW_ALIGNMENT_FEATURE(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_ALIGNMENT_FEATURE, zmapWindowAlignmentFeature))
#define ZMAP_WINDOW_ALIGNMENT_FEATURE_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_ALIGNMENT_FEATURE, zmapWindowAlignmentFeature const))
+#endif
+
#define ZMAP_WINDOW_ALIGNMENT_FEATURE_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_WINDOW_ALIGNMENT_FEATURE, zmapWindowAlignmentFeatureClass))
#define ZMAP_IS_WINDOW_ALIGNMENT_FEATURE(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_WINDOW_ALIGNMENT_FEATURE))
#define ZMAP_WINDOW_ALIGNMENT_FEATURE_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_WINDOW_ALIGNMENT_FEATURE, zmapWindowAlignmentFeatureClass))
diff --git a/src/zmapWindow/items/zmapWindowAssemblyFeature.h b/src/zmapWindow/items/zmapWindowAssemblyFeature.h
index 76fadc469..1b2ffb0ba 100755
--- a/src/zmapWindow/items/zmapWindowAssemblyFeature.h
+++ b/src/zmapWindow/items/zmapWindowAssemblyFeature.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Feb 16 10:16 2010 (edgrif)
* Created: Wed Dec 3 08:44:06 2008 (rds)
- * CVS info: $Id: zmapWindowAssemblyFeature.h,v 1.4 2010-03-04 15:11:44 mh17 Exp $
+ * CVS info: $Id: zmapWindowAssemblyFeature.h,v 1.5 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_WINDOW_ASSEMBLY_FEATURE_H
@@ -41,8 +41,15 @@
#define ZMAP_WINDOW_ASSEMBLY_FEATURE_NAME "ZMapWindowAssemblyFeature"
#define ZMAP_TYPE_WINDOW_ASSEMBLY_FEATURE (zMapWindowAssemblyFeatureGetType())
+
+#if GOBJ_CAST
+#define ZMAP_WINDOW_ASSEMBLY_FEATURE(obj) ((ZMapWindowAssemblyFeature) obj)
+#define ZMAP_WINDOW_ASSEMBLY_FEATURE_CONST(obj) ((ZMapWindowAssemblyFeature const) obj)
+#else
#define ZMAP_WINDOW_ASSEMBLY_FEATURE(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_ASSEMBLY_FEATURE, zmapWindowAssemblyFeature))
#define ZMAP_WINDOW_ASSEMBLY_FEATURE_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_ASSEMBLY_FEATURE, zmapWindowAssemblyFeature const))
+#endif
+
#define ZMAP_WINDOW_ASSEMBLY_FEATURE_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_WINDOW_ASSEMBLY_FEATURE, zmapWindowAssemblyFeatureClass))
#define ZMAP_IS_WINDOW_ASSEMBLY_FEATURE(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_WINDOW_ASSEMBLY_FEATURE))
#define ZMAP_WINDOW_ASSEMBLY_FEATURE_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_WINDOW_ASSEMBLY_FEATURE, zmapWindowAssemblyFeatureClass))
diff --git a/src/zmapWindow/items/zmapWindowBasicFeature.c b/src/zmapWindow/items/zmapWindowBasicFeature.c
index 52b14db5d..1d1e25616 100755
--- a/src/zmapWindow/items/zmapWindowBasicFeature.c
+++ b/src/zmapWindow/items/zmapWindowBasicFeature.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: May 26 12:54 2010 (edgrif)
* Created: Wed Dec 3 10:02:22 2008 (rds)
- * CVS info: $Id: zmapWindowBasicFeature.c,v 1.19 2010-05-26 12:47:40 edgrif Exp $
+ * CVS info: $Id: zmapWindowBasicFeature.c,v 1.20 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -135,7 +135,6 @@ static FooCanvasItem *zmap_window_basic_feature_add_interval(ZMapWindowCanvasIte
ZMapFeature feature;
gboolean interval_type_from_feature_type = TRUE; /* for now */
feature = basic->feature;
- style = (ZMAP_CANVAS_ITEM_GET_CLASS(basic)->get_style)(basic);
if (interval_type_from_feature_type)
@@ -169,12 +168,16 @@ static FooCanvasItem *zmap_window_basic_feature_add_interval(ZMapWindowCanvasIte
which = feature->boundary_type == ZMAPBOUNDARY_5_SPLICE ? 5 : 3;
}
- // style is as configured or retrofitted in zMapStyleMakeDrawable()
- // x and y coords are relative to main feature set up in CanvasItemCreate()
- item = FOO_CANVAS_ITEM(zMapWindowGlyphItemCreate(FOO_CANVAS_GROUP(basic),
- style, which, 0.0, 0.0, feature->score,strand));
+ style = (ZMAP_CANVAS_ITEM_GET_CLASS(basic)->get_style)(basic);
+ // style is as configured or retrofitted in zMapStyleMakeDrawable()
+ // x and y coords are relative to main feature set up in CanvasItemCreate()
- // colour should be set by caller, esp if style is frame specific
+ // style is as configured or retrofitted in zMapStyleMakeDrawable()
+ // x and y coords are relative to main feature set up in CanvasItemCreate()
+ item = FOO_CANVAS_ITEM(zMapWindowGlyphItemCreate(FOO_CANVAS_GROUP(basic),
+ style, which, 0.0, 0.0, feature->score,strand));
+
+ // colour should be set by caller, esp if style is frame specific
break;
}
diff --git a/src/zmapWindow/items/zmapWindowBasicFeature.h b/src/zmapWindow/items/zmapWindowBasicFeature.h
index 4926e13db..3abf83260 100755
--- a/src/zmapWindow/items/zmapWindowBasicFeature.h
+++ b/src/zmapWindow/items/zmapWindowBasicFeature.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: May 25 12:20 2010 (edgrif)
* Created: Wed Dec 3 08:44:06 2008 (rds)
- * CVS info: $Id: zmapWindowBasicFeature.h,v 1.5 2010-05-26 12:47:40 edgrif Exp $
+ * CVS info: $Id: zmapWindowBasicFeature.h,v 1.6 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_WINDOW_BASIC_FEATURE_H
@@ -41,8 +41,15 @@
#define ZMAP_WINDOW_BASIC_FEATURE_NAME "ZMapWindowBasicFeature"
#define ZMAP_TYPE_WINDOW_BASIC_FEATURE (zMapWindowBasicFeatureGetType())
+
+#if GOBJ_CAST
+#define ZMAP_WINDOW_BASIC_FEATURE(obj) ((ZMapWindowBasicFeature) obj)
+#define ZMAP_WINDOW_BASIC_FEATURE_CONST(obj) ((ZMapWindowBasicFeature const) obj)
+#else
#define ZMAP_WINDOW_BASIC_FEATURE(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_BASIC_FEATURE, zmapWindowBasicFeature))
#define ZMAP_WINDOW_BASIC_FEATURE_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_BASIC_FEATURE, zmapWindowBasicFeature const))
+#endif
+
#define ZMAP_WINDOW_BASIC_FEATURE_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_WINDOW_BASIC_FEATURE, zmapWindowBasicFeatureClass))
#define ZMAP_IS_WINDOW_BASIC_FEATURE(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_WINDOW_BASIC_FEATURE))
#define ZMAP_WINDOW_BASIC_FEATURE_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_WINDOW_BASIC_FEATURE, zmapWindowBasicFeatureClass))
diff --git a/src/zmapWindow/items/zmapWindowCanvasItem.c b/src/zmapWindow/items/zmapWindowCanvasItem.c
index 075d5cf43..7fa50eff2 100755
--- a/src/zmapWindow/items/zmapWindowCanvasItem.c
+++ b/src/zmapWindow/items/zmapWindowCanvasItem.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: May 26 13:13 2010 (edgrif)
* Created: Wed Dec 3 09:00:20 2008 (rds)
- * CVS info: $Id: zmapWindowCanvasItem.c,v 1.27 2010-05-26 12:49:21 edgrif Exp $
+ * CVS info: $Id: zmapWindowCanvasItem.c,v 1.28 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -249,7 +249,7 @@ ZMapWindowCanvasItem zMapWindowCanvasItemCreate(FooCanvasGroup *parent,
if (item && ZMAP_IS_CANVAS_ITEM(item))
{
- GObject *object ;
+
ZMapWindowCanvasItemClass canvas_item_class ;
@@ -262,21 +262,27 @@ ZMapWindowCanvasItem zMapWindowCanvasItemCreate(FooCanvasGroup *parent,
if (ZMAP_CANVAS_ITEM_GET_CLASS(canvas_item)->post_create)
(* ZMAP_CANVAS_ITEM_GET_CLASS(canvas_item)->post_create)(canvas_item) ;
-#ifdef AUTO_RESIZE_OFF
+#if 0
+{ GObject *object ;
+ #ifdef AUTO_RESIZE_OFF
expand_background(canvas_item, NULL, NULL, NULL, NULL);
#endif /* AUTO_RESIZE_OFF */
/* This needs to be removed and replaced by zMapWindowCanvasItemGetFeature() */
- object = G_OBJECT(item);
+
#ifdef RDS_DONT_INCLUDE
- g_object_set_data(object, ITEM_FEATURE_DATA, feature);
- g_object_set_data(object, ITEM_FEATURE_TYPE, GUINT_TO_POINTER(ITEM_FEATURE_SIMPLE));
+ object = G_OBJECT(item);
+ g_object_set_data(object, ITEM_FEATURE_DATA, feature);
+ g_object_set_data(object, ITEM_FEATURE_TYPE, GUINT_TO_POINTER(ITEM_FEATURE_SIMPLE));
+#endif
+}
#endif
-
canvas_item_class = ZMAP_CANVAS_ITEM_GET_CLASS(canvas_item) ;
zmapWindowItemStatsIncr(&(canvas_item_class->stats)) ;
+
}
+
}
return canvas_item;
@@ -422,6 +428,7 @@ FooCanvasItem *zMapWindowCanvasItemAddInterval(ZMapWindowCanvasItem canvas_ite
if(interval && ZMAP_IS_CANVAS(interval->canvas))
{
FooCanvasItem *long_interval;
+
long_interval = zmapWindowLongItemCheckPoint(interval);
if(long_interval != interval)
@@ -447,6 +454,7 @@ FooCanvasItem *zMapWindowCanvasItemAddInterval(ZMapWindowCanvasItem canvas_ite
(* canvas_item_class->set_colour)(canvas_item, interval, sub_feature,
colour_type, NULL);
}
+
}
}
@@ -1147,7 +1155,7 @@ void zMapWindowCanvasItemReparent(FooCanvasItem *item, FooCanvasGroup *new_group
-/*
+/*
* Internal routines.
*/
@@ -1445,9 +1453,9 @@ static gboolean canvasItemEventCB(FooCanvasItem *item, GdkEvent *event, gpointer
/* This function is kind of a disaster from the memory and processing point of view,
* it has taken the original basic feature item and bloated by adding:
- *
+ *
* FOO_TYPE_CANVAS_RECT, FOO_TYPE_CANVAS_GROUP & FOO_TYPE_CANVAS_GROUP
- *
+ *
* */
static void zmap_window_canvas_item_post_create(ZMapWindowCanvasItem canvas_item)
{
diff --git a/src/zmapWindow/items/zmapWindowCanvasItem.h b/src/zmapWindow/items/zmapWindowCanvasItem.h
index 7e56e93db..3c12eec3a 100755
--- a/src/zmapWindow/items/zmapWindowCanvasItem.h
+++ b/src/zmapWindow/items/zmapWindowCanvasItem.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Feb 15 17:45 2010 (edgrif)
* Created: Wed Dec 3 08:21:03 2008 (rds)
- * CVS info: $Id: zmapWindowCanvasItem.h,v 1.11 2010-03-04 15:11:52 mh17 Exp $
+ * CVS info: $Id: zmapWindowCanvasItem.h,v 1.12 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_WINDOW_CANVAS_ITEM_H
@@ -54,8 +54,15 @@
#define ZMAP_WINDOW_CANVAS_INTERVAL_TYPE "interval-type"
#define ZMAP_TYPE_CANVAS_ITEM (zMapWindowCanvasItemGetType())
+
+#if GOBJ_CAST
+#define ZMAP_CANVAS_ITEM(obj) ((ZMapWindowCanvasItem) obj)
+#define ZMAP_CANVAS_ITEM_CONST(obj) ((ZMapWindowCanvasItem const) obj)
+#else
#define ZMAP_CANVAS_ITEM(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_CANVAS_ITEM, zmapWindowCanvasItem))
#define ZMAP_CANVAS_ITEM_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_CANVAS_ITEM, zmapWindowCanvasItem const))
+#endif
+
#define ZMAP_CANVAS_ITEM_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_CANVAS_ITEM, zmapWindowCanvasItemClass))
#define ZMAP_IS_CANVAS_ITEM(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_CANVAS_ITEM))
#define ZMAP_CANVAS_ITEM_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_CANVAS_ITEM, zmapWindowCanvasItemClass))
@@ -80,7 +87,7 @@ ZMapWindowCanvasItem zMapWindowCanvasItemCreate(FooCanvasGroup *parent,
FooCanvasItem *zMapWindowCanvasItemAddInterval(ZMapWindowCanvasItem canvas_item,
ZMapFeatureSubPartSpan sub_feature,
- double top, double bottom,
+ double top, double bottom,
double left, double right);
ZMapFeature zMapWindowCanvasItemGetFeature(FooCanvasItem *any_feature_item) ;
diff --git a/src/zmapWindow/items/zmapWindowContainerAlignment.h b/src/zmapWindow/items/zmapWindowContainerAlignment.h
index cabc3b0b3..42821be22 100755
--- a/src/zmapWindow/items/zmapWindowContainerAlignment.h
+++ b/src/zmapWindow/items/zmapWindowContainerAlignment.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Jun 10 14:53 2009 (rds)
* Created: Wed Dec 3 08:21:03 2008 (rds)
- * CVS info: $Id: zmapWindowContainerAlignment.h,v 1.3 2010-03-04 15:11:58 mh17 Exp $
+ * CVS info: $Id: zmapWindowContainerAlignment.h,v 1.4 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -44,8 +44,15 @@
#define ZMAP_TYPE_CONTAINER_ALIGNMENT (zmapWindowContainerAlignmentGetType())
+
+#if GOBJ_CAST
+#define ZMAP_CONTAINER_ALIGNMENT(obj) ((ZMapWindowContainerAlignment) obj)
+#define ZMAP_CONTAINER_ALIGNMENT_CONST(obj) ((ZMapWindowContainerAlignment const) obj)
+#else
#define ZMAP_CONTAINER_ALIGNMENT(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_CONTAINER_ALIGNMENT, zmapWindowContainerAlignment))
#define ZMAP_CONTAINER_ALIGNMENT_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_CONTAINER_ALIGNMENT, zmapWindowContainerAlignment const))
+#endif
+
#define ZMAP_CONTAINER_ALIGNMENT_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_CONTAINER_ALIGNMENT, zmapWindowContainerAlignmentClass))
#define ZMAP_IS_CONTAINER_ALIGNMENT(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_CONTAINER_ALIGNMENT))
#define ZMAP_CONTAINER_ALIGNMENT_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_CONTAINER_ALIGNMENT, zmapWindowContainerAlignmentClass))
diff --git a/src/zmapWindow/items/zmapWindowContainerBlock.h b/src/zmapWindow/items/zmapWindowContainerBlock.h
index 99fdde3f9..3ac4b0a02 100755
--- a/src/zmapWindow/items/zmapWindowContainerBlock.h
+++ b/src/zmapWindow/items/zmapWindowContainerBlock.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Jan 21 22:01 2010 (roy)
* Created: Wed Dec 3 08:21:03 2008 (rds)
- * CVS info: $Id: zmapWindowContainerBlock.h,v 1.5 2010-03-04 15:12:01 mh17 Exp $
+ * CVS info: $Id: zmapWindowContainerBlock.h,v 1.6 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -46,8 +46,15 @@
#define ZMAP_TYPE_CONTAINER_BLOCK (zmapWindowContainerBlockGetType())
+
+#if GOBJ_CAST
+#define ZMAP_CONTAINER_BLOCK(obj) ((ZMapWindowContainerBlock) obj)
+#define ZMAP_CONTAINER_BLOCK_CONST(obj) ((ZMapWindowContainerBlock const ) obj)
+#else
#define ZMAP_CONTAINER_BLOCK(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_CONTAINER_BLOCK, zmapWindowContainerBlock))
#define ZMAP_CONTAINER_BLOCK_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_CONTAINER_BLOCK, zmapWindowContainerBlock const))
+#endif
+
#define ZMAP_CONTAINER_BLOCK_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_CONTAINER_BLOCK, zmapWindowContainerBlockClass))
#define ZMAP_IS_CONTAINER_BLOCK(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_CONTAINER_BLOCK))
#define ZMAP_CONTAINER_BLOCK_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_CONTAINER_BLOCK, zmapWindowContainerBlockClass))
@@ -65,10 +72,10 @@ typedef struct _zmapWindowContainerBlockClassStruct zmapWindowContainerBlockCla
GType zmapWindowContainerBlockGetType(void);
ZMapWindowContainerBlock zmapWindowContainerBlockAugment(ZMapWindowContainerBlock container_block,
ZMapFeatureBlock feature_block);
-void zmapWindowContainerBlockAddCompressedColumn(ZMapWindowContainerBlock block_data,
+void zmapWindowContainerBlockAddCompressedColumn(ZMapWindowContainerBlock block_data,
FooCanvasGroup *container);
GList *zmapWindowContainerBlockRemoveCompressedColumns(ZMapWindowContainerBlock block_data);
-void zmapWindowContainerBlockAddBumpedColumn(ZMapWindowContainerBlock block_data,
+void zmapWindowContainerBlockAddBumpedColumn(ZMapWindowContainerBlock block_data,
FooCanvasGroup *container);
GList *zmapWindowContainerBlockRemoveBumpedColumns(ZMapWindowContainerBlock block_data);
@@ -78,12 +85,12 @@ void zmapWindowContainerBlockUnmark(ZMapWindowContainerBlock container_block);
void zmapWindowContainerBlockFlagRegion(ZMapWindowContainerBlock block_data,
ZMapFeatureBlock block);
void zmapWindowContainerBlockFlagRegionForColumn(ZMapWindowContainerBlock container_block,
- ZMapFeatureBlock block,
+ ZMapFeatureBlock block,
ZMapWindowContainerFeatureSet container_set);
GList *zmapWindowContainerBlockFilterFlaggedColumns(ZMapWindowContainerBlock block_data,
GList *list, int world1, int world2);
gboolean zmapWindowContainerBlockIsColumnLoaded(ZMapWindowContainerBlock container_block,
- ZMapWindowContainerFeatureSet container_set,
+ ZMapWindowContainerFeatureSet container_set,
int world1, int world2);
diff --git a/src/zmapWindow/items/zmapWindowContainerChildren.h b/src/zmapWindow/items/zmapWindowContainerChildren.h
index 062345f55..e538e9c45 100755
--- a/src/zmapWindow/items/zmapWindowContainerChildren.h
+++ b/src/zmapWindow/items/zmapWindowContainerChildren.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Jun 4 08:32 2009 (rds)
* Created: Wed Dec 3 08:21:03 2008 (rds)
- * CVS info: $Id: zmapWindowContainerChildren.h,v 1.4 2010-03-04 15:12:04 mh17 Exp $
+ * CVS info: $Id: zmapWindowContainerChildren.h,v 1.5 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -61,8 +61,15 @@ typedef gboolean (*zmapWindowContainerItemTestCallback)(FooCanvasItem *item, gpo
#define ZMAP_TYPE_CONTAINER_FEATURES (zmapWindowContainerFeaturesGetType())
+
+#if GOBJ_CAST
+#define ZMAP_CONTAINER_FEATURES(obj) ((ZMapWindowContainerFeatures) obj)
+#define ZMAP_CONTAINER_FEATURES_CONST(obj) ((ZMapWindowContainerFeatures const) obj)
+#else
#define ZMAP_CONTAINER_FEATURES(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_CONTAINER_FEATURES, zmapWindowContainerFeatures))
#define ZMAP_CONTAINER_FEATURES_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_CONTAINER_FEATURES, zmapWindowContainerFeatures const))
+#endif
+
#define ZMAP_CONTAINER_FEATURES_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_CONTAINER_FEATURES, zmapWindowContainerFeaturesClass))
#define ZMAP_IS_CONTAINER_FEATURES(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_CONTAINER_FEATURES))
#define ZMAP_CONTAINER_FEATURES_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_CONTAINER_FEATURES, zmapWindowContainerFeaturesClass))
diff --git a/src/zmapWindow/items/zmapWindowContainerContext.h b/src/zmapWindow/items/zmapWindowContainerContext.h
index dbc1b31d3..99bfbadba 100755
--- a/src/zmapWindow/items/zmapWindowContainerContext.h
+++ b/src/zmapWindow/items/zmapWindowContainerContext.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: May 20 13:10 2009 (rds)
* Created: Wed Dec 3 08:21:03 2008 (rds)
- * CVS info: $Id: zmapWindowContainerContext.h,v 1.2 2010-03-04 15:12:07 mh17 Exp $
+ * CVS info: $Id: zmapWindowContainerContext.h,v 1.3 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -44,8 +44,15 @@
#define ZMAP_TYPE_CONTAINER_CONTEXT (zmapWindowContainerContextGetType())
+
+#if GOBJ_CAST
+#define ZMAP_CONTAINER_CONTEXT(obj) ((ZMapWindowContainerContext) obj)
+#define ZMAP_CONTAINER_CONTEXT_CONST(obj) ((ZMapWindowContainerContext const ) obj)
+#else
#define ZMAP_CONTAINER_CONTEXT(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_CONTAINER_CONTEXT, zmapWindowContainerContext))
#define ZMAP_CONTAINER_CONTEXT_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_CONTAINER_CONTEXT, zmapWindowContainerContext const))
+#endif
+
#define ZMAP_CONTAINER_CONTEXT_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_CONTAINER_CONTEXT, zmapWindowContainerContextClass))
#define ZMAP_IS_CONTAINER_CONTEXT(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_CONTAINER_CONTEXT))
#define ZMAP_CONTAINER_CONTEXT_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_CONTAINER_CONTEXT, zmapWindowContainerContextClass))
diff --git a/src/zmapWindow/items/zmapWindowContainerFeatureSet.c b/src/zmapWindow/items/zmapWindowContainerFeatureSet.c
index 9c3cff91a..72b3ef9ac 100755
--- a/src/zmapWindow/items/zmapWindowContainerFeatureSet.c
+++ b/src/zmapWindow/items/zmapWindowContainerFeatureSet.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: May 21 17:06 2010 (edgrif)
* Created: Mon Jul 30 13:09:33 2007 (rds)
- * CVS info: $Id: zmapWindowContainerFeatureSet.c,v 1.28 2010-05-25 14:17:01 mh17 Exp $
+ * CVS info: $Id: zmapWindowContainerFeatureSet.c,v 1.29 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
#include <string.h> /* memset */
@@ -173,6 +173,7 @@ GType zmapWindowContainerFeatureSetGetType(void)
* \return ZMapWindowContainerFeatureSet that was edited.
*/
+// this is only called on column creation
ZMapWindowContainerFeatureSet zmapWindowContainerFeatureSetAugment(ZMapWindowContainerFeatureSet container_set,
ZMapWindow window,
GQuark align_id,
@@ -210,8 +211,11 @@ ZMapWindowContainerFeatureSet zmapWindowContainerFeatureSetAugment(ZMapWindowCon
while((list = g_list_next(list)));
}
+ // try to guess the intended visibility mode to avoid extra foo_canvas activity
+ zmapWindowColumnSetState(window, FOO_CANVAS_GROUP(container_set),
+ ZMAPSTYLE_COLDISPLAY_INVALID, FALSE);
- zmapWindowContainerSetVisibility((FooCanvasGroup *)container_set, FALSE);
+// zmapWindowContainerSetVisibility((FooCanvasGroup *)container_set, FALSE);
}
return container_set;
@@ -659,7 +663,7 @@ void zmapWindowContainerFeatureSetStyleDisplay(ZMapWindowContainerFeatureSet con
value_data.gvalue = &value;
value_data.param_id = ITEM_FEATURE_SET_VISIBLE;
- value_to_each_style_in_table(GUINT_TO_POINTER(style_id), local_style, &value_data);
+ value_to_each_style_in_table(GUINT_TO_POINTER(style_id), (gpointer) local_style, &value_data);
g_value_unset(&value);
}
@@ -1069,6 +1073,8 @@ ZMapWindowContainerFeatureSet zmapWindowContainerFeatureSetDestroy(ZMapWindowCon
return item_feature_set;
}
+
+#if MH17_function_not_used
/* This function is written the wrong way round. It should be
* re-written, along with extract_value_from_style_table so that
* this function is part of utils and extract_value_from_style_table
@@ -1113,7 +1119,7 @@ gboolean zmapWindowStyleListGetSetting(GList *list_of_styles,
return result;
}
-
+#endif
/*
* OBJECT CODE
@@ -1575,7 +1581,9 @@ static void extract_value_from_style_table(gpointer key, gpointer value, gpointe
if(!current)
{
- if(zMapStyleGetJoinAligns(style, &style_version))
+// if(zMapStyleGetJoinAligns(style, &style_version))
+ style_version = zMapStyleGetWithinAlignError(style);
+ if(style_version) // if it's set we only care if it's not zero
{
g_value_set_uint(value_data->gvalue, style_version);
}
diff --git a/src/zmapWindow/items/zmapWindowContainerFeatureSet.h b/src/zmapWindow/items/zmapWindowContainerFeatureSet.h
index 4b9a4f8f7..ab50fe7ba 100755
--- a/src/zmapWindow/items/zmapWindowContainerFeatureSet.h
+++ b/src/zmapWindow/items/zmapWindowContainerFeatureSet.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: May 24 15:40 2010 (edgrif)
* Created: Wed Dec 3 08:21:03 2008 (rds)
- * CVS info: $Id: zmapWindowContainerFeatureSet.h,v 1.12 2010-05-24 14:41:11 edgrif Exp $
+ * CVS info: $Id: zmapWindowContainerFeatureSet.h,v 1.13 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -49,8 +49,15 @@
#define ZMAP_TYPE_CONTAINER_FEATURESET (zmapWindowContainerFeatureSetGetType())
+
+#if GOBJ_CAST
+#define ZMAP_CONTAINER_FEATURESET(obj) ((ZMapWindowContainerFeatureSet) obj)
+#define ZMAP_CONTAINER_FEATURESET_CONST(obj) ((ZMapWindowContainerFeatureSet const) obj)
+#else
#define ZMAP_CONTAINER_FEATURESET(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_CONTAINER_FEATURESET, zmapWindowContainerFeatureSet))
#define ZMAP_CONTAINER_FEATURESET_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_CONTAINER_FEATURESET, zmapWindowContainerFeatureSet const))
+#endif
+
#define ZMAP_CONTAINER_FEATURESET_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_CONTAINER_FEATURESET, zmapWindowContainerFeatureSetClass))
#define ZMAP_IS_CONTAINER_FEATURESET(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_CONTAINER_FEATURESET))
#define ZMAP_CONTAINER_FEATURESET_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_CONTAINER_FEATURESET, zmapWindowContainerFeatureSetClass))
@@ -99,7 +106,7 @@ ZMapStrand zmapWindowContainerFeatureSetGetStrand(ZMapWindowContainerFeatureSet
ZMapFrame zmapWindowContainerFeatureSetGetFrame (ZMapWindowContainerFeatureSet container_set);
double zmapWindowContainerFeatureSetGetWidth(ZMapWindowContainerFeatureSet container_set);
double zmapWindowContainerFeatureGetBumpSpacing(ZMapWindowContainerFeatureSet container_set);
-gboolean zmapWindowContainerFeatureSetGetMagValues(ZMapWindowContainerFeatureSet container_set,
+gboolean zmapWindowContainerFeatureSetGetMagValues(ZMapWindowContainerFeatureSet container_set,
double *min_mag_out, double *max_mag_out);
ZMapStyleBumpMode zmapWindowContainerFeatureSetGetBumpUnmarked(ZMapWindowContainerFeatureSet container_set) ;
@@ -135,9 +142,9 @@ void zmapWindowContainerFeatureSetPushHiddenStack(ZMapWindowContainerFeatureSet
void zmapWindowContainerFeatureSetRemoveAllItems(ZMapWindowContainerFeatureSet container_set);
-void zmapWindowContainerFeatureSetSortFeatures(ZMapWindowContainerFeatureSet container_set,
+void zmapWindowContainerFeatureSetSortFeatures(ZMapWindowContainerFeatureSet container_set,
gint direction);
-
+
void zMapWindowContainerFeatureSetMarkUnsorted(ZMapWindowContainerFeatureSet container_set);
/* Finished with this container */
diff --git a/src/zmapWindow/items/zmapWindowContainerFeatureSetUtils.c b/src/zmapWindow/items/zmapWindowContainerFeatureSetUtils.c
index 954c523ac..827a08e14 100755
--- a/src/zmapWindow/items/zmapWindowContainerFeatureSetUtils.c
+++ b/src/zmapWindow/items/zmapWindowContainerFeatureSetUtils.c
@@ -30,7 +30,7 @@
* HISTORY:
* Last edited: May 24 12:05 2010 (edgrif)
* Created: Wed Dec 3 10:02:22 2008 (rds)
- * CVS info: $Id: zmapWindowContainerFeatureSetUtils.c,v 1.2 2010-05-26 12:02:50 mh17 Exp $
+ * CVS info: $Id: zmapWindowContainerFeatureSetUtils.c,v 1.3 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
#include <math.h>
@@ -586,11 +586,27 @@ static gboolean fragments_splice(char *fragment_a, char *fragment_b)
spliceosome[4] = fragment_b[1];
spliceosome[5] = '\0';
+#define NEW_RULES 0
+#if NEW_RULES
if(!g_ascii_strcasecmp(fragment_b, "AG"))
{
if(!g_ascii_strcasecmp(&spliceosome[1], "GT") || !g_ascii_strcasecmp(&spliceosome[0], "GGC"))
splice = TRUE;
}
+#else
+ if(g_ascii_strcasecmp(&spliceosome[1], "GTAG") == 0)
+ {
+ splice = TRUE;
+ }
+ else if(g_ascii_strcasecmp(&spliceosome[1], "GCAG") == 0)
+ {
+ splice = TRUE;
+ }
+ else if(g_ascii_strcasecmp(&spliceosome[1], "ATAC") == 0)
+ {
+ splice = TRUE;
+ }
+#endif
}
diff --git a/src/zmapWindow/items/zmapWindowContainerGroup.c b/src/zmapWindow/items/zmapWindowContainerGroup.c
index 705f0ab24..52b6c888d 100755
--- a/src/zmapWindow/items/zmapWindowContainerGroup.c
+++ b/src/zmapWindow/items/zmapWindowContainerGroup.c
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: May 24 15:23 2010 (edgrif)
* Created: Wed Dec 3 10:02:22 2008 (rds)
- * CVS info: $Id: zmapWindowContainerGroup.c,v 1.13 2010-05-24 14:23:50 edgrif Exp $
+ * CVS info: $Id: zmapWindowContainerGroup.c,v 1.14 2010-06-08 08:31:27 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -58,7 +58,7 @@ typedef struct
static void zmap_window_container_group_class_init (ZMapWindowContainerGroupClass container_class);
static void zmap_window_container_group_init (ZMapWindowContainerGroup group);
-static void zmap_window_container_group_set_property(GObject *object,
+static void zmap_window_container_group_set_property(GObject *object,
guint param_id,
const GValue *value,
GParamSpec *pspec);
@@ -72,19 +72,19 @@ static void zmap_window_container_group_destroy (GtkObject *gtkobject);
static void zmap_window_container_group_draw (FooCanvasItem *item, GdkDrawable *drawable,
GdkEventExpose *expose);
static void zmap_window_container_group_update (FooCanvasItem *item, double i2w_dx, double i2w_dy, int flags);
-static void zmap_window_container_group_reposition(ZMapWindowContainerGroup container_group,
+static void zmap_window_container_group_reposition(ZMapWindowContainerGroup container_group,
double rect_x1, double rect_y1,
double rect_x2, double rect_y2,
double *dx_repos, double *dy_repos);
-static void maximise_background_rectangle(ZMapWindowContainerGroup this_container,
+static void maximise_background_rectangle(ZMapWindowContainerGroup this_container,
FooCanvasItem *container_item,
FooCanvasRE *rect);
static void crop_rectangle_to_scroll_region(gpointer rectangle_data, gpointer points_data);
static void zmap_window_container_scroll_region_get_item_bounds(FooCanvasItem *item,
double *x1, double *y1,
double *x2, double *y2);
-static void zmap_window_container_update_with_crop(FooCanvasItem *item,
+static void zmap_window_container_update_with_crop(FooCanvasItem *item,
double i2w_dx, double i2w_dy,
FooCanvasPoints *itemised_scroll_region,
int flags);
@@ -108,16 +108,16 @@ static FooCanvasItemClass *item_parent_class_G = NULL;
/*!
* \brief Get the GType for the ZMapWindowContainerGroup GObjects
- *
+ *
* \return GType corresponding to the GObject as registered by glib.
*/
GType zmapWindowContainerGroupGetType(void)
{
static GType group_type = 0;
-
+
if (!group_type) {
- static const GTypeInfo group_info =
+ static const GTypeInfo group_info =
{
sizeof (zmapWindowContainerGroupClass),
(GBaseInitFunc) NULL,
@@ -128,21 +128,21 @@ GType zmapWindowContainerGroupGetType(void)
sizeof (zmapWindowContainerGroup),
0, /* n_preallocs */
(GInstanceInitFunc) zmap_window_container_group_init
-
+
};
-
+
group_type = g_type_register_static (FOO_TYPE_CANVAS_GROUP,
ZMAP_WINDOW_CONTAINER_GROUP_NAME,
&group_info,
0);
}
-
+
return group_type;
}
/*!
* \brief Create a new ZMapWindowContainerGroup object.
- *
+ *
* \param parent This is the parent ZMapWindowContainerFeatures
* \param level The level the new ZMapWindowContainerGroup should be.
* \param child_spacing The distance between the children of this container.
@@ -171,7 +171,7 @@ ZMapWindowContainerGroup zmapWindowContainerGroupCreate(ZMapWindowContainerFeatu
/*!
* \brief Create a new ZMapWindowContainerGroup object.
- *
+ *
* \param parent This is the parent FooCanvasGroup.
* \param level The level the new ZMapWindowContainerGroup should be.
* \param child_spacing The distance between the children of this container.
@@ -202,7 +202,7 @@ ZMapWindowContainerGroup zmapWindowContainerGroupCreateFromFoo(FooCanvasGroup
if(ZMAP_IS_CONTAINER_GROUP(parent))
{
zMapAssertNotReached();
-
+
parent = (FooCanvasGroup *)zmapWindowContainerGetFeatures((ZMapWindowContainerGroup)parent);
}
else
@@ -213,9 +213,9 @@ ZMapWindowContainerGroup zmapWindowContainerGroupCreateFromFoo(FooCanvasGroup
level = parent_container->level + 1;
}
}
-
+
container_type = ZMAP_TYPE_CONTAINER_GROUP;
-
+
switch(level)
{
case ZMAPCONTAINER_LEVEL_ROOT:
@@ -238,11 +238,11 @@ ZMapWindowContainerGroup zmapWindowContainerGroupCreateFromFoo(FooCanvasGroup
break;
}
- item = foo_canvas_item_new(parent, container_type,
+ item = foo_canvas_item_new(parent, container_type,
"x", 0.0,
"y", 0.0,
NULL);
-
+
if(item && ZMAP_IS_CONTAINER_GROUP(item))
{
group = FOO_CANVAS_GROUP(item);
@@ -265,13 +265,13 @@ ZMapWindowContainerGroup zmapWindowContainerGroupCreateFromFoo(FooCanvasGroup
if(ZMAP_CONTAINER_GROUP_GET_CLASS(container)->post_create)
(ZMAP_CONTAINER_GROUP_GET_CLASS(container)->post_create)(container);
}
-
+
return container;
}
/*!
* \brief Set the visibility of a whole ZMapWindowContainerGroup.
- *
+ *
* \param container_parent A FooCanvasGroup which _must_ be a ZMapWindowContainerGroup.
* \param visible A boolean to specify visibility. TRUE = visible, FALSE = hidden.
*
@@ -294,6 +294,8 @@ gboolean zmapWindowContainerSetVisibility(FooCanvasGroup *container_parent, gboo
else
foo_canvas_item_hide((FooCanvasItem *)container_parent);
+ zMapStopTimer("SetVis",visible ? "true" : "false");
+
setable = TRUE;
}
@@ -343,7 +345,7 @@ void zmapWindowContainerGroupBackgroundSize(ZMapWindowContainerGroup container,
}
/*!
- * \brief A ZMapWindowContainerGroup may need to redraw it's children.
+ * \brief A ZMapWindowContainerGroup may need to redraw it's children.
* This sets a flag so that it happens
*
* \param container The container that needs its flag set.
@@ -352,7 +354,7 @@ void zmapWindowContainerGroupBackgroundSize(ZMapWindowContainerGroup container,
* \return void
*/
-void zmapWindowContainerGroupChildRedrawRequired(ZMapWindowContainerGroup container,
+void zmapWindowContainerGroupChildRedrawRequired(ZMapWindowContainerGroup container,
gboolean redraw_required)
{
container->flags.column_redraw = redraw_required;
@@ -417,7 +419,7 @@ void zmapWindowContainerGroupAddPreUpdateHook(ZMapWindowContainerGroup container
update_hook->hook_func = hook;
update_hook->hook_data = user_data;
- container->pre_update_hooks = g_slist_append(container->pre_update_hooks,
+ container->pre_update_hooks = g_slist_append(container->pre_update_hooks,
update_hook);
}
@@ -449,7 +451,7 @@ void zmapWindowContainerGroupRemovePreUpdateHook(ZMapWindowContainerGroup contai
*
* Internally the containers hold a list of these hook which get
* called every time the container gets drawn. This can be done
- * on a per container basis, rather than across all containers.
+ * on a per container basis, rather than across all containers.
* In terms of utility and use case the block marking and navigator
* are users of this.
*
@@ -471,7 +473,7 @@ void zmapWindowContainerGroupAddUpdateHook(ZMapWindowContainerGroup container,
update_hook->hook_func = hook;
update_hook->hook_data = user_data;
- container->post_update_hooks = g_slist_append(container->post_update_hooks,
+ container->post_update_hooks = g_slist_append(container->post_update_hooks,
update_hook);
}
@@ -480,7 +482,7 @@ void zmapWindowContainerGroupAddUpdateHook(ZMapWindowContainerGroup container,
/*!
* \brief Remove an update hook on a ZMapWindowContainerGroup.
- *
+ *
* Exactly the opposite of Add. Both the hook and the data are required
* to successfully remove the hook.
*
@@ -512,11 +514,11 @@ void zmapWindowContainerGroupRemoveUpdateHook(ZMapWindowContainerGroup container
/*!
* \brief Time to free the memory associated with the ZMapWindowContainerGroup.
- *
+ *
* \code container = zmapWindowContainerGroupDestroy(container);
- *
+ *
* \param container The container to be free'd
- *
+ *
* \return The container that has been free'd. i.e. NULL
*/
@@ -597,7 +599,7 @@ static void zmap_window_container_group_init (ZMapWindowContainerGroup co
return ;
}
-static void zmap_window_container_group_set_property(GObject *object,
+static void zmap_window_container_group_set_property(GObject *object,
guint param_id,
const GValue *value,
GParamSpec *pspec)
@@ -698,23 +700,23 @@ static void zmap_window_container_group_get_property(GObject *obje
return ;
}
#ifdef POINT_REQUIRED
-static double window_container_group_invoke_point (FooCanvasItem *item,
- double x, double y,
+static double window_container_group_invoke_point (FooCanvasItem *item,
+ double x, double y,
int cx, int cy,
FooCanvasItem **actual_item)
{
/* Calculate x & y in item local coordinates */
-
+
if (FOO_CANVAS_ITEM_GET_CLASS (item)->point)
return FOO_CANVAS_ITEM_GET_CLASS (item)->point (item, x, y, cx, cy, actual_item);
-
+
return 1e18;
}
/* Point handler for canvas groups */
-static double zmap_window_container_group_item_point (FooCanvasItem *item,
- double x, double y,
+static double zmap_window_container_group_item_point (FooCanvasItem *item,
+ double x, double y,
int cx, int cy,
FooCanvasItem **actual_item)
{
@@ -726,15 +728,15 @@ static double zmap_window_container_group_item_point (FooCanvasItem *item,
double dist, best;
group = FOO_CANVAS_GROUP (item);
-
+
x1 = cx - item->canvas->close_enough;
y1 = cy - item->canvas->close_enough;
x2 = cx + item->canvas->close_enough;
y2 = cy + item->canvas->close_enough;
-
+
best = 0.0;
*actual_item = NULL;
-
+
gx = x - group->xpos;
gy = y - group->ypos;
@@ -747,7 +749,7 @@ static double zmap_window_container_group_item_point (FooCanvasItem *item,
child = list->data;
if ((child->object.flags & FOO_CANVAS_ITEM_MAPPED)
- && FOO_CANVAS_ITEM_GET_CLASS (child)->point)
+ && FOO_CANVAS_ITEM_GET_CLASS (child)->point)
{
dist = window_container_group_invoke_point (child, gx, gy, cx, cy, &point_item);
if(point_item && ((int)(dist * item->canvas->pixels_per_unit_x + 0.5) <= item->canvas->close_enough) &&
@@ -756,10 +758,10 @@ static double zmap_window_container_group_item_point (FooCanvasItem *item,
best = dist;
*actual_item = point_item;
}
- }
+ }
list = list->next;
}
-
+
if(actual_item == NULL && item_parent_class_G->point)
best = (item_parent_class_G->point)(item, x, y, cx, cy, actual_item);
@@ -781,7 +783,7 @@ static void zmap_window_container_group_destroy (GtkObject *gtkobject)
g_slist_free(container->pre_update_hooks);
container->pre_update_hooks = NULL;
}
-
+
if(container->post_update_hooks)
{
g_slist_foreach(container->post_update_hooks, (GFunc)g_free, NULL);
@@ -805,15 +807,15 @@ static void zmap_window_container_group_draw (FooCanvasItem *item, GdkDrawable *
return ;
}
-static void maximise_background_rectangle(ZMapWindowContainerGroup this_container,
+static void maximise_background_rectangle(ZMapWindowContainerGroup this_container,
FooCanvasItem *container_item,
FooCanvasRE *rect)
{
FooCanvasItem *rect_item;
double irx1, irx2, iry1, iry2;
int container_x2, container_y2; /* container canvas coords, calculated from group->update above. */
-
-
+
+
/* We can't trust item->x1 and item->y1 as empty child
* groups return 0,0->0,0 hence extend all parents to
* 0,0! */
@@ -828,7 +830,7 @@ static void maximise_background_rectangle(ZMapWindowContainerGroup this_containe
if((iry2 - iry1 + 1) < this_container->height)
iry2 = this_container->height + iry1 ;
-
+
rect->x1 = irx1;
rect->y1 = iry1;
rect->x2 = irx2;
@@ -853,7 +855,7 @@ static void crop_rectangle_to_scroll_region(gpointer rectangle_data, gpointer po
FooCanvasPoints *scroll_region = (FooCanvasPoints *)points_data;
double scroll_x1, scroll_y1, scroll_x2, scroll_y2;
double iwx1, iwy1, iwx2, iwy2;
-
+
rect = (FooCanvasRE *)rectangle_data;
crop_item = (FooCanvasItem *)rect;
foo_canvas = crop_item->canvas;
@@ -868,10 +870,10 @@ static void crop_rectangle_to_scroll_region(gpointer rectangle_data, gpointer po
/* x unused ATM */
scroll_x1 = foo_canvas->scroll_x1;
scroll_x2 = foo_canvas->scroll_x2;
-
+
scroll_y1 = foo_canvas->scroll_y1;
scroll_y2 = foo_canvas->scroll_y2;
-
+
foo_canvas_item_w2i(crop_item, &scroll_x1, &scroll_y1);
foo_canvas_item_w2i(crop_item, &scroll_x2, &scroll_y2);
}
@@ -889,7 +891,7 @@ static void crop_rectangle_to_scroll_region(gpointer rectangle_data, gpointer po
{
rect->y1 = scroll_y1 - 1.0;
}
-
+
if(iwy2 > scroll_y2)
{
rect->y2 = scroll_y2 + 1.0;
@@ -913,10 +915,10 @@ static void zmap_window_container_scroll_region_get_item_bounds(FooCanvasItem *i
scroll_y1 = foo_canvas->scroll_y1;
scroll_y2 = foo_canvas->scroll_y2;
-
+
foo_canvas_item_w2i(item, &scroll_x1, &scroll_y1);
foo_canvas_item_w2i(item, &scroll_x2, &scroll_y2);
-
+
if(x1)
*x1 = scroll_x1;
if(y1)
@@ -929,7 +931,7 @@ static void zmap_window_container_scroll_region_get_item_bounds(FooCanvasItem *i
return ;
}
-static void zmap_window_container_update_with_crop(FooCanvasItem *item,
+static void zmap_window_container_update_with_crop(FooCanvasItem *item,
double i2w_dx, double i2w_dy,
FooCanvasPoints *itemised_scroll_region,
int flags)
@@ -955,7 +957,7 @@ static void zmap_window_container_update_with_crop(FooCanvasItem *item,
do
{
- zmap_window_container_update_with_crop((FooCanvasItem *)(list->data),
+ zmap_window_container_update_with_crop((FooCanvasItem *)(list->data),
sub_i2w_dx, sub_i2w_dy,
itemised_scroll_region, flags);
}
@@ -997,16 +999,16 @@ static void invoke_update_hooks(ZMapWindowContainerGroup container, GSList *hook
coords[1] = y1;
coords[2] = x2;
coords[3] = y2;
-
+
bounds.coords = &coords[0];
bounds.ref_count = 1;
bounds.num_points = 2;
-
+
item = (FooCanvasItem *)container;
if(canvas_in_update) /* actually we might not want to do this. */
canvas_in_update = item->canvas->doing_update;
-
+
if(canvas_in_update)
{
@@ -1024,9 +1026,9 @@ static void invoke_update_hooks(ZMapWindowContainerGroup container, GSList *hook
do
{
ContainerUpdateHook update_hook;
-
+
update_hook = (ContainerUpdateHook)(hooks->data);
-
+
if(update_hook->hook_func)
(update_hook->hook_func)(container, &bounds, container->level, update_hook->hook_data);
}
@@ -1120,7 +1122,7 @@ static void zmap_window_container_group_update (FooCanvasItem *item, double i2w_
if(doing_reposition)
{
- GList *list, *list_end, tmp_features = {NULL}, tmp_background = {NULL};
+ GList *list, *list_end, tmp_features = {NULL}, tmp_background = {NULL};
gboolean print_debug = FALSE;
if((item_list = canvas_group->item_list))
@@ -1131,12 +1133,12 @@ static void zmap_window_container_group_update (FooCanvasItem *item, double i2w_
if(FOO_IS_CANVAS_GROUP(item_list->data))
{
FooCanvasGroup *group = (FooCanvasGroup *)(item_list->data);
-
+
if(group->xpos != 0.0)
group->xpos = 0.0;
if(group->ypos != 0.0)
group->ypos = 0.0;
-
+
if(ZMAP_IS_CONTAINER_OVERLAY(item_list->data))
overlay = (ZMapWindowContainerOverlay)(item_list->data);
else if(ZMAP_IS_CONTAINER_UNDERLAY(item_list->data))
@@ -1145,12 +1147,12 @@ static void zmap_window_container_group_update (FooCanvasItem *item, double i2w_
else if(ZMAP_IS_CONTAINER_BACKGROUND(item_list->data))
{
rect = FOO_CANVAS_RE(item_list->data);
-
+
if(rect->x1 != 0.0)
rect->x1 = 0.0;
if(rect->y1 != 0.0)
rect->y1 = 0.0;
-
+
rect->x2 = 1.0; /* There's no way to know width */
rect->y2 = this_container->height; /* We know height though. */
}
@@ -1172,7 +1174,7 @@ static void zmap_window_container_group_update (FooCanvasItem *item, double i2w_
default:
break;
}
-
+
printf("current_x=%f, current_y=%f\n", current_x, current_y);
}
@@ -1226,18 +1228,18 @@ static void zmap_window_container_group_update (FooCanvasItem *item, double i2w_
if(parent_container)
{
double dx, dy;
-
+
if(ZMAP_CONTAINER_GROUP_GET_CLASS(this_container)->reposition_group)
- (ZMAP_CONTAINER_GROUP_GET_CLASS(this_container)->reposition_group)(this_container,
- rect->x1, rect->y1,
- rect->x2, rect->y2,
+ (ZMAP_CONTAINER_GROUP_GET_CLASS(this_container)->reposition_group)(this_container,
+ rect->x1, rect->y1,
+ rect->x2, rect->y2,
&dx, &dy);
-
+
parent_container->reposition_x += dx;
parent_container->reposition_y += dy;
}
- zmap_window_container_invoke_post_update_hooks(this_container,
+ zmap_window_container_invoke_post_update_hooks(this_container,
rect->x1, rect->y1,
rect->x2, rect->y2);
}
@@ -1260,7 +1262,7 @@ static void zmap_window_container_group_update (FooCanvasItem *item, double i2w_
update_items[i++] = (FooCanvasItem *)overlay;
update_items[i++] = (FooCanvasItem *)underlay;
- zmap_window_container_scroll_region_get_item_bounds(update_items[0],
+ zmap_window_container_scroll_region_get_item_bounds(update_items[0],
&coords[0], &coords[1],
&coords[2], &coords[3]);
scroll_region.coords = &coords[0];
@@ -1269,12 +1271,12 @@ static void zmap_window_container_group_update (FooCanvasItem *item, double i2w_
/* We need to maximise overlays and underlays if required too. */
if(overlay)
- zmapWindowContainerOverlayMaximiseItems(overlay,
+ zmapWindowContainerOverlayMaximiseItems(overlay,
rect->x1, rect->y1,
rect->x2, rect->y2);
if(underlay)
- zmapWindowContainerUnderlayMaximiseItems(underlay,
+ zmapWindowContainerUnderlayMaximiseItems(underlay,
rect->x1, rect->y1,
rect->x2, rect->y2);
@@ -1295,7 +1297,7 @@ static void zmap_window_container_group_update (FooCanvasItem *item, double i2w_
}
-static void zmap_window_container_group_reposition(ZMapWindowContainerGroup container_group,
+static void zmap_window_container_group_reposition(ZMapWindowContainerGroup container_group,
double rect_x1, double rect_y1,
double rect_x2, double rect_y2,
double *dx_repos, double *dy_repos)
diff --git a/src/zmapWindow/items/zmapWindowContainerGroup.h b/src/zmapWindow/items/zmapWindowContainerGroup.h
index a1c64aaf4..a9b39e048 100755
--- a/src/zmapWindow/items/zmapWindowContainerGroup.h
+++ b/src/zmapWindow/items/zmapWindowContainerGroup.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: May 20 11:13 2010 (edgrif)
* Created: Wed Dec 3 08:21:03 2008 (rds)
- * CVS info: $Id: zmapWindowContainerGroup.h,v 1.9 2010-05-24 14:24:21 edgrif Exp $
+ * CVS info: $Id: zmapWindowContainerGroup.h,v 1.10 2010-06-08 08:31:27 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_WINDOW_CONTAINER_GROUP_H
@@ -50,7 +50,7 @@
/*!
* ZMapWindowContainerGroup for containing and positioning of canvas items.
* Each ZMapWindowContainerGroup consists of:
- *
+ *
* -------- parent_group -----------
* / / \ \
* / / \ \
@@ -74,14 +74,14 @@
* group then we make a container root, i.e. the top of the container tree.
*
* The new object code means that each container member including the member itself
- * has a G_TYPE* This means code that does ZMAP_IS_CONTAINER_GROUP(pointer) is
- * simpler and hopefully more readable.
+ * has a G_TYPE* This means code that does ZMAP_IS_CONTAINER_GROUP(pointer) is
+ * simpler and hopefully more readable.
*
* The ZMapWindowContainerGroup are sub classes of FooCanvasGroup and implement the
* FooCanvasItem interface (draw, update, bounds, etc...). The update code takes
- * care of cropping the Container "owned" items, such as the background and any
- * overlays/underlays that might be being drawn. It also includes hooks to
- * provide similar functionality to the ContainerExecute callbacks. These are
+ * care of cropping the Container "owned" items, such as the background and any
+ * overlays/underlays that might be being drawn. It also includes hooks to
+ * provide similar functionality to the ContainerExecute callbacks. These are
* attached/owned by each specific container so only get called by the container
* they relate to. This again leads to simpler code, without the switch on the
* container level.
@@ -96,8 +96,14 @@
#define ZMAP_TYPE_CONTAINER_GROUP (zmapWindowContainerGroupGetType())
+
+#if GOBJ_CAST
+#define ZMAP_CONTAINER_GROUP(obj) ((ZMapWindowContainerGroup) obj)
+#define ZMAP_CONTAINER_GROUP_CONST(obj) ((ZMapWindowContainerGroup const) obj)
+#else
#define ZMAP_CONTAINER_GROUP(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_CONTAINER_GROUP, zmapWindowContainerGroup))
#define ZMAP_CONTAINER_GROUP_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_CONTAINER_GROUP, zmapWindowContainerGroup const))
+#endif
#define ZMAP_CONTAINER_GROUP_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_CONTAINER_GROUP, zmapWindowContainerGroupClass))
#define ZMAP_IS_CONTAINER_GROUP(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_CONTAINER_GROUP))
#define ZMAP_CONTAINER_GROUP_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_CONTAINER_GROUP, zmapWindowContainerGroupClass))
@@ -126,7 +132,7 @@ typedef struct _zmapWindowContainerGroupStruct zmapWindowContainerGroup, *ZMapW
typedef struct _zmapWindowContainerGroupClassStruct zmapWindowContainerGroupClass, *ZMapWindowContainerGroupClass ;
-typedef gboolean (* ZMapWindowContainerUpdateHook)(ZMapWindowContainerGroup group_updated,
+typedef gboolean (* ZMapWindowContainerUpdateHook)(ZMapWindowContainerGroup group_updated,
FooCanvasPoints *group_bounds,
ZMapContainerLevelType group_level,
gpointer user_data);
@@ -147,7 +153,7 @@ ZMapWindowContainerGroup zmapWindowContainerGroupCreateFromFoo(FooCanvasGroup
gboolean zmapWindowContainerSetVisibility(FooCanvasGroup *container_parent, gboolean visible);
void zmapWindowContainerRequestReposition(ZMapWindowContainerGroup container);
void zmapWindowContainerGroupBackgroundSize(ZMapWindowContainerGroup container, double height);
-void zmapWindowContainerGroupChildRedrawRequired(ZMapWindowContainerGroup container,
+void zmapWindowContainerGroupChildRedrawRequired(ZMapWindowContainerGroup container,
gboolean redraw_required);
void zmapWindowContainerGroupSetBackgroundColour(ZMapWindowContainerGroup container,
GdkColor *new_colour);
diff --git a/src/zmapWindow/items/zmapWindowContainerStrand.h b/src/zmapWindow/items/zmapWindowContainerStrand.h
index 5e4112d8a..e1e98e0aa 100755
--- a/src/zmapWindow/items/zmapWindowContainerStrand.h
+++ b/src/zmapWindow/items/zmapWindowContainerStrand.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Jun 4 09:42 2009 (rds)
* Created: Wed Dec 3 08:21:03 2008 (rds)
- * CVS info: $Id: zmapWindowContainerStrand.h,v 1.3 2010-03-04 15:12:14 mh17 Exp $
+ * CVS info: $Id: zmapWindowContainerStrand.h,v 1.4 2010-06-08 08:31:27 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -44,8 +44,15 @@
#define ZMAP_TYPE_CONTAINER_STRAND (zmapWindowContainerStrandGetType())
+
+#if GOBJ_CAST
+#define ZMAP_CONTAINER_STRAND(obj) ((ZMapWindowContainerStrand) obj)
+#define ZMAP_CONTAINER_STRAND_CONST(obj) ((ZMapWindowContainerStrand const) obj)
+#else
#define ZMAP_CONTAINER_STRAND(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_CONTAINER_STRAND, zmapWindowContainerStrand))
#define ZMAP_CONTAINER_STRAND_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_CONTAINER_STRAND, zmapWindowContainerStrand const))
+#endif
+
#define ZMAP_CONTAINER_STRAND_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_CONTAINER_STRAND, zmapWindowContainerStrandClass))
#define ZMAP_IS_CONTAINER_STRAND(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_CONTAINER_STRAND))
#define ZMAP_CONTAINER_STRAND_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_CONTAINER_STRAND, zmapWindowContainerStrandClass))
diff --git a/src/zmapWindow/items/zmapWindowGlyphItem.h b/src/zmapWindow/items/zmapWindowGlyphItem.h
index f7f3f3dd3..a43e076e8 100755
--- a/src/zmapWindow/items/zmapWindowGlyphItem.h
+++ b/src/zmapWindow/items/zmapWindowGlyphItem.h
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Apr 6 14:45 2009 (rds)
* Created: Fri Jan 16 14:01:12 2009 (rds)
- * CVS info: $Id: zmapWindowGlyphItem.h,v 1.6 2010-04-15 11:19:04 mh17 Exp $
+ * CVS info: $Id: zmapWindowGlyphItem.h,v 1.7 2010-06-08 08:31:27 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -42,8 +42,14 @@
#define ZMAP_WINDOW_GLYPH_ITEM_NAME "ZMapWindowGlyphItem"
#define ZMAP_TYPE_WINDOW_GLYPH_ITEM (zMapWindowGlyphItemGetType())
+
+#if GOBJ_CAST
+#define ZMAP_WINDOW_GLYPH_ITEM(obj) ((ZMapWindowGlyphItem) obj)
+#define ZMAP_WINDOW_GLYPH_ITEM_CONST(obj) ((ZMapWindowGlyphItem const) obj)
+#else
#define ZMAP_WINDOW_GLYPH_ITEM(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_GLYPH_ITEM, zmapWindowGlyphItem))
#define ZMAP_WINDOW_GLYPH_ITEM_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_GLYPH_ITEM, zmapWindowGlyphItem const))
+#endif
#define ZMAP_WINDOW_GLYPH_ITEM_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_WINDOW_GLYPH_ITEM, zmapWindowGlyphItemClass))
#define ZMAP_IS_WINDOW_GLYPH_ITEM(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_WINDOW_GLYPH_ITEM))
#define ZMAP_WINDOW_GLYPH_ITEM_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_WINDOW_GLYPH_ITEM, zmapWindowGlyphItemClass))
diff --git a/src/zmapWindow/items/zmapWindowLongItem.h b/src/zmapWindow/items/zmapWindowLongItem.h
index b8b84fd53..cc2ddabc0 100755
--- a/src/zmapWindow/items/zmapWindowLongItem.h
+++ b/src/zmapWindow/items/zmapWindowLongItem.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Jul 9 10:07 2009 (rds)
* Created: Fri Jan 16 14:01:12 2009 (rds)
- * CVS info: $Id: zmapWindowLongItem.h,v 1.3 2010-03-04 15:12:25 mh17 Exp $
+ * CVS info: $Id: zmapWindowLongItem.h,v 1.4 2010-06-08 08:31:27 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -39,8 +39,15 @@
#define ZMAP_WINDOW_LONG_ITEM_NAME "ZMapWindowLongItem"
#define ZMAP_TYPE_WINDOW_LONG_ITEM (zMapWindowLongItemGetType())
+
+#if GOBJ_CAST
+#define ZMAP_WINDOW_LONG_ITEM(obj) ((ZMapWindowLongItem) obj)
+#define ZMAP_WINDOW_LONG_ITEM_CONST(obj) ((ZMapWindowLongItem const) obj)
+#else
#define ZMAP_WINDOW_LONG_ITEM(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_LONG_ITEM, zmapWindowLongItem))
#define ZMAP_WINDOW_LONG_ITEM_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_LONG_ITEM, zmapWindowLongItem const))
+#endif
+
#define ZMAP_WINDOW_LONG_ITEM_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_WINDOW_LONG_ITEM, zmapWindowLongItemClass))
#define ZMAP_IS_WINDOW_LONG_ITEM(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_WINDOW_LONG_ITEM))
#define ZMAP_WINDOW_LONG_ITEM_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_WINDOW_LONG_ITEM, zmapWindowLongItemClass))
@@ -60,7 +67,7 @@ GType zMapWindowLongItemGetType(void);
FooCanvasItem *zmapWindowLongItemCheckPoint(FooCanvasItem *possibly_long_item);
FooCanvasItem *zmapWindowLongItemCheckPointFull(FooCanvasItem *possibly_long_item,
FooCanvasPoints *points,
- double x1, double y1,
+ double x1, double y1,
double x2, double y2);
int zmapWindowIsLongItem(FooCanvasItem *foo);
diff --git a/src/zmapWindow/items/zmapWindowSequenceFeature.h b/src/zmapWindow/items/zmapWindowSequenceFeature.h
index 62b66927a..e17cc32d2 100755
--- a/src/zmapWindow/items/zmapWindowSequenceFeature.h
+++ b/src/zmapWindow/items/zmapWindowSequenceFeature.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Feb 16 09:58 2010 (edgrif)
* Created: Wed Dec 3 08:44:06 2008 (rds)
- * CVS info: $Id: zmapWindowSequenceFeature.h,v 1.7 2010-03-04 15:12:29 mh17 Exp $
+ * CVS info: $Id: zmapWindowSequenceFeature.h,v 1.8 2010-06-08 08:31:27 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -42,8 +42,15 @@
#define ZMAP_TYPE_WINDOW_SEQUENCE_FEATURE (zMapWindowSequenceFeatureGetType())
+
+#if GOBJ_CAST
+#define ZMAP_WINDOW_SEQUENCE_FEATURE(obj) ((ZMapWindowSequenceFeature) obj)
+#define ZMAP_WINDOW_SEQUENCE_FEATURE_CONST(obj) ((ZMapWindowSequenceFeature const) obj)
+#else
#define ZMAP_WINDOW_SEQUENCE_FEATURE(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_SEQUENCE_FEATURE, zmapWindowSequenceFeature))
#define ZMAP_WINDOW_SEQUENCE_FEATURE_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_SEQUENCE_FEATURE, zmapWindowSequenceFeature const))
+#endif
+
#define ZMAP_WINDOW_SEQUENCE_FEATURE_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_WINDOW_SEQUENCE_FEATURE, zmapWindowSequenceFeatureClass))
#define ZMAP_IS_WINDOW_SEQUENCE_FEATURE(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_WINDOW_SEQUENCE_FEATURE))
#define ZMAP_WINDOW_SEQUENCE_FEATURE_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_WINDOW_SEQUENCE_FEATURE, zmapWindowSequenceFeatureClass))
diff --git a/src/zmapWindow/items/zmapWindowTextFeature.h b/src/zmapWindow/items/zmapWindowTextFeature.h
index add83de8e..6ffe194ac 100755
--- a/src/zmapWindow/items/zmapWindowTextFeature.h
+++ b/src/zmapWindow/items/zmapWindowTextFeature.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Jan 13 13:40 2009 (rds)
* Created: Wed Dec 3 08:44:06 2008 (rds)
- * CVS info: $Id: zmapWindowTextFeature.h,v 1.2 2010-03-04 15:12:32 mh17 Exp $
+ * CVS info: $Id: zmapWindowTextFeature.h,v 1.3 2010-06-08 08:31:27 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -39,8 +39,15 @@
#define ZMAP_WINDOW_TEXT_FEATURE_NAME "ZMapWindowTextFeature"
#define ZMAP_TYPE_WINDOW_TEXT_FEATURE (zMapWindowTextFeatureGetType())
+
+#if GOBJ_CAST
+#define ZMAP_WINDOW_TEXT_FEATURE(obj) ((ZMapWindowTextFeature) obj)
+#define ZMAP_WINDOW_TEXT_FEATURE_CONST(obj) ((ZMapWindowTextFeature const) obj)
+#else
#define ZMAP_WINDOW_TEXT_FEATURE(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_TEXT_FEATURE, zmapWindowTextFeature))
#define ZMAP_WINDOW_TEXT_FEATURE_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_TEXT_FEATURE, zmapWindowTextFeature const))
+#endif
+
#define ZMAP_WINDOW_TEXT_FEATURE_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_WINDOW_TEXT_FEATURE, zmapWindowTextFeatureClass))
#define ZMAP_IS_WINDOW_TEXT_FEATURE(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_WINDOW_TEXT_FEATURE))
#define ZMAP_WINDOW_TEXT_FEATURE_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_WINDOW_TEXT_FEATURE, zmapWindowTextFeatureClass))
diff --git a/src/zmapWindow/items/zmapWindowTextItem.h b/src/zmapWindow/items/zmapWindowTextItem.h
index 0325efa9b..ad096dc73 100755
--- a/src/zmapWindow/items/zmapWindowTextItem.h
+++ b/src/zmapWindow/items/zmapWindowTextItem.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Jun 18 15:01 2009 (rds)
* Created: Fri Jan 16 14:01:12 2009 (rds)
- * CVS info: $Id: zmapWindowTextItem.h,v 1.3 2010-03-04 15:12:35 mh17 Exp $
+ * CVS info: $Id: zmapWindowTextItem.h,v 1.4 2010-06-08 08:31:27 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -42,8 +42,14 @@
#define ZMAP_WINDOW_TEXT_ITEM_NAME "ZMapWindowTextItem"
#define ZMAP_TYPE_WINDOW_TEXT_ITEM (zMapWindowTextItemGetType())
+
+#if GOBJ_CAST
+#define ZMAP_WINDOW_TEXT_ITEM(obj) ((ZMapWindowTextItem) obj)
+#define ZMAP_WINDOW_TEXT_ITEM_CONST(obj) ((ZMapWindowTextItem const) obj)
+#else
#define ZMAP_WINDOW_TEXT_ITEM(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_TEXT_ITEM, zmapWindowTextItem))
#define ZMAP_WINDOW_TEXT_ITEM_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_TEXT_ITEM, zmapWindowTextItem const))
+#endif
#define ZMAP_WINDOW_TEXT_ITEM_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_WINDOW_TEXT_ITEM, zmapWindowTextItemClass))
#define ZMAP_IS_WINDOW_TEXT_ITEM(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_WINDOW_TEXT_ITEM))
#define ZMAP_WINDOW_TEXT_ITEM_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_WINDOW_TEXT_ITEM, zmapWindowTextItemClass))
@@ -82,10 +88,10 @@ typedef gint (* ZMapTextItemAllocateCB)(FooCanvasItem *item,
gint buffer_size,
gpointer user_data);
-typedef gint (* ZMapTextItemFetchTextCB)(FooCanvasItem *item,
+typedef gint (* ZMapTextItemFetchTextCB)(FooCanvasItem *item,
ZMapTextItemDrawData draw_data,
- char *buffer,
- gint buffer_size,
+ char *buffer,
+ gint buffer_size,
gpointer user_data);
@@ -98,7 +104,7 @@ typedef gboolean (* ZMapWindowTextItemSelectionCB)(ZMapWindowTextItem text_item,
GType zMapWindowTextItemGetType(void);
-void zMapWindowTextItemSelect(ZMapWindowTextItem text_item, int start, int end,
+void zMapWindowTextItemSelect(ZMapWindowTextItem text_item, int start, int end,
gboolean deselect_first, gboolean emit_signal);
void zMapWindowTextItemDeselect(ZMapWindowTextItem text_item,
gboolean emit_signal);
diff --git a/src/zmapWindow/items/zmapWindowTranscriptFeature.h b/src/zmapWindow/items/zmapWindowTranscriptFeature.h
index ea9e44531..18c1e132a 100755
--- a/src/zmapWindow/items/zmapWindowTranscriptFeature.h
+++ b/src/zmapWindow/items/zmapWindowTranscriptFeature.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Feb 16 10:01 2010 (edgrif)
* Created: Wed Dec 3 08:44:06 2008 (rds)
- * CVS info: $Id: zmapWindowTranscriptFeature.h,v 1.3 2010-03-04 15:12:38 mh17 Exp $
+ * CVS info: $Id: zmapWindowTranscriptFeature.h,v 1.4 2010-06-08 08:31:27 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_WINDOW_TRANSCRIPT_FEATURE_H
@@ -39,8 +39,15 @@
#define ZMAP_WINDOW_TRANSCRIPT_FEATURE_NAME "ZMapWindowTranscriptFeature"
#define ZMAP_TYPE_WINDOW_TRANSCRIPT_FEATURE (zMapWindowTranscriptFeatureGetType())
+
+#if GOBJ_CAST
+#define ZMAP_WINDOW_TRANSCRIPT_FEATURE(obj) ((ZMapWindowTranscriptFeature) obj)
+#define ZMAP_WINDOW_TRANSCRIPT_FEATURE_CONST(obj) ((ZMapWindowTranscriptFeature const) obj)
+#else
#define ZMAP_WINDOW_TRANSCRIPT_FEATURE(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_TRANSCRIPT_FEATURE, zmapWindowTranscriptFeature))
#define ZMAP_WINDOW_TRANSCRIPT_FEATURE_CONST(obj) (G_TYPE_CHECK_INSTANCE_CAST((obj), ZMAP_TYPE_WINDOW_TRANSCRIPT_FEATURE, zmapWindowTranscriptFeature const))
+#endif
+
#define ZMAP_WINDOW_TRANSCRIPT_FEATURE_CLASS(klass) (G_TYPE_CHECK_CLASS_CAST((klass), ZMAP_TYPE_WINDOW_TRANSCRIPT_FEATURE, zmapWindowTranscriptFeatureClass))
#define ZMAP_IS_WINDOW_TRANSCRIPT_FEATURE(obj) (G_TYPE_CHECK_INSTANCE_TYPE((obj), ZMAP_TYPE_WINDOW_TRANSCRIPT_FEATURE))
#define ZMAP_WINDOW_TRANSCRIPT_FEATURE_GET_CLASS(obj) (G_TYPE_INSTANCE_GET_CLASS((obj), ZMAP_TYPE_WINDOW_TRANSCRIPT_FEATURE, zmapWindowTranscriptFeatureClass))
diff --git a/src/zmapWindow/zmapWindow.c b/src/zmapWindow/zmapWindow.c
index d581c4380..d3dd1ea5a 100755
--- a/src/zmapWindow/zmapWindow.c
+++ b/src/zmapWindow/zmapWindow.c
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: May 24 16:04 2010 (edgrif)
* Created: Thu Jul 24 14:36:27 2003 (edgrif)
- * CVS info: $Id: zmapWindow.c,v 1.322 2010-05-24 15:04:55 edgrif Exp $
+ * CVS info: $Id: zmapWindow.c,v 1.323 2010-06-08 08:31:25 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -61,8 +61,8 @@ typedef struct
{
ZMapFeatureContext current_features ;
ZMapFeatureContext new_features ;
- GData *all_styles ;
- GData *new_styles ;
+ GHashTable *all_styles ;
+ GHashTable *new_styles ;
GHashTable *featuresets_2_stylelist ;
ZMapWindowState state ; /* Can be NULL! */
} FeatureSetsStateStruct, *FeatureSetsState ;
@@ -367,7 +367,7 @@ ZMapWindow zMapWindowCreate(GtkWidget *parent_widget,
ZMapWindow zMapWindowCopy(GtkWidget *parent_widget, char *sequence,
void *app_data, ZMapWindow original_window,
ZMapFeatureContext feature_context,
- GData *read_only_styles, GData *display_styles,
+ GHashTable *read_only_styles, GHashTable *display_styles,
ZMapWindowLockType window_locking)
{
ZMapWindow new_window = NULL ;
@@ -399,7 +399,7 @@ ZMapWindow zMapWindowCopy(GtkWidget *parent_widget, char *sequence,
/* Update styles lists in original window, new window is done by display call. */
zMapAssert(read_only_styles && display_styles) ;
- if (!zmapWindowUpdateStyles(original_window, &read_only_styles, &display_styles))
+ if (!zmapWindowUpdateStyles(original_window, read_only_styles, display_styles))
zMapLogWarning("%s", "Errors in copying read only and display styles for original window.") ;
/* Lock windows together for scrolling/zooming if requested. */
@@ -511,7 +511,7 @@ void zMapWindowBusyFull(ZMapWindow window, gboolean busy, const char *file, cons
* */
void zMapWindowDisplayData(ZMapWindow window, ZMapWindowState state,
ZMapFeatureContext current_features, ZMapFeatureContext new_features,
- GData *all_styles, GData *new_styles,
+ GHashTable *all_styles, GHashTable *new_styles,
GHashTable *new_featuresets_2_stylelist)
{
FeatureSetsState feature_sets ;
@@ -523,8 +523,8 @@ void zMapWindowDisplayData(ZMapWindow window, ZMapWindowState state,
feature_sets->current_features = current_features ;
feature_sets->new_features = new_features ;
- zMapStyleCopyAllStyles(&all_styles, &(feature_sets->all_styles)) ;
- zMapStyleCopyAllStyles(&new_styles, &(feature_sets->new_styles)) ;
+ zMapStyleCopyAllStyles(all_styles, &(feature_sets->all_styles)) ;
+ zMapStyleCopyAllStyles(new_styles, &(feature_sets->new_styles)) ;
feature_sets->featuresets_2_stylelist = new_featuresets_2_stylelist ;
@@ -715,7 +715,7 @@ void zMapWindowStats(ZMapWindow window, GString *text)
* We also need the information so that we can maintain window position after a revcomp.
* We really do need to know even though it feels a bit hacky... */
void zMapWindowFeatureRedraw(ZMapWindow window, ZMapFeatureContext feature_context,
- GData *all_styles, GData *new_styles,
+ GHashTable *all_styles, GHashTable *new_styles,
gboolean features_are_revcomped)
{
int x, y ;
@@ -725,6 +725,7 @@ void zMapWindowFeatureRedraw(ZMapWindow window, ZMapFeatureContext feature_conte
gboolean state_saves_position = TRUE;
+ zMapStartTimer("WindowFeatureRedraw","");
state = zmapWindowStateCreate();
/* Note that currently we lose the 3 frame state and other state such as columns */
@@ -787,15 +788,19 @@ void zMapWindowFeatureRedraw(ZMapWindow window, ZMapFeatureContext feature_conte
free_child_windows = TRUE ;
}
+ zMapStopTimer("WindowFeatureRedraw","Revcomp");
+
/* wrap the resetCanvas and set scroll region in a expose free cape */
zmapWindowInterruptExpose(window);
resetCanvas(window, free_child_windows, free_revcomp_safe_windows) ; /* Resets scrolled region and much else. */
+ zMapStopTimer("WindowFeatureRedraw","ResetCanvas");
if(window->strand_separator_context)
zMapFeatureContextDestroy(window->strand_separator_context, TRUE);
window->strand_separator_context = NULL;
+ zMapStopTimer("WindowFeatureRedraw","Separator");
/* You cannot just draw the features here as the canvas needs to be realised so we send
* an event to get the data drawn which means that the canvas is guaranteed to be
@@ -803,6 +808,8 @@ void zMapWindowFeatureRedraw(ZMapWindow window, ZMapFeatureContext feature_conte
zMapWindowDisplayData(window, state, feature_context, feature_context,
all_styles, new_styles, window->featureset_2_styles) ;
+ zMapStopTimer("WindowFeatureRedraw","Display");
+
/* stop the expose avoidance */
zmapWindowUninterruptExpose(window);
@@ -815,6 +822,7 @@ void zMapWindowFeatureRedraw(ZMapWindow window, ZMapFeatureContext feature_conte
* Code moved to the correct place, dataEventCB()
*/
}
+ zMapStopTimer("WindowFeatureRedraw","");
return ;
@@ -1125,9 +1133,9 @@ void zMapWindowDestroy(ZMapWindow window)
unlockWindow(window, FALSE) ;
if (window->read_only_styles)
- zMapStyleDestroyStyles(&(window->read_only_styles)) ;
+ zMapStyleDestroyStyles(window->read_only_styles) ;
if (window->display_styles)
- zMapStyleDestroyStyles(&(window->display_styles)) ;
+ zMapStyleDestroyStyles(window->display_styles) ;
/* free the array of feature list windows and the windows themselves */
zmapWindowFreeWindowArray(&(window->featureListWindows), TRUE) ;
@@ -2482,7 +2490,7 @@ static gboolean dataEventCB(GtkWidget *widget, GdkEventClient *event, gpointer c
diff_context = feature_sets->current_features ;
/* Reload the styles lists. */
- if (!zmapWindowUpdateStyles(window, &(feature_sets->all_styles), &(feature_sets->new_styles)))
+ if (!zmapWindowUpdateStyles(window, feature_sets->all_styles, feature_sets->new_styles))
zMapLogWarning("%s", "Errors in copying read only and display styles.") ;
@@ -2566,8 +2574,8 @@ static gboolean dataEventCB(GtkWidget *widget, GdkEventClient *event, gpointer c
zMapLogMessage("%s", "event handler for canvas already registered.");
- zMapStyleDestroyStyles(&(feature_sets->all_styles)) ;
- zMapStyleDestroyStyles(&(feature_sets->new_styles)) ;
+ zMapStyleDestroyStyles(feature_sets->all_styles) ;
+ zMapStyleDestroyStyles(feature_sets->new_styles) ;
g_free(feature_sets) ;
g_free(window_data) ; /* Free the WindowData struct. */
@@ -3861,7 +3869,7 @@ GList *zmapWindowDeferredColumns(ZMapWindow window)
{
GList *list = NULL;
- //g_datalist_foreach(&(window->read_only_styles), filter_deferred_styles, &list);
+ //g_hash_table_foreach(&(window->read_only_styles), filter_deferred_styles, &list);
list = g_list_copy(window->feature_set_names);
@@ -4192,9 +4200,6 @@ static gboolean keyboardEvent(ZMapWindow window, GdkEventKey *key_event)
compress_mode = ZMAPWINDOW_COMPRESS_ALL ;
}
-
- zMapResetTimer(NULL) ;
-
zmapWindowColumnBumpRange(FOO_CANVAS_ITEM(focus_column), bump_mode, compress_mode) ;
zmapWindowFullReposition(window) ;
diff --git a/src/zmapWindow/zmapWindowColBump.c b/src/zmapWindow/zmapWindowColBump.c
index abbfd9258..73248eff0 100755
--- a/src/zmapWindow/zmapWindowColBump.c
+++ b/src/zmapWindow/zmapWindowColBump.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: May 24 16:01 2010 (edgrif)
* Created: Tue Sep 4 10:52:09 2007 (edgrif)
- * CVS info: $Id: zmapWindowColBump.c,v 1.74 2010-05-26 15:28:09 mh17 Exp $
+ * CVS info: $Id: zmapWindowColBump.c,v 1.75 2010-06-08 08:31:25 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -414,7 +414,8 @@ void zmapWindowColumnBumpRange(FooCanvasItem *bump_item, ZMapStyleBumpMode bump_
ZMAPSTYLE_PROPERTY_DISPLAY_MODE, &(bump_properties.display_state),
NULL);
- zMapStyleGetJoinAligns(style, &(bump_properties.match_threshold));
+// zMapStyleGetJoinAligns(style, &(bump_properties.match_threshold));
+ bump_properties.match_threshold = zMapStyleGetWithinAlignError(style);
zMapStyleSetBumpMode(style, bump_mode);
}
diff --git a/src/zmapWindow/zmapWindowDraw.c b/src/zmapWindow/zmapWindowDraw.c
index 1698d8f1c..6a7a4b2d0 100755
--- a/src/zmapWindow/zmapWindowDraw.c
+++ b/src/zmapWindow/zmapWindowDraw.c
@@ -30,7 +30,7 @@
* HISTORY:
* Last edited: Feb 15 11:52 2010 (edgrif)
* Created: Thu Sep 8 10:34:49 2005 (edgrif)
- * CVS info: $Id: zmapWindowDraw.c,v 1.123 2010-05-26 12:02:50 mh17 Exp $
+ * CVS info: $Id: zmapWindowDraw.c,v 1.124 2010-06-08 08:31:25 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -67,6 +67,7 @@ typedef struct execOnChildrenStruct_
} execOnChildrenStruct, *execOnChildren ;
+#if 0
/* For 3 frame display/normal display. */
typedef struct
{
@@ -83,7 +84,7 @@ typedef struct
ZMapFeatureTypeStyle style;
} RedrawDataStruct, *RedrawData ;
-
+#endif
typedef struct
@@ -103,7 +104,7 @@ typedef struct
/* Records which alignment, block, set, type we are processing. */
ZMapFeatureContext full_context ;
- GData *styles ;
+ GHashTable *styles ;
ZMapFeatureAlignment curr_alignment ;
ZMapFeatureBlock curr_block ;
ZMapFeatureSet curr_set ;
@@ -168,6 +169,7 @@ void zMapWindowToggle3Frame(ZMapWindow window)
zMapWindowBusy(window, TRUE) ;
+ zMapStartTimer("3Frame" ,window->display_3_frame ? "off" : "on");
// yuk...
three_frame_id = GUINT_TO_POINTER(zMapStyleCreateID(ZMAP_FIXED_STYLE_3FRAME));
three_frame_Id = GUINT_TO_POINTER(g_quark_from_string(ZMAP_FIXED_STYLE_3FRAME));
@@ -184,11 +186,13 @@ void zMapWindowToggle3Frame(ZMapWindow window)
// remove always columns or 3-frame depending on mode
zmapWindowDrawRemove3FrameFeatures(window);
+ zMapStopTimer("3FrameRemove","");
window->display_3_frame = !window->display_3_frame;
// draw always columns or 3-frame depending on mode
zmapWindowDraw3FrameFeatures(window);
+ zMapStopTimer("3FrameDraw","");
/* Now we've drawn all the features we can position them all. */
zmapWindowColOrderColumns(window);
@@ -200,6 +204,8 @@ void zMapWindowToggle3Frame(ZMapWindow window)
else
zMapWarning("%s", "No '" ZMAP_FIXED_STYLE_3FRAME "' column in config file.");
+ zMapStopTimer("3Frame" ,window->display_3_frame ? "off" : "on");
+
zMapWindowBusy(window, FALSE) ;
return ;
@@ -245,10 +251,12 @@ void zmapWindowCanvasGroupChildSort(FooCanvasGroup *group_inout)
*
* */
void zmapWindowColumnSetState(ZMapWindow window, FooCanvasGroup *column_group,
+ // new_col_state = NULL if new (empty) column
ZMapStyleColumnDisplayState new_col_state, gboolean redraw_if_needed)
{
ZMapWindowContainerFeatureSet container;
ZMapStyleColumnDisplayState curr_col_state ;
+ gboolean test_mag = TRUE;
container = (ZMapWindowContainerFeatureSet)column_group;
@@ -260,8 +268,14 @@ void zmapWindowColumnSetState(ZMapWindow window, FooCanvasGroup *column_group,
gboolean redraw = FALSE ;
if (!new_col_state)
- new_col_state = curr_col_state ;
-
+ {
+ test_mag = FALSE;
+ // we are creating the column: mag not vis due to no features
+ // but we still want it to be visible
+ // a bit hacky, but less grief than adding a new flag
+
+ new_col_state = curr_col_state ;
+ }
switch(new_col_state)
{
case ZMAPSTYLE_COLDISPLAY_HIDE:
@@ -276,23 +290,13 @@ void zmapWindowColumnSetState(ZMapWindow window, FooCanvasGroup *column_group,
{
gboolean mag_visible, frame_visible ;
- mag_visible = zmapWindowColumnIsMagVisible(window, column_group) ;
+// ha ha ... this runs nearly 2x slower and we get blank columns
+// mag_visible = test_mag ? zmapWindowColumnIsMagVisible(window, column_group) : TRUE ;
+ mag_visible = zmapWindowColumnIsMagVisible(window, column_group);;
frame_visible = zmapWindowColumnIs3frameVisible(window, column_group) ;
- if (mag_visible && frame_visible)
- {
- zmapWindowContainerSetVisibility(column_group, TRUE) ;
- redraw = TRUE;
- }
- else if (!mag_visible || !frame_visible)
- {
- zmapWindowContainerSetVisibility(column_group, FALSE) ;
- redraw = TRUE;
- }
-
-
/* Check mag, mark, compress etc. etc....probably need some funcs in compress/mark/mag
* packages to return whether a column should be hidden.... */
if ((curr_col_state == ZMAPSTYLE_COLDISPLAY_HIDE || curr_col_state == ZMAPSTYLE_COLDISPLAY_SHOW_HIDE)
@@ -319,14 +323,14 @@ void zmapWindowColumnSetState(ZMapWindow window, FooCanvasGroup *column_group,
break ;
}
}
-
+ zMapStopTimer("DrawFeatureSet","SetVis");
/* Set the new display for the column _and_ all styles within the column. */
zmapWindowContainerFeatureSetSetDisplay(container, new_col_state) ;
/* Only do redraw if it was requested _and_ state change needs it. */
if (redraw_if_needed && redraw)
- zmapWindowFullReposition(window) ;
+ zmapWindowFullReposition(window) ;
}
diff --git a/src/zmapWindow/zmapWindowDrawFeatures.c b/src/zmapWindow/zmapWindowDrawFeatures.c
index c26c4b750..684b86705 100755
--- a/src/zmapWindow/zmapWindowDrawFeatures.c
+++ b/src/zmapWindow/zmapWindowDrawFeatures.c
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: Mar 11 14:19 2010 (edgrif)
* Created: Thu Jul 29 10:45:00 2004 (rnc)
- * CVS info: $Id: zmapWindowDrawFeatures.c,v 1.272 2010-05-26 12:02:50 mh17 Exp $
+ * CVS info: $Id: zmapWindowDrawFeatures.c,v 1.273 2010-06-08 08:31:25 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -60,7 +60,7 @@ typedef struct _ZMapCanvasDataStruct
/* Records which alignment, block, set, type we are processing. */
ZMapFeatureContext full_context ;
- GData *styles ;
+ GHashTable *styles ;
ZMapFeatureAlignment curr_alignment ;
ZMapFeatureBlock curr_block ;
ZMapFeatureSet curr_set ;
@@ -106,7 +106,7 @@ typedef struct
typedef struct
{
ZMapWindow window ;
- GData *styles ;
+ GHashTable *styles ;
GHashTable *feature_hash ;
int feature_count;
ZMapWindowContainerFeatures curr_forward_col ;
@@ -116,7 +116,7 @@ typedef struct
} CreateFeatureSetDataStruct, *CreateFeatureSetData ;
static void windowDrawContext(ZMapCanvasData canvas_data,
- GData *styles,
+ GHashTable *styles,
ZMapFeatureContext full_context,
ZMapFeatureContext diff_context);
static ZMapFeatureContextExecuteStatus windowDrawContextCB(GQuark key_id,
@@ -448,7 +448,7 @@ gboolean zmapWindowCreateSetColumns(ZMapWindow window,
ZMapWindowContainerFeatures reverse_strand_group,
ZMapFeatureBlock block,
ZMapFeatureSet feature_set,
- GData *styles,
+ GHashTable *styles,
ZMapFrame frame,
FooCanvasGroup **forward_col_out,
FooCanvasGroup **reverse_col_out,
@@ -620,7 +620,7 @@ gboolean zmapWindowCreateSetColumns(ZMapWindow window,
* ProcessFeature splits the feature sets features into the separate strands.
*/
void zmapWindowDrawFeatureSet(ZMapWindow window,
- GData *styles,
+ GHashTable *styles,
ZMapFeatureSet feature_set,
FooCanvasGroup *forward_col_wcp,
FooCanvasGroup *reverse_col_wcp,
@@ -670,7 +670,9 @@ void zmapWindowDrawFeatureSet(ZMapWindow window,
featureset_data.feature_count = 0;
/* Now draw all the features in the column. */
+ zMapStartTimer("DrawFeatureSet","ProcessFeature");
g_hash_table_foreach(feature_set->features, ProcessFeature, &featureset_data) ;
+ zMapStopTimer("DrawFeatureSet","ProcessFeature");
if(featureset_data.feature_count > 0)
{
@@ -689,6 +691,7 @@ void zmapWindowDrawFeatureSet(ZMapWindow window,
}
}
+ zMapStartTimer("DrawFeatureSet","Bump");
/* We should be bumping columns here if required... */
if (bump_required && view_feature_set)
{
@@ -708,6 +711,7 @@ void zmapWindowDrawFeatureSet(ZMapWindow window,
* already loaded in this column a COMPRESS_ALL will bump the whole column
* _not_ just the newly loaded ones... */
+
if (forward_col_wcp)
{
if ((bump_mode = zmapWindowContainerFeatureSetGetBumpMode((ZMapWindowContainerFeatureSet)forward_container)) != ZMAPBUMP_UNBUMP)
@@ -715,8 +719,10 @@ void zmapWindowDrawFeatureSet(ZMapWindow window,
/* Some columns are hidden initially, could be mag. level, 3 frame only display or
* set explicitly in the style for the column. */
+ zMapStartTimer("DrawFeatureSet","SetState");
zmapWindowColumnSetState(window, forward_col_wcp, ZMAPSTYLE_COLDISPLAY_INVALID, FALSE) ;
- }
+ zMapStopTimer("DrawFeatureSet","SetState");
+ }
if (reverse_col_wcp)
{
@@ -728,7 +734,7 @@ void zmapWindowDrawFeatureSet(ZMapWindow window,
zmapWindowColumnSetState(window, reverse_col_wcp, ZMAPSTYLE_COLDISPLAY_INVALID, FALSE) ;
}
}
-
+ zMapStopTimer("DrawFeatureSet","Bump");
return ;
}
@@ -937,7 +943,7 @@ static void toggleColumnInMultipleBlocks(ZMapWindow window, char *name,
*/
static void windowDrawContext(ZMapCanvasData canvas_data,
- GData *styles,
+ GHashTable *styles,
ZMapFeatureContext full_context,
ZMapFeatureContext diff_context)
{
@@ -1515,6 +1521,8 @@ static ZMapFeatureContextExecuteStatus windowDrawContextCB(GQuark key_id,
double x, y;
gboolean block_created = FALSE;
+ zMapStartTimer("DrawBlock","");
+
feature_block = (ZMapFeatureBlock)feature_any;
#ifdef MH17_REVCOMP_DEBUG
printf("\ndrawFeatures block %d-%d",feature_block->block_to_sequence.t1,feature_block->block_to_sequence.t2);
@@ -1678,14 +1686,18 @@ printf("\ndrawFeatures block %d-%d",feature_block->block_to_sequence.t1,feature_
canvas_data->curr_forward_group = zmapWindowContainerGetFeatures(forward_group) ;
+ zMapStartTimer("CreateColumns","");
/* We create the columns here now. */
/* Why? So that we always have the column, even though it's empty... */
g_list_foreach(window->feature_set_names,
set_name_create_set_columns,
canvas_data);
+
+ zMapStopTimer("CreateColumns","");
}
+ zMapStopTimer("DrawBlock","");
break;
}
@@ -1711,6 +1723,8 @@ printf("drawFeatures set %s",feature_set->description);
{
int i, got_columns = 0;
+//printf("drawFeatures set %s\n",g_quark_to_string(feature_set->unique_id));
+
/* re-written for(i = frame_start; i <= frame_end; i++) */
i = frame_start;
do
@@ -1731,7 +1745,7 @@ printf("drawFeatures set %s",feature_set->description);
#ifdef MH17_REVCOMP_DEBUG
printf("\nFeatures...\n");
#endif
-
+ zMapStartTimer("DrawFeatureSet",g_quark_to_string(feature_set->unique_id));
zmapWindowDrawFeatureSet(window,
canvas_data->styles,
@@ -1739,6 +1753,7 @@ printf("drawFeatures set %s",feature_set->description);
tmp_forward,
tmp_reverse,
canvas_data->current_frame);
+ zMapStopTimer("DrawFeatureSet",g_quark_to_string(feature_set->unique_id));
}
i++;
}
@@ -2049,11 +2064,15 @@ static void ProcessFeature(gpointer key, gpointer data, gpointer user_data)
featureset_data->feature_count++;
- style = zMapFindStyle(featureset_data->styles, feature->style_id) ;
+ style = feature->style; // fails: no display. fixed it for pipe via GFF2parser, ACE seems to call it???
+ // features paint so it musk be ok!
+// style = zMapFindStyle(featureset_data->styles, feature->style_id) ;
+
#ifdef MH17_REVCOMP_DEBUG
if(!style) printf("no style 1 ");
#endif
+#if MH17_FEATURESET_HAS_OWN_COPY_POINTED_AT_BY_FEATURE
if(style)
style = zmapWindowContainerFeatureSetStyleFromStyle((ZMapWindowContainerFeatureSet)column_group, style) ;
else
@@ -2065,13 +2084,15 @@ static void ProcessFeature(gpointer key, gpointer data, gpointer user_data)
if(!style) printf("no style 2");
printf("\n");
#endif
+
+#endif
+
if(style)
feature_item = zmapWindowFeatureDraw(window, style, (FooCanvasGroup *)column_group, feature) ;
else
g_warning("definitely need a style '%s' for feature '%s'",
g_quark_to_string(feature->style_id),
g_quark_to_string(feature->original_id));
-
return ;
}
diff --git a/src/zmapWindow/zmapWindowDump.c b/src/zmapWindow/zmapWindowDump.c
index 69f14bcfe..e881e8b4d 100755
--- a/src/zmapWindow/zmapWindowDump.c
+++ b/src/zmapWindow/zmapWindowDump.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Jun 19 13:38 2009 (rds)
* Created: Thu Mar 30 16:48:34 2006 (edgrif)
- * CVS info: $Id: zmapWindowDump.c,v 1.15 2010-05-17 14:41:16 mh17 Exp $
+ * CVS info: $Id: zmapWindowDump.c,v 1.16 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -1184,7 +1184,7 @@ static void dumpFeatureCB(gpointer data, gpointer user_data)
double x, y ;
// so I can look at them in the debugger
-ZMapWindowTextItem zwt = ZMAP_WINDOW_TEXT_ITEM(text_item);
+//ZMapWindowTextItem zwt = ZMAP_WINDOW_TEXT_ITEM(text_item);
// "GLib-GObject-WARNING **: invalid cast from `ZMapWindowTextItem' to `FooCanvasZMapText'"
//FooCanvasZMapText *fzt = FOO_CANVAS_ZMAP_TEXT(text_item);
diff --git a/src/zmapWindow/zmapWindowFeature.c b/src/zmapWindow/zmapWindowFeature.c
index 535e38da3..1bf411865 100755
--- a/src/zmapWindow/zmapWindowFeature.c
+++ b/src/zmapWindow/zmapWindowFeature.c
@@ -30,7 +30,7 @@
* HISTORY:
* Last edited: May 5 16:32 2010 (edgrif)
* Created: Mon Jan 9 10:25:40 2006 (edgrif)
- * CVS info: $Id: zmapWindowFeature.c,v 1.185 2010-05-26 12:02:50 mh17 Exp $
+ * CVS info: $Id: zmapWindowFeature.c,v 1.186 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -207,7 +207,7 @@ static gboolean mouse_debug_G = FALSE ;
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-GData *zMapWindowFeatureAllStyles(ZMapWindow window)
+GHashTable *zMapWindowFeatureAllStyles(ZMapWindow window)
{
zMapAssert(window && window->feature_context);
@@ -474,7 +474,8 @@ ZMapStrand zmapWindowFeatureStrand(ZMapWindow window, ZMapFeature feature)
ZMapFeatureTypeStyle style = NULL;
ZMapStrand strand = ZMAPSTRAND_FORWARD ;
- style = zMapFindStyle(window->read_only_styles, feature->style_id) ;
+// style = zMapFindStyle(window->read_only_styles, feature->style_id) ;
+ style = feature->style; // safe failure...
g_return_val_if_fail(style != NULL, strand);
@@ -552,6 +553,7 @@ FooCanvasItem *zmapWindowFeatureDraw(ZMapWindow window,
block,
set,
feature);
+
return new_feature;
}
diff --git a/src/zmapWindow/zmapWindowItemFactory.c b/src/zmapWindow/zmapWindowItemFactory.c
index d51efba23..68c2a2200 100755
--- a/src/zmapWindow/zmapWindowItemFactory.c
+++ b/src/zmapWindow/zmapWindowItemFactory.c
@@ -30,7 +30,7 @@
* HISTORY:
* Last edited: Apr 28 09:49 2010 (edgrif)
* Created: Mon Sep 25 09:09:52 2006 (rds)
- * CVS info: $Id: zmapWindowItemFactory.c,v 1.81 2010-04-28 08:51:43 edgrif Exp $
+ * CVS info: $Id: zmapWindowItemFactory.c,v 1.82 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -550,7 +550,7 @@ FooCanvasItem *zmapWindowFToIFactoryRunSingle(ZMapWindowFToIFactory factory,
ZMapFrame frame;
ZMapStrand strand;
- g_object_set_data(G_OBJECT(item), ITEM_FEATURE_ITEM_STYLE, style) ;
+ g_object_set_data(G_OBJECT(item), ITEM_FEATURE_ITEM_STYLE, (gpointer) style) ;
frame = zmapWindowContainerFeatureSetGetFrame((ZMapWindowContainerFeatureSet)parent_container);
strand = zmapWindowContainerFeatureSetGetStrand((ZMapWindowContainerFeatureSet)parent_container);
@@ -701,6 +701,7 @@ static FooCanvasItem *drawSimpleFeature(RunSet run_data, ZMapFeature feature,
* We just need to Seq2CanOffset */
zmapWindowSeq2CanOffset(&y1, &y2, feature_offset);
+
if((new_canvas_item = zMapWindowCanvasItemCreate(parent, y1, feature, style)))
{
zMapWindowCanvasItemAddInterval(new_canvas_item, NULL, 0.0, y2 - y1, x1, x2);
diff --git a/src/zmapWindow/zmapWindowNavigator.c b/src/zmapWindow/zmapWindowNavigator.c
index 9e9d7bc0a..fc44efa06 100755
--- a/src/zmapWindow/zmapWindowNavigator.c
+++ b/src/zmapWindow/zmapWindowNavigator.c
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Apr 23 13:59 2010 (edgrif)
* Created: Wed Sep 6 11:22:24 2006 (rds)
- * CVS info: $Id: zmapWindowNavigator.c,v 1.60 2010-04-23 14:40:32 edgrif Exp $
+ * CVS info: $Id: zmapWindowNavigator.c,v 1.61 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -51,7 +51,7 @@ typedef struct
/* inputs */
ZMapWindowNavigator navigate;
ZMapFeatureContext context;
- GData *styles;
+ GHashTable *styles;
/* The current features in the recursion */
ZMapFeatureAlignment current_align;
@@ -61,7 +61,7 @@ typedef struct
ZMapWindowContainerGroup container_block;
ZMapWindowContainerGroup container_strand;
ZMapWindowContainerGroup container_feature_set;
- double current;
+ double current;
} NavigateDrawStruct, *NavigateDraw;
@@ -75,7 +75,7 @@ typedef struct
/* We need this because the locator is drawn as a foo_canvas_rect with
* a transparent background, that will not receive events! Therefore as
- * a work around we set up a handler on the root background and test
+ * a work around we set up a handler on the root background and test
* whether we're within the bounds of the locator. */
typedef struct
{
@@ -99,18 +99,18 @@ static void container_group_add_highlight_area_item(ZMapWindowNavigator navigate
ZMapWindowContainerGroup container);
/* draw some features... */
-static ZMapFeatureContextExecuteStatus drawContext(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus drawContext(GQuark key,
+ gpointer data,
gpointer user_data,
char **err_out);
static void createColumnCB(gpointer data, gpointer user_data);
-static void clampCoords(ZMapWindowNavigator navigate,
- double pre_scale, double post_scale,
+static void clampCoords(ZMapWindowNavigator navigate,
+ double pre_scale, double post_scale,
double *c1_inout, double *c2_inout);
-static void clampScaled(ZMapWindowNavigator navigate,
+static void clampScaled(ZMapWindowNavigator navigate,
double *s1_inout, double *s2_inout);
-static void clampWorld2Scaled(ZMapWindowNavigator navigate,
+static void clampWorld2Scaled(ZMapWindowNavigator navigate,
double *w1_inout, double *w2_inout);
static void updateLocatorDragger(ZMapWindowNavigator navigate, double button_y, double size);
static gboolean rootBGEventCB(FooCanvasItem *item, GdkEvent *event, gpointer data);
@@ -126,7 +126,7 @@ static void navigateDrawFunc(NavigateDraw nav_draw, GtkWidget *widget);
static void expose_handler_disconn_cb(gpointer user_data, GClosure *unused);
static gboolean nav_draw_expose_handler(GtkWidget *widget,
- GdkEventExpose *expose,
+ GdkEventExpose *expose,
gpointer user_data);
static gboolean navCanvasItemEventCB(FooCanvasItem *item, GdkEvent *event, gpointer data);
@@ -140,17 +140,17 @@ static gboolean factoryItemHandler(FooCanvasItem *new_item,
ZMapFeature feature,
gpointer handler_data);
-static gboolean factoryFeatureSizeReq(ZMapFeature feature,
- double *limits_array,
- double *points_array_inout,
+static gboolean factoryFeatureSizeReq(ZMapFeature feature,
+ double *limits_array,
+ double *points_array_inout,
gpointer handler_data);
static void customiseFactory(ZMapWindowNavigator navigator);
static GHashTable *zmapWindowNavigatorLDHCreate(void);
static LocusEntry zmapWindowNavigatorLDHFind(GHashTable *hash, GQuark key);
-static LocusEntry zmapWindowNavigatorLDHInsert(GHashTable *hash,
- ZMapFeature feature,
+static LocusEntry zmapWindowNavigatorLDHInsert(GHashTable *hash,
+ ZMapFeature feature,
double start, double end);
static void zmapWindowNavigatorLDHDestroy(GHashTable **destroy);
static void destroyLocusEntry(gpointer data);
@@ -161,13 +161,13 @@ static void default_locus_names_filter(GList **filter_out);
static gint strcmp_list_find(gconstpointer list_data, gconstpointer user_data);
/* The container update hooks */
-static gboolean highlight_locator_area_cb(ZMapWindowContainerGroup container, FooCanvasPoints *points,
+static gboolean highlight_locator_area_cb(ZMapWindowContainerGroup container, FooCanvasPoints *points,
ZMapContainerLevelType level, gpointer user_data);
-static gboolean positioning_cb(ZMapWindowContainerGroup container, FooCanvasPoints *points,
+static gboolean positioning_cb(ZMapWindowContainerGroup container, FooCanvasPoints *points,
ZMapContainerLevelType level, gpointer user_data);
-static gboolean container_draw_locator(ZMapWindowContainerGroup container, FooCanvasPoints *points,
+static gboolean container_draw_locator(ZMapWindowContainerGroup container, FooCanvasPoints *points,
ZMapContainerLevelType level, gpointer user_data);
/* create the items which get updated during hooks */
@@ -276,19 +276,19 @@ ZMapWindowNavigator zMapWindowNavigatorCreate(GtkWidget *canvas_widget)
int gdkcolor_size = 0;
gdkcolor_size = sizeof(GdkColor);
canvas_color = &(gtk_widget_get_style(canvas_widget)->bg[GTK_STATE_NORMAL]);
- memcpy(&(navigate->root_background),
+ memcpy(&(navigate->root_background),
canvas_color,
gdkcolor_size);
- memcpy(&(navigate->align_background),
+ memcpy(&(navigate->align_background),
canvas_color,
gdkcolor_size);
- memcpy(&(navigate->block_background),
+ memcpy(&(navigate->block_background),
canvas_color,
gdkcolor_size);
- memcpy(&(navigate->strand_background),
+ memcpy(&(navigate->strand_background),
canvas_color,
gdkcolor_size);
- memcpy(&(navigate->column_background),
+ memcpy(&(navigate->column_background),
canvas_color,
gdkcolor_size);
}
@@ -318,7 +318,7 @@ ZMapWindowNavigator zMapWindowNavigatorCreate(GtkWidget *canvas_widget)
navigate->container_root = zmapWindowContainerGroupCreateFromFoo(root, ZMAPCONTAINER_LEVEL_ROOT,
- ROOT_CHILD_SPACING,
+ ROOT_CHILD_SPACING,
&(navigate->root_background), NULL);
g_object_set_data(G_OBJECT(navigate->container_root), ZMAP_WINDOW_POINTER, navigate->current_window) ;
@@ -331,8 +331,8 @@ ZMapWindowNavigator zMapWindowNavigatorCreate(GtkWidget *canvas_widget)
container_group_add_locator(navigate, navigate->container_root);
- zmapWindowContainerGroupAddUpdateHook(navigate->container_root,
- container_draw_locator,
+ zmapWindowContainerGroupAddUpdateHook(navigate->container_root,
+ container_draw_locator,
navigate);
g_object_set(G_OBJECT(navigate->container_root),
@@ -344,7 +344,7 @@ ZMapWindowNavigator zMapWindowNavigatorCreate(GtkWidget *canvas_widget)
default_locus_names_filter(&(navigate->hide_filter));
- available_locus_names_filter(&(navigate->available_filters));
+ available_locus_names_filter(&(navigate->available_filters));
}
zMapAssert(navigate);
@@ -394,7 +394,7 @@ void zMapWindowNavigatorReset(ZMapWindowNavigator navigate)
return ;
}
-void zMapWindowNavigatorFocus(ZMapWindowNavigator navigate,
+void zMapWindowNavigatorFocus(ZMapWindowNavigator navigate,
gboolean true_eq_focus)
{
FooCanvasItem *root;
@@ -426,7 +426,7 @@ void zMapWindowNavigatorSetCurrentWindow(ZMapWindowNavigator navigate, ZMapWindo
return ;
}
-void zMapWindowNavigatorMergeInFeatureSetNames(ZMapWindowNavigator navigate,
+void zMapWindowNavigatorMergeInFeatureSetNames(ZMapWindowNavigator navigate,
GList *navigator_sets)
{
/* This needs to do more that just concat!! ha, it'll break something down the line ... column ordering at least */
@@ -437,9 +437,9 @@ void zMapWindowNavigatorMergeInFeatureSetNames(ZMapWindowNavigator navigate,
}
/* draw features */
-void zMapWindowNavigatorDrawFeatures(ZMapWindowNavigator navigate,
+void zMapWindowNavigatorDrawFeatures(ZMapWindowNavigator navigate,
ZMapFeatureContext full_context,
- GData *styles)
+ GHashTable *styles)
{
FooCanvas *canvas = NULL;
NavigateDrawStruct draw_data = {NULL};
@@ -562,7 +562,7 @@ static gboolean nav_draw_expose_handler(GtkWidget *widget, GdkEventExpose *expos
gulong expose_id;
expose_id = draw_data->navigate->draw_expose_handler_id;
-
+
if(draw_data->navigate->current_window)
{
g_signal_handler_block(G_OBJECT(widget), expose_id);
@@ -593,7 +593,7 @@ static void locus_gh_func(gpointer hash_key, gpointer hash_value, gpointer user_
end = locus_data->end;
if((item = zmapWindowFToIFindFeatureItem(data->navigate->ftoi_hash,
- locus_data->strand, ZMAPFRAME_NONE,
+ locus_data->strand, ZMAPFRAME_NONE,
feature)))
{
FooCanvasItem *line_item;
@@ -603,23 +603,23 @@ static void locus_gh_func(gpointer hash_key, gpointer hash_value, gpointer user_
text_height = data->wheight;
mid = start + ((end - start + 1.0) / 2.0);
draw_here = mid - (text_height / 2.0);
-
+
iy1 = wy1 = start;
iy2 = wy2 = start + text_height;
-
+
foo_canvas_item_get_bounds(item, &x1, &y1, &x2, &y2);
-
+
/* move to the start of the locus... */
foo_canvas_item_move(item, 0.0, start - y1);
-
+
foo_canvas_item_get_bounds(item, &x1, &(iy1), &x2, &(iy2));
-
+
wy1 = iy1;
wy2 = iy2;
-
+
foo_canvas_item_i2w(item, &dummy_x, &(wy1));
foo_canvas_item_i2w(item, &dummy_x, &(wy2));
-
+
foo_canvas_w2c(item->canvas, dummy_x, wy1, &cx, &(cy1));
foo_canvas_w2c(item->canvas, dummy_x, wy2, &cx, &(cy2));
@@ -650,7 +650,7 @@ static void locus_gh_func(gpointer hash_key, gpointer hash_value, gpointer user_
{
GList *match;
char *text = NULL;
-
+
g_object_get(G_OBJECT(item),
"text", &text,
NULL);
@@ -669,7 +669,7 @@ static void locus_gh_func(gpointer hash_key, gpointer hash_value, gpointer user_
else
zmapWindowTextPositionerAddItem(data->positioner, item);
}
-
+
return ;
}
@@ -684,10 +684,10 @@ static void repositionText(ZMapWindowNavigator navigate)
canvas = fetchCanvas(navigate);
repos_data.navigate = navigate;
- repos_data.positioner = zmapWindowTextPositionerCreate(navigate->full_span.x1 * navigate->scaling_factor,
+ repos_data.positioner = zmapWindowTextPositionerCreate(navigate->full_span.x1 * navigate->scaling_factor,
navigate->full_span.x2 * navigate->scaling_factor);
- zmapWindowNavigatorTextSize(GTK_WIDGET(canvas),
+ zmapWindowNavigatorTextSize(GTK_WIDGET(canvas),
NULL, &(repos_data.wheight));
g_hash_table_foreach(navigate->locus_display_hash,
@@ -697,7 +697,7 @@ static void repositionText(ZMapWindowNavigator navigate)
zmapWindowTextPositionerUnOverlap(repos_data.positioner, TRUE);
zmapWindowTextPositionerDestroy(repos_data.positioner);
}
-
+
return ;
}
@@ -709,9 +709,9 @@ static void navigateDrawFunc(NavigateDraw nav_draw, GtkWidget *widget)
zMapAssert(navigate->current_window);
/* Everything to get a context drawn, raised to top and visible. */
- zMapFeatureContextExecuteComplete((ZMapFeatureAny)(nav_draw->context),
- ZMAPFEATURE_STRUCT_FEATURE,
- drawContext,
+ zMapFeatureContextExecuteComplete((ZMapFeatureAny)(nav_draw->context),
+ ZMAPFEATURE_STRUCT_FEATURE,
+ drawContext,
NULL, nav_draw);
repositionText(navigate);
@@ -726,8 +726,8 @@ static void navigateDrawFunc(NavigateDraw nav_draw, GtkWidget *widget)
}
-static ZMapFeatureContextExecuteStatus drawContext(GQuark key_id,
- gpointer data,
+static ZMapFeatureContextExecuteStatus drawContext(GQuark key_id,
+ gpointer data,
gpointer user_data,
char **error_out)
{
@@ -758,7 +758,7 @@ static ZMapFeatureContextExecuteStatus drawContext(GQuark key_id,
if(!navigate->container_align)
{
navigate->container_align = zmapWindowContainerGroupCreate(container_features, ZMAPCONTAINER_LEVEL_ALIGN,
- ALIGN_CHILD_SPACING,
+ ALIGN_CHILD_SPACING,
&(navigate->align_background), NULL);
g_object_set_data(G_OBJECT(navigate->container_align), ZMAP_WINDOW_POINTER, navigate->current_window) ;
@@ -768,9 +768,9 @@ static ZMapFeatureContextExecuteStatus drawContext(GQuark key_id,
zmapWindowContainerGroupAddUpdateHook(navigate->container_align,
positioning_cb,
navigate);
-#endif
+#endif
zmapWindowContainerGroupAddUpdateHook(navigate->container_align,
- highlight_locator_area_cb,
+ highlight_locator_area_cb,
navigate);
hash_status = zmapWindowFToIAddAlign(navigate->ftoi_hash, key_id, (FooCanvasGroup *)(navigate->container_align));
@@ -789,11 +789,11 @@ static ZMapFeatureContextExecuteStatus drawContext(GQuark key_id,
block_start = feature_block->block_to_sequence.q1;
block_end = feature_block->block_to_sequence.q2;
-
+
/* create the block and add the item to the hash */
features = zmapWindowContainerGetFeatures(draw_data->navigate->container_align);
draw_data->container_block = zmapWindowContainerGroupCreate(features, ZMAPCONTAINER_LEVEL_BLOCK,
- BLOCK_CHILD_SPACING,
+ BLOCK_CHILD_SPACING,
&(navigate->block_background), NULL);
g_object_set_data(G_OBJECT(draw_data->container_block),
@@ -802,10 +802,10 @@ static ZMapFeatureContextExecuteStatus drawContext(GQuark key_id,
container_group_add_highlight_area_item(navigate, draw_data->container_block);
zmapWindowContainerGroupAddUpdateHook(draw_data->container_block,
- highlight_locator_area_cb,
+ highlight_locator_area_cb,
draw_data->navigate);
- g_object_set_data(G_OBJECT(draw_data->container_block), ITEM_FEATURE_STATS,
+ g_object_set_data(G_OBJECT(draw_data->container_block), ITEM_FEATURE_STATS,
zmapWindowStatsCreate((ZMapFeatureAny)draw_data->current_block)) ;
hash_status = zmapWindowFToIAddBlock(navigate->ftoi_hash, draw_data->current_align->unique_id,
@@ -816,7 +816,7 @@ static ZMapFeatureContextExecuteStatus drawContext(GQuark key_id,
features = zmapWindowContainerGetFeatures(draw_data->container_block);
/* The strand container doesn't get added to the hash! */
draw_data->container_strand = zmapWindowContainerGroupCreate(features, ZMAPCONTAINER_LEVEL_STRAND,
- STRAND_CHILD_SPACING,
+ STRAND_CHILD_SPACING,
&(navigate->strand_background), NULL);
g_object_set_data(G_OBJECT(draw_data->container_strand),
@@ -825,7 +825,7 @@ static ZMapFeatureContextExecuteStatus drawContext(GQuark key_id,
container_group_add_highlight_area_item(navigate, draw_data->container_strand);
zmapWindowContainerGroupAddUpdateHook(draw_data->container_strand,
- highlight_locator_area_cb,
+ highlight_locator_area_cb,
draw_data->navigate);
/* create a column per set ... */
@@ -844,7 +844,7 @@ static ZMapFeatureContextExecuteStatus drawContext(GQuark key_id,
status = ZMAP_CONTEXT_EXEC_STATUS_DONT_DESCEND;
- if((item = zmapWindowFToIFindSetItem(draw_data->navigate->ftoi_hash, feature_set,
+ if((item = zmapWindowFToIFindSetItem(draw_data->navigate->ftoi_hash, feature_set,
ZMAPSTRAND_NONE, ZMAPFRAME_NONE)))
{
ZMapWindowContainerFeatureSet container_feature_set;
@@ -854,8 +854,8 @@ static ZMapFeatureContextExecuteStatus drawContext(GQuark key_id,
group_feature_set = FOO_CANVAS_GROUP(item);
container_feature_set = (ZMapWindowContainerFeatureSet)item;
- zmapWindowFToIFactoryRunSet(draw_data->navigate->item_factory,
- feature_set,
+ zmapWindowFToIFactoryRunSet(draw_data->navigate->item_factory,
+ feature_set,
group_feature_set, ZMAPFRAME_NONE);
if ((bump_mode = zmapWindowContainerFeatureSetGetBumpMode(container_feature_set)) != ZMAPBUMP_UNBUMP)
@@ -925,7 +925,7 @@ static gboolean drawScaleRequired(NavigateDraw draw_data)
static void drawScale(NavigateDraw draw_data)
{
FooCanvasItem *item = NULL;
-
+
GQuark scale_id = 0;
int min, max, origin;
@@ -939,7 +939,7 @@ static void drawScale(NavigateDraw draw_data)
{
FooCanvasGroup *scale_group = NULL;
FooCanvasGroup *features = NULL;
-
+
scale_group = FOO_CANVAS_GROUP(item);
features = (FooCanvasGroup *)zmapWindowContainerGetFeatures((ZMapWindowContainerGroup)scale_group);
@@ -981,13 +981,13 @@ static void createColumnCB(gpointer data, gpointer user_data)
if(style_list && draw_data->current_set)
{
ZMapWindowContainerFeatureSet container_set;
-
+
features = zmapWindowContainerGetFeatures(ZMAP_CONTAINER_GROUP(draw_data->container_strand));
- draw_data->container_feature_set = zmapWindowContainerGroupCreate(features,
+ draw_data->container_feature_set = zmapWindowContainerGroupCreate(features,
ZMAPCONTAINER_LEVEL_FEATURESET,
- SET_CHILD_SPACING,
- &(draw_data->navigate->column_background),
+ SET_CHILD_SPACING,
+ &(draw_data->navigate->column_background),
NULL);
g_object_set_data(G_OBJECT(draw_data->container_feature_set),
@@ -996,43 +996,43 @@ static void createColumnCB(gpointer data, gpointer user_data)
container_group_add_highlight_area_item(draw_data->navigate, draw_data->container_feature_set);
zmapWindowContainerGroupAddUpdateHook(draw_data->container_feature_set,
- highlight_locator_area_cb,
+ highlight_locator_area_cb,
draw_data->navigate);
-
- status = zmapWindowFToIAddSet(draw_data->navigate->ftoi_hash,
+
+ status = zmapWindowFToIAddSet(draw_data->navigate->ftoi_hash,
draw_data->current_align->unique_id,
draw_data->current_block->unique_id,
set_id, ZMAPSTRAND_NONE, ZMAPFRAME_NONE,
(FooCanvasGroup *)draw_data->container_feature_set);
zMapAssert(status);
-
+
container_set = (ZMapWindowContainerFeatureSet)draw_data->container_feature_set;
-
+
zmapWindowContainerFeatureSetAugment(container_set,
draw_data->navigate->current_window,
draw_data->current_align->unique_id,
draw_data->current_block->unique_id,
set_id, 0, style_list,
ZMAPSTRAND_FORWARD, ZMAPFRAME_NONE);
-
- zmapWindowContainerFeatureSetAttachFeatureSet(container_set,
+
+ zmapWindowContainerFeatureSetAttachFeatureSet(container_set,
draw_data->current_set);
-
+
g_list_free(style_list);
-
+
zmapWindowContainerSetVisibility(FOO_CANVAS_GROUP(draw_data->container_feature_set), TRUE);
-
+
container_background = zmapWindowContainerGetBackground(draw_data->container_feature_set);
-
- zmapWindowContainerGroupBackgroundSize(draw_data->container_feature_set,
+
+ zmapWindowContainerGroupBackgroundSize(draw_data->container_feature_set,
(draw_data->current_block->block_to_sequence.t2 - draw_data->current_block->block_to_sequence.t1)
* draw_data->navigate->scaling_factor);
-
+
/* scale doesn't need this. */
if(set_id != g_quark_from_string(ZMAP_FIXED_STYLE_SCALE_NAME))
g_signal_connect(G_OBJECT(container_set), "event",
- G_CALLBACK(columnBackgroundEventCB),
+ G_CALLBACK(columnBackgroundEventCB),
(gpointer)draw_data->navigate);
}
else
@@ -1041,13 +1041,13 @@ static void createColumnCB(gpointer data, gpointer user_data)
return ;
}
-static void clampCoords(ZMapWindowNavigator navigate,
- double pre_scale, double post_scale,
+static void clampCoords(ZMapWindowNavigator navigate,
+ double pre_scale, double post_scale,
double *c1_inout, double *c2_inout)
{
double top, bot;
double min, max;
-
+
min = (double)(navigate->full_span.x1) * pre_scale;
max = (double)(navigate->full_span.x2) * pre_scale;
@@ -1065,8 +1065,8 @@ static void clampCoords(ZMapWindowNavigator navigate,
static void clampScaled(ZMapWindowNavigator navigate, double *s1_inout, double *s2_inout)
{
- clampCoords(navigate,
- navigate->scaling_factor,
+ clampCoords(navigate,
+ navigate->scaling_factor,
1.0,
s1_inout,
s2_inout);
@@ -1076,9 +1076,9 @@ static void clampScaled(ZMapWindowNavigator navigate, double *s1_inout, double *
static void clampWorld2Scaled(ZMapWindowNavigator navigate, double *w1_inout, double *w2_inout)
{
- clampCoords(navigate,
+ clampCoords(navigate,
1.0,
- navigate->scaling_factor,
+ navigate->scaling_factor,
w1_inout,
w2_inout);
return ;
@@ -1090,9 +1090,9 @@ static void updateLocatorDragger(ZMapWindowNavigator navigate, double button_y,
a = button_y;
b = button_y + size - 1.0;
-
+
clampScaled(navigate, &a, &b);
-
+
if(locator_debug_G)
{
double sf = navigate->scaling_factor;
@@ -1104,12 +1104,12 @@ static void updateLocatorDragger(ZMapWindowNavigator navigate, double button_y,
top = start / sf;
bot = end / sf;
- printf("%s: [nav] %f -> %f (%f) = [wrld] %f -> %f (%f)\n",
- "updateLocatorDragger",
+ printf("%s: [nav] %f -> %f (%f) = [wrld] %f -> %f (%f)\n",
+ "updateLocatorDragger",
start, end, end - start + 1.0,
top, bot, bot - top + 1.0);
}
-
+
foo_canvas_item_set(FOO_CANVAS_ITEM(navigate->locator_drag),
"y1", a,
"y2", b,
@@ -1171,12 +1171,12 @@ static gboolean rootBGEventCB(FooCanvasItem *item, GdkEvent *event, gpointer dat
locator_y2 -= LOCATOR_LINE_WIDTH / 2.0;
locator_size = locator_y2 - locator_y1 + 1.0;
-
+
foo_canvas_item_show(navigate->locator_drag);
foo_canvas_item_lower_to_bottom(navigate->locator_drag);
-
+
updateLocatorDragger(navigate, y_coord - transp_data->click_correction, locator_size);
-
+
event_handled = transp_data->locator_click = TRUE;
}
}
@@ -1186,7 +1186,7 @@ static gboolean rootBGEventCB(FooCanvasItem *item, GdkEvent *event, gpointer dat
{
double locator_y1, locator_y2, origin_y1, origin_y2, dummy;
zMapAssert(navigate->locator_drag);
-
+
if(transp_data->locator_click == TRUE)
{
foo_canvas_item_get_bounds(FOO_CANVAS_ITEM(navigate->locator_drag), NULL, &locator_y1, NULL, &locator_y2);
@@ -1197,7 +1197,7 @@ static gboolean rootBGEventCB(FooCanvasItem *item, GdkEvent *event, gpointer dat
origin_y1 += LOCATOR_LINE_WIDTH / 2.0;
origin_y2 -= LOCATOR_LINE_WIDTH / 2.0;
-
+
foo_canvas_item_i2w(FOO_CANVAS_ITEM(navigate->locator_drag), &dummy, &locator_y1);
foo_canvas_item_i2w(FOO_CANVAS_ITEM(navigate->locator_drag), &dummy, &locator_y2);
@@ -1209,39 +1209,39 @@ static gboolean rootBGEventCB(FooCanvasItem *item, GdkEvent *event, gpointer dat
origin_y1 /= navigate->scaling_factor;
origin_y2 /= navigate->scaling_factor;
-
+
foo_canvas_item_hide(navigate->locator_drag);
-
+
zMapWindowNavigatorDrawLocator(navigate, locator_y1, locator_y2);
if(locator_y1 != origin_y1 && locator_y2 != origin_y2)
zmapWindowNavigatorValueChanged(NAVIGATOR_WIDGET(navigate), locator_y1, locator_y2);
-
+
transp_data->locator_click = FALSE;
-
+
event_handled = TRUE;
}
}
break;
case GDK_MOTION_NOTIFY:
{
- double button_y = 0.0, locator_y1,
+ double button_y = 0.0, locator_y1,
locator_y2, locator_size = 0.0;
zMapAssert(navigate->locator_drag);
-
+
if(transp_data->locator_click == TRUE)
{
button_y = (double)event->button.y - transp_data->click_correction;
foo_canvas_item_get_bounds(FOO_CANVAS_ITEM(navigate->locator), NULL, &locator_y1, NULL, &locator_y2);
-
+
locator_y1 += LOCATOR_LINE_WIDTH / 2.0;
locator_y2 -= LOCATOR_LINE_WIDTH / 2.0;
locator_size = locator_y2 - locator_y1 + 1.0;
updateLocatorDragger(navigate, button_y, locator_size);
-
+
event_handled = TRUE;
}
}
@@ -1252,9 +1252,9 @@ static gboolean rootBGEventCB(FooCanvasItem *item, GdkEvent *event, gpointer dat
event_handled = FALSE ;
break ;
}
-
+
}
-
+
return event_handled;
}
@@ -1297,17 +1297,17 @@ static void makeMenuFromCanvasItem(GdkEventButton *button, FooCanvasItem *item,
menu_sets = g_list_append(menu_sets, zmapWindowNavigatorMakeMenuLocusColumnOps(NULL, NULL, menu_data));
menu_sets = g_list_append(menu_sets, separator);
}
-
+
container = (ZMapWindowContainerFeatureSet)zmapWindowContainerCanvasItemGetContainer(item);
}
else
{
/* get set_data->style */
-
+
if(ZMAP_IS_CONTAINER_FEATURESET(item))
{
container = ZMAP_CONTAINER_FEATURESET(item);
-
+
if(container->unique_id == menu_data->navigate->locus_id)
{
menu_sets = g_list_append(menu_sets, zmapWindowNavigatorMakeMenuLocusColumnOps(NULL, NULL, menu_data));
@@ -1375,7 +1375,7 @@ static gboolean navCanvasItemEventCB(FooCanvasItem *item, GdkEvent *event, gpoin
case GDK_2BUTTON_PRESS:
{
GdkEventButton *button = (GdkEventButton *)event ;
-
+
/* Retrieve the feature item info from the canvas item. */
feature = zmapWindowItemGetFeature(item);
zMapAssert(feature) ;
@@ -1395,7 +1395,7 @@ static gboolean navCanvasItemEventCB(FooCanvasItem *item, GdkEvent *event, gpoin
}
}
last_but_press = button->time ;
-
+
event_handled = TRUE ;
}
else
@@ -1432,7 +1432,7 @@ static gboolean factoryItemHandler(FooCanvasItem *new_item,
ZMapFeature feature,
gpointer handler_data)
{
- g_signal_connect(GTK_OBJECT(new_item), "event",
+ g_signal_connect(GTK_OBJECT(new_item), "event",
GTK_SIGNAL_FUNC(navCanvasItemEventCB), handler_data);
g_signal_connect(GTK_OBJECT(new_item), "destroy",
GTK_SIGNAL_FUNC(navCanvasItemDestroyCB), handler_data);
@@ -1443,9 +1443,9 @@ static gboolean factoryItemHandler(FooCanvasItem *new_item,
return TRUE;
}
-static gboolean factoryFeatureSizeReq(ZMapFeature feature,
- double *limits_array,
- double *points_array_inout,
+static gboolean factoryFeatureSizeReq(ZMapFeature feature,
+ double *limits_array,
+ double *points_array_inout,
gpointer handler_data)
{
ZMapWindowNavigator navigate = (ZMapWindowNavigator)handler_data;
@@ -1461,7 +1461,7 @@ static gboolean factoryFeatureSizeReq(ZMapFeature feature,
block_start = limits_array[1] * scale_factor;
block_end = limits_array[3] * scale_factor;
-
+
*x1_inout = *x1_inout * scale_factor;
*x2_inout = *x2_inout * scale_factor;
@@ -1470,7 +1470,7 @@ static gboolean factoryFeatureSizeReq(ZMapFeature feature,
points_array_inout[0] += 20;
points_array_inout[2] += 20;
- if((hash_entry = zmapWindowNavigatorLDHFind(navigate->locus_display_hash,
+ if((hash_entry = zmapWindowNavigatorLDHFind(navigate->locus_display_hash,
feature->original_id)))
{
/* we only ever draw the first one of these. */
@@ -1486,23 +1486,23 @@ static gboolean factoryFeatureSizeReq(ZMapFeature feature,
zMapAssertNotReached();
}
}
-
+
/* shift according to how we cross, like this for ease of debugging, not speed */
start_end_crossing |= ((*x1_inout < block_start) << 1);
start_end_crossing |= ((*x2_inout > block_end) << 2);
start_end_crossing |= ((*x1_inout > block_end) << 3);
start_end_crossing |= ((*x2_inout < block_start) << 4);
-
+
/* Now check whether we cross! */
- if(start_end_crossing & 8 ||
+ if(start_end_crossing & 8 ||
start_end_crossing & 16) /* everything is out of range don't display! */
outside = TRUE;
-
+
if(start_end_crossing & 2)
*x1_inout = block_start;
if(start_end_crossing & 4)
*x2_inout = block_end;
-
+
if(hash_entry)
{
/* extend the values in the hash list */
@@ -1520,8 +1520,8 @@ static gboolean factoryFeatureSizeReq(ZMapFeature feature,
static void customiseFactory(ZMapWindowNavigator navigate)
{
ZMapWindowFToIFactoryProductionTeamStruct factory_helpers = {NULL};
-
- /* create a factory and set up */
+
+ /* create a factory and set up */
navigate->item_factory = zmapWindowFToIFactoryOpen(navigate->ftoi_hash, NULL);
factory_helpers.feature_size_request = factoryFeatureSizeReq;
factory_helpers.top_item_created = factoryItemHandler;
@@ -1536,20 +1536,20 @@ static void customiseFactory(ZMapWindowNavigator navigate)
/* mini package for the locus_display_hash ... */
/*
* \brief Create a hash for the locus display.
- *
+ *
* Hash is keyed on GUINT_TO_POINTER(feature->original_id)
* Contains LocusEntry items.
*/
static GHashTable *zmapWindowNavigatorLDHCreate(void)
{
GHashTable *hash = NULL;
-
+
hash = g_hash_table_new_full(NULL, NULL, NULL, destroyLocusEntry);
return hash;
}
-/*
+/*
* \brief finds the entry.
*/
static LocusEntry zmapWindowNavigatorLDHFind(GHashTable *hash, GQuark key)
@@ -1560,11 +1560,11 @@ static LocusEntry zmapWindowNavigatorLDHFind(GHashTable *hash, GQuark key)
return hash_entry;
}
-/*
+/*
* \brief creates a new entry from feature, start and end (scaled) and returns it.
*/
-static LocusEntry zmapWindowNavigatorLDHInsert(GHashTable *hash,
- ZMapFeature feature,
+static LocusEntry zmapWindowNavigatorLDHInsert(GHashTable *hash,
+ ZMapFeature feature,
double start, double end)
{
LocusEntry hash_entry = NULL;
@@ -1575,8 +1575,8 @@ static LocusEntry zmapWindowNavigatorLDHInsert(GHashTable *hash,
hash_entry->end = end;
hash_entry->strand = feature->strand;
hash_entry->feature = feature; /* So we can find the item */
- g_hash_table_insert(hash,
- GUINT_TO_POINTER(feature->original_id),
+ g_hash_table_insert(hash,
+ GUINT_TO_POINTER(feature->original_id),
(gpointer)hash_entry);
}
else
@@ -1584,7 +1584,7 @@ static LocusEntry zmapWindowNavigatorLDHInsert(GHashTable *hash,
return hash_entry;
}
-/*
+/*
* \brief Destroy the hash **! NULL's for you.
*/
static void zmapWindowNavigatorLDHDestroy(GHashTable **destroy_me)
@@ -1605,7 +1605,7 @@ static void destroyLocusEntry(gpointer data)
zMapAssert(data);
locus_entry->feature = NULL;
-
+
g_free(locus_entry);
return ;
@@ -1673,7 +1673,7 @@ static gint strcmp_list_find(gconstpointer list_data, gconstpointer user_data)
/* container update hooks */
-static gboolean highlight_locator_area_cb(ZMapWindowContainerGroup container, FooCanvasPoints *points,
+static gboolean highlight_locator_area_cb(ZMapWindowContainerGroup container, FooCanvasPoints *points,
ZMapContainerLevelType level, gpointer user_data)
{
ZMapWindowNavigator navigate = (ZMapWindowNavigator)user_data;
@@ -1698,7 +1698,7 @@ static gboolean highlight_locator_area_cb(ZMapWindowContainerGroup container, Fo
if(FOO_IS_CANVAS_RE(item_list->data))
{
item = FOO_CANVAS_ITEM(item_list->data);
-
+
foo_canvas_item_set(item,
"x1", points->coords[0],
"x2", points->coords[2],
@@ -1735,7 +1735,7 @@ static gboolean idle_resize_widget_cb(gpointer navigate_data)
return FALSE; /* only run once! */
}
-static gboolean positioning_cb(ZMapWindowContainerGroup container, FooCanvasPoints *points,
+static gboolean positioning_cb(ZMapWindowContainerGroup container, FooCanvasPoints *points,
ZMapContainerLevelType level, gpointer user_data)
{
ZMapWindowNavigator navigate = (ZMapWindowNavigator)user_data;
@@ -1763,7 +1763,7 @@ static gboolean positioning_cb(ZMapWindowContainerGroup container, FooCanvasPoin
}
-static gboolean container_draw_locator(ZMapWindowContainerGroup container, FooCanvasPoints *points,
+static gboolean container_draw_locator(ZMapWindowContainerGroup container, FooCanvasPoints *points,
ZMapContainerLevelType level, gpointer user_data)
{
ZMapWindowNavigator navigate = (ZMapWindowNavigator)user_data;
@@ -1776,17 +1776,17 @@ static gboolean container_draw_locator(ZMapWindowContainerGroup container, FooCa
if(GTK_WIDGET_MAPPED(GTK_WIDGET(navigate->locator->canvas)))
{
-
+
x1 = points->coords[0];
x2 = points->coords[2];
-
+
y1 = navigate->locator_y_coords.x1;
y2 = navigate->locator_y_coords.x2;
-
+
clampWorld2Scaled(navigate, &y1, &y2);
-
+
overlay = (FooCanvasGroup *)zmapWindowContainerGetOverlay(container);
-
+
if((list = g_list_first(overlay->item_list)))
{
do
@@ -1806,11 +1806,11 @@ static gboolean container_draw_locator(ZMapWindowContainerGroup container, FooCa
while((list = list->next));
}
-
+
foo_canvas_item_raise_to_top(navigate->locator);
foo_canvas_item_show(navigate->locator);
-
+
positioning_cb(container, points, level, user_data);
}
@@ -1888,11 +1888,11 @@ static void container_group_add_locator(ZMapWindowNavigator navigate,
int i;
GdkColor blue;
gdk_color_parse("lightblue", &blue);
-
- /* These are just some markers to draw that show where the
+
+ /* These are just some markers to draw that show where the
* 1000 "scaled" world coords are. i.e. 1000 world coords
* of _this_ canvas, which does not equal the feature
- * coords here... They get updated in x by the
+ * coords here... They get updated in x by the
* container_draw_locator update hook. */
for(i = 0; i < 26; i+=2)
@@ -1914,13 +1914,13 @@ static void container_group_add_locator(ZMapWindowNavigator navigate,
if((transp_data = g_new0(TransparencyEventStruct, 1)))
{
FooCanvasItem *root_bg = NULL;
-
+
root_bg = (FooCanvasItem *)(navigate->container_root);
-
+
transp_data->navigate = navigate;
transp_data->locator_click = FALSE;
transp_data->click_correction = 0.0;
-
+
g_signal_connect(GTK_OBJECT(root_bg), "event",
GTK_SIGNAL_FUNC(rootBGEventCB), transp_data);
}
diff --git a/src/zmapWindow/zmapWindowRemoteReceive.c b/src/zmapWindow/zmapWindowRemoteReceive.c
index 9e0aa64c4..eab30bea9 100755
--- a/src/zmapWindow/zmapWindowRemoteReceive.c
+++ b/src/zmapWindow/zmapWindowRemoteReceive.c
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Sep 8 08:51 2009 (edgrif)
* Created: Thu Jul 19 11:45:36 2007 (rds)
- * CVS info: $Id: zmapWindowRemoteReceive.c,v 1.12 2010-03-04 15:13:20 mh17 Exp $
+ * CVS info: $Id: zmapWindowRemoteReceive.c,v 1.13 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -79,7 +79,7 @@ typedef struct
ZMapFeatureSet feature_set;
ZMapFeature feature;
- GData *styles;
+ GHashTable *styles;
GList *locations, *feature_list;
@@ -107,22 +107,22 @@ static void loadFeatures(ZMapWindow window, RequestData input_data, ResponseData
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-static gboolean xml_zmap_start_cb(gpointer user_data,
- ZMapXMLElement zmap_element,
+static gboolean xml_zmap_start_cb(gpointer user_data,
+ ZMapXMLElement zmap_element,
ZMapXMLParser parser);
-static gboolean xml_request_start_cb(gpointer user_data,
- ZMapXMLElement zmap_element,
+static gboolean xml_request_start_cb(gpointer user_data,
+ ZMapXMLElement zmap_element,
ZMapXMLParser parser);
#if NOT_USED
-static gboolean xml_featureset_start_cb(gpointer user_data,
- ZMapXMLElement zmap_element,
+static gboolean xml_featureset_start_cb(gpointer user_data,
+ ZMapXMLElement zmap_element,
ZMapXMLParser parser);
-static gboolean xml_feature_start_cb(gpointer user_data,
- ZMapXMLElement zmap_element,
+static gboolean xml_feature_start_cb(gpointer user_data,
+ ZMapXMLElement zmap_element,
ZMapXMLParser parser);
#endif
-static gboolean xml_return_true_cb(gpointer user_data,
- ZMapXMLElement zmap_element,
+static gboolean xml_return_true_cb(gpointer user_data,
+ ZMapXMLElement zmap_element,
ZMapXMLParser parser);
static char *actions_G[ZMAPWINDOW_REMOTE_UNKNOWN + 1] =
@@ -204,10 +204,10 @@ static char *window_execute_command(char *command_text, gpointer user_data, int
if((zMapXMLParserParseBuffer(parser, command_text, strlen(command_text))) == TRUE)
{
ResponseDataStruct output_data = {0};
-
+
output_data.code = 0;
output_data.messages = g_string_sized_new(512);
-
+
switch(input.common.action)
{
@@ -244,7 +244,7 @@ static char *window_execute_command(char *command_text, gpointer user_data, int
{
zMapLogWarning("%s", response);
g_free(response);
- response = g_strdup("Broken code. Check zmap.log file");
+ response = g_strdup("Broken code. Check zmap.log file");
}
if(response == NULL){ response = g_strdup("Broken code."); }
@@ -253,8 +253,8 @@ static char *window_execute_command(char *command_text, gpointer user_data, int
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-static ZMapFeatureContextExecuteStatus zoomToFeatureCB(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus zoomToFeatureCB(GQuark key,
+ gpointer data,
gpointer user_data,
char **error_out)
{
@@ -267,7 +267,7 @@ static ZMapFeatureContextExecuteStatus zoomToFeatureCB(GQuark key,
case ZMAPFEATURE_STRUCT_FEATURE:
if(!input_data->zoomed)
{
- zMapWindowZoomToFeature(input_data->window, (ZMapFeature)feature_any);
+ zMapWindowZoomToFeature(input_data->window, (ZMapFeature)feature_any);
input_data->zoomed = TRUE;
}
break;
@@ -312,17 +312,17 @@ static void zoomWindowToFeature(ZMapWindow window, RequestData input_data, Respo
else if ((list = g_list_first(input_data->locations)))
{
span = (ZMapSpan)(list->data);
- zMapWindowZoomToWorldPosition(window, FALSE,
+ zMapWindowZoomToWorldPosition(window, FALSE,
0.0, span->x1,
100.0, span->x2);
- g_string_append_printf(output_data->messages,
+ g_string_append_printf(output_data->messages,
"Zoom to location %d-%d executed",
span->x1, span->x2);
}
else
{
- g_string_append_printf(output_data->messages,
- "No data for %s action",
+ g_string_append_printf(output_data->messages,
+ "No data for %s action",
actions_G[ZMAPWINDOW_REMOTE_ZOOM_TO]);
output_data->code = ZMAPXREMOTE_BADREQUEST;
}
@@ -396,13 +396,13 @@ static void loadFeatures(ZMapWindow window, RequestData input_data, ResponseData
static void populate_request_data(RequestData input_data)
{
input_data->orig_context = input_data->window->feature_context;
-
+
/* Copy basics of original context. */
input_data->edit_context = (ZMapFeatureContext)zMapFeatureAnyCopy((ZMapFeatureAny)(input_data->orig_context)) ;
//input_data->edit_context->styles = NULL ;
-
+
input_data->styles = input_data->window->read_only_styles ;
-
+
return ;
}
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
@@ -410,8 +410,8 @@ static void populate_request_data(RequestData input_data)
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-static gboolean setupStyles(ZMapFeatureSet set, ZMapFeature feature,
- GData *styles, GQuark style_id)
+static gboolean setupStyles(ZMapFeatureSet set, ZMapFeature feature,
+ GHashTable *styles, GQuark style_id)
{
gboolean got_style = TRUE;
@@ -421,7 +421,7 @@ static gboolean setupStyles(ZMapFeatureSet set, ZMapFeature feature,
-static gboolean xml_zmap_start_cb(gpointer user_data,
+static gboolean xml_zmap_start_cb(gpointer user_data,
ZMapXMLElement zmap_element,
ZMapXMLParser parser)
{
@@ -516,7 +516,7 @@ static gboolean xml_zmap_start_cb(gpointer user_data,
return result ;
}
-static gboolean xml_request_start_cb(gpointer user_data,
+static gboolean xml_request_start_cb(gpointer user_data,
ZMapXMLElement zmap_element,
ZMapXMLParser parser)
{
@@ -759,75 +759,75 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
case ZMAPWINDOW_REMOTE_ZOOM_TO:
{
zMapXMLParserCheckIfTrueErrorReturn(request_data->block == NULL,
- parser,
+ parser,
"feature tag not contained within featureset tag");
-
+
if((attr = zMapXMLElementGetAttributeByName(feature_element, "name")))
{
feature_name_q = zMapXMLAttributeGetValue(attr);
}
else
zMapXMLParserRaiseParsingError(parser, "name is a required attribute for feature.");
-
+
if((attr = zMapXMLElementGetAttributeByName(feature_element, "style")))
{
style_q = zMapXMLAttributeGetValue(attr);
}
else
zMapXMLParserRaiseParsingError(parser, "style is a required attribute for feature.");
-
+
if((attr = zMapXMLElementGetAttributeByName(feature_element, "start")))
{
- start = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
+ start = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
(char **)NULL, 10);
}
else
zMapXMLParserRaiseParsingError(parser, "start is a required attribute for feature.");
-
+
if((attr = zMapXMLElementGetAttributeByName(feature_element, "end")))
{
- end = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
+ end = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
(char **)NULL, 10);
}
else
zMapXMLParserRaiseParsingError(parser, "end is a required attribute for feature.");
-
+
if((attr = zMapXMLElementGetAttributeByName(feature_element, "strand")))
{
zMapFeatureFormatStrand((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
&(strand));
}
-
+
if((attr = zMapXMLElementGetAttributeByName(feature_element, "score")))
{
score = zMapXMLAttributeValueToDouble(attr);
has_score = TRUE;
}
-
+
if((attr = zMapXMLElementGetAttributeByName(feature_element, "suid")))
{
/* Nothing done here yet. */
zMapXMLAttributeGetValue(attr);
}
-
+
if(!zMapXMLParserLastErrorMsg(parser))
{
style_name = (char *)g_quark_to_string(style_q);
style_id = zMapStyleCreateID(style_name);
feature_name = (char *)g_quark_to_string(feature_name_q);
-
+
if(!(request_data->feature_set = zMapFeatureBlockGetSetByID(request_data->block, style_id)))
{
request_data->feature_set = zMapFeatureSetCreate(style_name , NULL);
zMapFeatureBlockAddFeatureSet(request_data->block, request_data->feature_set);
}
-
- if((request_data->feature = zMapFeatureCreateFromStandardData(feature_name, NULL, "",
+
+ if((request_data->feature = zMapFeatureCreateFromStandardData(feature_name, NULL, "",
ZMAPSTYLE_MODE_BASIC, NULL,
start, end, has_score,
score, strand, ZMAPPHASE_NONE)))
{
- if (setupStyles(request_data->feature_set, request_data->feature,
+ if (setupStyles(request_data->feature_set, request_data->feature,
request_data->styles, style_id))
{
@@ -865,7 +865,7 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
g_free(error);
}
}
-
+
/* This must go and instead use a feature create call... */
feature_any = g_new0(ZMapFeatureAnyStruct, 1) ;
@@ -891,8 +891,8 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-static gboolean xml_return_true_cb(gpointer user_data,
- ZMapXMLElement zmap_element,
+static gboolean xml_return_true_cb(gpointer user_data,
+ ZMapXMLElement zmap_element,
ZMapXMLParser parser)
{
return TRUE;
diff --git a/src/zmapWindow/zmapWindowSearch.c b/src/zmapWindow/zmapWindowSearch.c
index 40eee8d92..a3d264795 100755
--- a/src/zmapWindow/zmapWindowSearch.c
+++ b/src/zmapWindow/zmapWindowSearch.c
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -25,12 +25,12 @@
* Description: Implements a search window which allows a user to
* specify align, block, set and feature patterns to
* find sets of features.
- *
+ *
* Exported functions: See zmapWindow_P.h
* HISTORY:
* Last edited: Jun 12 08:58 2009 (rds)
* Created: Fri Aug 12 16:53:21 2005 (edgrif)
- * CVS info: $Id: zmapWindowSearch.c,v 1.42 2010-03-04 15:13:22 mh17 Exp $
+ * CVS info: $Id: zmapWindowSearch.c,v 1.43 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -46,7 +46,7 @@ typedef struct
ZMapWindow window ;
FooCanvasItem *feature_item ;
ZMapFeatureAny feature_any ;
- GData *styles ;
+ GHashTable *styles ;
GHashTable *context_to_item;
ZMapWindowListGetFToIHash get_hash_func;
@@ -135,15 +135,15 @@ static void setFilterDefaults(SearchData search_data) ;
static void addToComboBoxText(gpointer list_data, gpointer combo_data);
static void addToComboBoxQuark(gpointer list_data, gpointer combo_data);
static GtkWidget *createPopulateComboBox(GList *list, gboolean quarks);
-static void fetchAllComboLists(ZMapFeatureAny feature_any,
+static void fetchAllComboLists(ZMapFeatureAny feature_any,
GList **align_list_out,
GList **block_list_out,
GList **set_list_out);
-static ZMapFeatureContextExecuteStatus fillAllComboList(GQuark key, gpointer data,
+static ZMapFeatureContextExecuteStatus fillAllComboList(GQuark key, gpointer data,
gpointer user_data, char **err_out);
-static GList *getStyleQuarks(GData *styles) ;
-static void getQuark(GQuark style_id, gpointer data, gpointer user_data) ;
+static GList *getStyleQuarks(GHashTable *styles) ;
+static void getQuark(gpointer key, gpointer data, gpointer user_data) ;
gboolean searchPredCB(FooCanvasItem *canvas_item, gpointer user_data) ;
@@ -166,7 +166,7 @@ static GHashTable *access_window_context_to_item(gpointer user_data)
}
-void zmapWindowCreateSearchWindow(ZMapWindow window,
+void zmapWindowCreateSearchWindow(ZMapWindow window,
ZMapWindowListGetFToIHash get_hash_func,
gpointer get_hash_data,
FooCanvasItem *feature_item)
@@ -231,9 +231,9 @@ void zmapWindowCreateSearchWindow(ZMapWindow window,
buttonBox = gtk_hbutton_box_new();
gtk_button_box_set_layout (GTK_BUTTON_BOX (buttonBox), GTK_BUTTONBOX_END);
- gtk_box_set_spacing (GTK_BOX(buttonBox),
+ gtk_box_set_spacing (GTK_BOX(buttonBox),
ZMAP_WINDOW_GTK_BUTTON_BOX_SPACING);
- gtk_container_set_border_width (GTK_CONTAINER (buttonBox),
+ gtk_container_set_border_width (GTK_CONTAINER (buttonBox),
ZMAP_WINDOW_GTK_CONTAINER_BORDER_WIDTH);
search_button = gtk_button_new_with_label("Search") ;
@@ -245,7 +245,7 @@ void zmapWindowCreateSearchWindow(ZMapWindow window,
gtk_window_set_default(GTK_WINDOW(toplevel), search_button) ;
frame = gtk_frame_new("") ;
- gtk_container_set_border_width(GTK_CONTAINER(frame),
+ gtk_container_set_border_width(GTK_CONTAINER(frame),
ZMAP_WINDOW_GTK_CONTAINER_BORDER_WIDTH);
gtk_box_pack_start(GTK_BOX(vbox), frame, FALSE, FALSE, 0) ;
@@ -381,7 +381,7 @@ static GtkWidget *makeFiltersPanel(SearchData search_data)
GtkWidget *frame ;
GtkWidget *topbox, *hbox, *entrybox, *labelbox, *entry, *label, *combo ;
ZMapFeatureContext context ;
- GData *styles ;
+ GHashTable *styles ;
GList *style_quarks ;
context = (ZMapFeatureContext)zMapFeatureGetParentGroup(search_data->feature_any,
@@ -389,7 +389,7 @@ static GtkWidget *makeFiltersPanel(SearchData search_data)
search_data->styles = styles = search_data->window->read_only_styles ;
style_quarks = getStyleQuarks(styles) ;
-
+
setFilterDefaults(search_data) ;
@@ -569,7 +569,7 @@ static GQuark entry_get_text_quark(GtkEntry *entry, char *wildcard)
else if((entry_text = g_strdup(entry_text)))
{
entry_text = g_strstrip(entry_text);
-
+
entry_quark = g_quark_from_string(entry_text);
/* The Quark table has a reference to this now... Free it. */
@@ -580,11 +580,11 @@ static GQuark entry_get_text_quark(GtkEntry *entry, char *wildcard)
}
/* return either usable, wildcard or canonicalized(user_set) */
-static GQuark manage_quark_from_entry(GQuark user_set, GQuark original,
+static GQuark manage_quark_from_entry(GQuark user_set, GQuark original,
GQuark usable, GQuark wildcard)
{
GQuark managed_quark = 0;
-
+
managed_quark = user_set;
if(managed_quark == original)
@@ -615,7 +615,7 @@ static void searchCB(GtkWidget *widget, gpointer cb_data)
char *wild_card_str = "*" ;
GQuark wild_card_id ;
char *style_text ;
-
+
wild_card_id = g_quark_from_string(wild_card_str) ;
@@ -636,11 +636,11 @@ static void searchCB(GtkWidget *widget, gpointer cb_data)
/* Needed in more than one place. */
start_txt = (char *)gtk_entry_get_text(GTK_ENTRY(search_data->start_entry)) ;
end_text = (char *)gtk_entry_get_text(GTK_ENTRY(search_data->end_entry)) ;
-
+
if((align_id = entry_get_text_quark(GTK_ENTRY(search_data->align_entry), wild_card_str)) != 0)
{
/* fix up align_id */
- align_id = manage_quark_from_entry(align_id, search_data->align_original_id,
+ align_id = manage_quark_from_entry(align_id, search_data->align_original_id,
search_data->align_id, wild_card_id);
/* fix up block_id */
@@ -654,7 +654,7 @@ static void searchCB(GtkWidget *widget, gpointer cb_data)
{
set_id = manage_quark_from_entry(set_id, search_data->set_original_id,
search_data->set_id, wild_card_id);
-
+
/* fix up feature_id */
if((feature_id = entry_get_text_quark(GTK_ENTRY(search_data->feature_entry), wild_card_str)) != 0)
{
@@ -718,7 +718,7 @@ static void searchCB(GtkWidget *widget, gpointer cb_data)
search_pred_ptr = &search_pred ;
search_pred.start = atoi(start_txt) ;
-
+
search_pred.end = atoi(end_text) ;
search_pred.locus = locus ;
@@ -778,9 +778,9 @@ static void searchCB(GtkWidget *widget, gpointer cb_data)
{
char *title = NULL;
title = g_strdup_printf("Results '%s'", feature_txt);
- zmapWindowListWindow(search_data->window,
+ zmapWindowListWindow(search_data->window,
NULL, title,
- search_data->get_hash_func,
+ search_data->get_hash_func,
search_data->get_hash_data,
NULL, NULL, NULL,
zoom_to_item);
@@ -789,7 +789,7 @@ static void searchCB(GtkWidget *widget, gpointer cb_data)
}
else
{
- zMapMessage("Sorry, list windows of %ss within a feature context not currently supported.",
+ zMapMessage("Sorry, list windows of %ss within a feature context not currently supported.",
zMapFeatureStructType2Str(any_feature->struct_type)) ;
}
@@ -803,7 +803,7 @@ static void searchCB(GtkWidget *widget, gpointer cb_data)
SearchPredCBData search_pred_data = NULL ;
gboolean zoom_to_item = TRUE;
char *title = NULL;
-
+
title = g_strdup_printf("Results '%s'", feature_txt);
if(callback && search_pred_ptr)
@@ -1078,7 +1078,7 @@ static GtkWidget *createPopulateComboBox(GList *list, gboolean quarks)
return combo;
}
-static ZMapFeatureContextExecuteStatus fillAllComboList(GQuark key, gpointer data,
+static ZMapFeatureContextExecuteStatus fillAllComboList(GQuark key, gpointer data,
gpointer user_data, char **err_out)
{
ZMapFeatureAny feature_any = (ZMapFeatureAny)data;
@@ -1114,7 +1114,7 @@ static ZMapFeatureContextExecuteStatus fillAllComboList(GQuark key, gpointer dat
return ZMAP_CONTEXT_EXEC_STATUS_OK;
}
-static void fetchAllComboLists(ZMapFeatureAny feature_any,
+static void fetchAllComboLists(ZMapFeatureAny feature_any,
GList **align_list_out,
GList **block_list_out,
GList **set_list_out)
@@ -1136,7 +1136,7 @@ static void addToComboBoxText(gpointer list_data, gpointer combo_data)
{
GtkWidget *combo = (GtkWidget *)combo_data;
char *text = (char *)list_data;
-
+
gtk_combo_box_append_text(GTK_COMBO_BOX(combo), text);
return ;
@@ -1147,7 +1147,7 @@ static void addToComboBoxQuark(gpointer list_data, gpointer combo_data)
GtkWidget *combo = (GtkWidget *)combo_data;
GQuark textId = GPOINTER_TO_UINT(list_data);
const char *text = NULL;
-
+
if(textId)
{
text = g_quark_to_string(textId);
@@ -1248,18 +1248,18 @@ static void locusCB(GtkToggleButton *toggle_button, gpointer cb_data)
-static GList *getStyleQuarks(GData *styles)
+static GList *getStyleQuarks(GHashTable *styles)
{
GList *style_quarks = NULL ;
- g_datalist_foreach(&styles, getQuark, &style_quarks) ;
+ g_hash_table_foreach(styles, getQuark, &style_quarks) ;
return style_quarks ;
}
-static void getQuark(GQuark style_id, gpointer data, gpointer user_data)
+static void getQuark(gpointer key, gpointer data, gpointer user_data)
{
ZMapFeatureTypeStyle style = (ZMapFeatureTypeStyle)data ;
GList *style_quarks = *((GList **)user_data) ;
diff --git a/src/zmapWindow/zmapWindowUtils.c b/src/zmapWindow/zmapWindowUtils.c
index 6a39b394b..4358987a8 100755
--- a/src/zmapWindow/zmapWindowUtils.c
+++ b/src/zmapWindow/zmapWindowUtils.c
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: Jan 22 11:22 2010 (edgrif)
* Created: Thu Jan 20 14:43:12 2005 (edgrif)
- * CVS info: $Id: zmapWindowUtils.c,v 1.61 2010-05-17 14:41:16 mh17 Exp $
+ * CVS info: $Id: zmapWindowUtils.c,v 1.62 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -307,22 +307,22 @@ void zMapWindowGetVisible(ZMapWindow window, double *top_out, double *bottom_out
*
*/
-gboolean zmapWindowUpdateStyles(ZMapWindow window, GData **read_only_styles, GData **display_styles)
+gboolean zmapWindowUpdateStyles(ZMapWindow window, GHashTable *read_only_styles, GHashTable *display_styles)
{
gboolean result = FALSE ;
- if (*read_only_styles)
+ if (read_only_styles)
{
if (window->read_only_styles)
- zMapStyleDestroyStyles(&(window->read_only_styles)) ;
+ zMapStyleDestroyStyles(window->read_only_styles) ;
result = zMapStyleCopyAllStyles(read_only_styles, &(window->read_only_styles)) ;
}
- if (*display_styles)
+ if (display_styles)
{
if (window->display_styles)
- zMapStyleDestroyStyles(&(window->display_styles)) ;
+ zMapStyleDestroyStyles(window->display_styles) ;
result = zMapStyleCopyAllStyles(display_styles, &(window->display_styles)) ;
}
@@ -403,7 +403,7 @@ ZMapFeatureTypeStyle zmapWindowStyleTableAddCopy(GHashTable *style_table, ZMapFe
{
style = zMapFeatureStyleCopy(new_style) ;
- g_hash_table_insert(style_table, GINT_TO_POINTER(zMapStyleGetUniqueID(new_style)), style) ;
+ g_hash_table_insert(style_table, GINT_TO_POINTER(zMapStyleGetUniqueID(new_style)), (gpointer) style) ;
}
return style ;
@@ -455,10 +455,10 @@ void zmapWindowStyleTableDestroy(GHashTable *style_table)
/* Free the list, but not the styles ......um, what does this mean.....EG */
-/* It means there's no copying of the style from GData[all_styles] ->
+/* It means there's no copying of the style from GHashTable[all_styles] ->
* GList[some_styles] going on in this function. Just allocation of
* GList items to hold onto the styles pointers. */
-GList *zmapWindowFeatureSetStyles(ZMapWindow window, GData *all_styles, GQuark feature_set_id)
+GList *zmapWindowFeatureSetStyles(ZMapWindow window, GHashTable *all_styles, GQuark feature_set_id)
{
GList *styles_list = NULL;
GList *styles_quark_list = NULL;
@@ -480,7 +480,7 @@ GList *zmapWindowFeatureSetStyles(ZMapWindow window, GData *all_styles, GQuark f
if((style = zMapFindStyle(all_styles, style_id))) // add styles needed by featuresets
{
- styles_list = g_list_append(styles_list, style);
+ styles_list = g_list_append(styles_list, (gpointer) style);
for(i = 1;i < ZMAPSTYLE_SUB_FEATURE_MAX;i++) // add styles needed by this style
{
@@ -491,7 +491,7 @@ GList *zmapWindowFeatureSetStyles(ZMapWindow window, GData *all_styles, GQuark f
{
if((sub = zMapFindStyle(all_styles, sub_id)))
{
- styles_list = g_list_append(styles_list, sub);
+ styles_list = g_list_append(styles_list, (gpointer) sub);
}
}
}
@@ -499,12 +499,11 @@ GList *zmapWindowFeatureSetStyles(ZMapWindow window, GData *all_styles, GQuark f
else
{
- static int fred = 0;
- void printStyle(GQuark style_id, gpointer data, gpointer user_data);
+ //void printStyle(gpointer key, gpointer data, gpointer user_data);
+ //g_hash_table_foreach(&all_styles, printStyle, "FeatureSetStyles") ;
zMapLogWarning("could not find style %s for featureset %s\n",
g_quark_to_string(style_id),g_quark_to_string(feature_set_id));
- //g_datalist_foreach(&all_styles, printStyle, "FeatureSetStyles") ;
}
}
while((list = g_list_next(list)));
diff --git a/src/zmapWindow/zmapWindow_P.h b/src/zmapWindow/zmapWindow_P.h
index 33c397b09..4267035cb 100755
--- a/src/zmapWindow/zmapWindow_P.h
+++ b/src/zmapWindow/zmapWindow_P.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,11 +23,11 @@
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
* Description: Defines internal interfaces/data structures of zMapWindow.
- *
+ *
* HISTORY:
* Last edited: May 24 13:37 2010 (edgrif)
* Created: Fri Aug 1 16:45:58 2003 (edgrif)
- * CVS info: $Id: zmapWindow_P.h,v 1.260 2010-05-24 12:37:43 edgrif Exp $
+ * CVS info: $Id: zmapWindow_P.h,v 1.261 2010-06-08 08:31:26 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_WINDOW_P_H
@@ -46,13 +46,13 @@
#include <zmapWindowContainerUtils.h>
-/* set a KNOWN initial size for the foo_canvas!
+/* set a KNOWN initial size for the foo_canvas!
* ... the same size as foo_canvas sets ...
*/
#define ZMAP_CANVAS_INIT_SIZE (100.0)
-/*
+/*
* This section details data that we attach to the foocanvas items that represent
* contexts, aligns etc. Each data structure is accessed via a key given by the
* string in the hash define for each struct.
@@ -162,7 +162,7 @@ typedef struct
GQuark block_id;
GQuark set_id;
GQuark feature_id;
-
+
char *strand_str;
char *frame_str;
@@ -231,22 +231,22 @@ typedef struct
* be changed any time soon...they impinge on the canvas which could have a very
* large windows indeed. Unfortunately X just silently resets the window to size
* 1 when you try to create larger windows....now read on...
- *
+ *
* The largest X window that can be created has max dimensions of 65535 (i.e. an
* unsigned short), you can easily test this for a server by creating a window and
* then querying its size, you should find this is the max. window size you can have.
- *
+ *
* BUT....you can't really make use of a window this size _because_ when positioning
* anything (other windows, lines etc.), the coordinates are given via _signed_ ints.
* This means that the maximum position you can specify must in the range -32768
* to 32767. In a way this makes sense because it means that you can have a window
* that covers this entire span and so position things anywhere inside it. In a way
* its completely crap and confusing.......
- *
+ *
* BUT....it means that in the visible window you are limited to the range 0 - 32767.
* by sticking at 30,000 we allow ourselves a margin for error that should work on any
* machine.
- *
+ *
*/
enum
@@ -262,13 +262,13 @@ enum
ZMAP_WINDOW_INTRON_POINTS = 3 /* Number of points to draw an intron. */
} ;
-enum
+enum
{
ZMAP_WINDOW_GTK_BOX_SPACING = 5, /* Size in pixels for the GTK_BOX spacing between children */
ZMAP_WINDOW_GTK_BUTTON_BOX_SPACING = 10
};
-enum
+enum
{
ZMAP_WINDOW_GTK_CONTAINER_BORDER_WIDTH = 5
};
@@ -308,7 +308,7 @@ typedef enum
/* Controls what data is displayed in the feature list window. */
typedef enum
- {
+ {
ZMAP_WINDOW_LIST_COL_NAME, /*!< feature name column */
ZMAP_WINDOW_LIST_COL_TYPE, /*!< feature type column */
ZMAP_WINDOW_LIST_COL_STRAND, /*!< feature strand */
@@ -334,7 +334,7 @@ typedef enum
/* Controls what data is displayed in the dna list window. */
typedef enum
- {
+ {
ZMAP_WINDOW_LIST_DNA_SCREEN_START, /* match screen start coord */
ZMAP_WINDOW_LIST_DNA_SCREEN_END, /* match screen end coord */
ZMAP_WINDOW_LIST_DNA_SCREEN_STRAND, /* match strand */
@@ -418,7 +418,7 @@ typedef void (*ZMapWindowRulerCanvasCallback)(gpointer data,
typedef struct _ZMapWindowRulerCanvasCallbackListStruct
{
ZMapWindowRulerCanvasCallback paneResize;
-
+
gpointer user_data; /* Goes to all! */
} ZMapWindowRulerCanvasCallbackListStruct, *ZMapWindowRulerCanvasCallbackList;
@@ -531,7 +531,7 @@ typedef struct _ZMapWindowStruct
/* Max canvas window size can either be set in pixels or in DNA bases, the latter overrides the
- * former. In either case the window cannot be more than 30,000 pixels (32k is the actual
+ * former. In either case the window cannot be more than 30,000 pixels (32k is the actual
* X windows limit. */
int canvas_maxwin_size ;
int canvas_maxwin_bases ;
@@ -563,8 +563,8 @@ typedef struct _ZMapWindowStruct
ZMapFeatureContext feature_context ; /* Currently displayed features. */
- GData *read_only_styles ; /* Original styles list from server. */
- GData *display_styles ; /* Styles used for current display. */
+ GHashTable *read_only_styles ; /* Original styles list from server. */
+ GHashTable *display_styles ; /* Styles used for current display. */
ZMapFeatureContext strand_separator_context ; /* context to display non-feature context "features" with. */
@@ -583,7 +583,7 @@ typedef struct _ZMapWindowStruct
/* The stupid foocanvas can generate graphics items that are greater than the X Windows 32k
* limit, so we have to keep a list of the canvas items that can generate graphics greater
* than this limit as we zoom in and crop them ourselves. */
- ZMapWindowLongItems long_items ;
+ ZMapWindowLongItems long_items ;
ZMapWindowFToIFactory item_factory;
/* Lists of dialog windows associated with this zmap window, these must be destroyed when
@@ -720,8 +720,8 @@ void zmapWindowPrintLocalCoords(char *msg_prefix, FooCanvasItem *item) ;
void zmapWindowShowItem(FooCanvasItem *item) ;
-void zmapWindowListWindowCreate(ZMapWindow window,
- FooCanvasItem *current_item,
+void zmapWindowListWindowCreate(ZMapWindow window,
+ FooCanvasItem *current_item,
char *title,
ZMapWindowListGetFToIHash get_hash_func,
gpointer get_hash_data,
@@ -729,8 +729,8 @@ void zmapWindowListWindowCreate(ZMapWindow window,
gpointer search_hash_data,
GDestroyNotify search_hash_free,
gboolean zoom_to_item);
-void zmapWindowListWindow(ZMapWindow window,
- FooCanvasItem *current_item,
+void zmapWindowListWindow(ZMapWindow window,
+ FooCanvasItem *current_item,
char *title,
ZMapWindowListGetFToIHash get_hash_func,
gpointer get_hash_data,
@@ -740,7 +740,7 @@ void zmapWindowListWindow(ZMapWindow window,
gboolean zoom_to_item);
void zmapWindowListWindowReread(GtkWidget *window_list_widget) ;
-void zmapWindowCreateSearchWindow(ZMapWindow zmapWindow,
+void zmapWindowCreateSearchWindow(ZMapWindow zmapWindow,
ZMapWindowListGetFToIHash get_hash_func,
gpointer get_hash_data,
FooCanvasItem *feature_item) ;
@@ -769,7 +769,7 @@ void zmapWindowLongItemPrint(ZMapWindowLongItems long_items) ;
void zmapWindowLongItemFree(ZMapWindowLongItems long_items) ;
void zmapWindowLongItemDestroy(ZMapWindowLongItems long_item) ;
-void zmapWindowDrawFeatures(ZMapWindow window,
+void zmapWindowDrawFeatures(ZMapWindow window,
ZMapFeatureContext current_context, ZMapFeatureContext new_context) ;
void zmapWindowreDrawContainerExecute(ZMapWindow window,
ZMapContainerUtilsExecFunc enter_cb,
@@ -827,7 +827,7 @@ GList *zmapWindowFToIFindItemSetFull(GHashTable *feature_to_context_hash,
GQuark align_id, GQuark block_id, GQuark set_id,
char *strand_spec, char *frame_spec,
GQuark feature_id,
- ZMapWindowFToIPredFuncCB pred_func, gpointer user_data) ;
+ ZMapWindowFToIPredFuncCB pred_func, gpointer user_data) ;
GList *zmapWindowFToIFindSameNameItems(GHashTable *feature_to_context_hash,
char *set_strand, char *set_frame, ZMapFeature feature) ;
@@ -905,9 +905,9 @@ ZMapFeatureSet zmapWindowItemFeatureSetRecoverFeatureSet(ZMapWindowItemFeatureSe
-void zmapWindowItemHighlightRegionTranslations(ZMapWindow window, FooCanvasItem *item,
+void zmapWindowItemHighlightRegionTranslations(ZMapWindow window, FooCanvasItem *item,
int region_start, int region_end);
-void zmapWindowItemHighlightTranslationRegion(ZMapWindow window, FooCanvasItem *item,
+void zmapWindowItemHighlightTranslationRegion(ZMapWindow window, FooCanvasItem *item,
ZMapFrame required_frame,
int region_start, int region_end) ;
FooCanvasItem *zmapWindowItemGetShowTranslationColumn(ZMapWindow window, FooCanvasItem *item) ;
@@ -927,7 +927,7 @@ gboolean zmapWindowWorld2SeqCoords(ZMapWindow window,
FooCanvasGroup **block_grp_out, int *y1_out, int *y2_out) ;
gboolean zmapWindowItem2SeqCoords(FooCanvasItem *item, int *y1, int *y2) ;
-void zmapWindowItemGetVisibleCanvas(ZMapWindow window,
+void zmapWindowItemGetVisibleCanvas(ZMapWindow window,
double *wx1, double *wy1,
double *wx2, double *wy2);
@@ -956,17 +956,17 @@ void zmapWindowGetScrollRegion(ZMapWindow window,
void zmapWindowSetScrollRegion(ZMapWindow window,
double *x1_inout, double *y1_inout,
double *x2_inout, double *y2_inout);
-ZMapGUIClampType zmapWindowClampSpan(ZMapWindow window,
- double *top_inout,
+ZMapGUIClampType zmapWindowClampSpan(ZMapWindow window,
+ double *top_inout,
double *bot_inout) ;
-ZMapGUIClampType zmapWindowClampedAtStartEnd(ZMapWindow window,
- double *top_inout,
+ZMapGUIClampType zmapWindowClampedAtStartEnd(ZMapWindow window,
+ double *top_inout,
double *bot_inout) ;
void zMapWindowMoveItem(ZMapWindow window, ZMapFeature origFeature,
ZMapFeature modFeature, FooCanvasItem *item);
-void zMapWindowMoveSubFeatures(ZMapWindow window,
- ZMapFeature originalFeature,
+void zMapWindowMoveSubFeatures(ZMapWindow window,
+ ZMapFeature originalFeature,
ZMapFeature modifiedFeature,
GArray *origArray, GArray *modArray,
gboolean isExon);
@@ -1004,7 +1004,7 @@ void zmapWindowColumnSetState(ZMapWindow window, FooCanvasGroup *column_group,
void zmapWindowGetPosFromScore(ZMapFeatureTypeStyle style, double score,
double *curr_x1_inout, double *curr_x2_out) ;
void zmapWindowFreeWindowArray(GPtrArray **window_array_inout, gboolean free_array) ;
-ZMapWindowFeatureShow zmapWindowFeatureShowCreate(ZMapWindow zmapWindow, FooCanvasItem *item) ;
+ZMapWindowFeatureShow zmapWindowFeatureShowCreate(ZMapWindow zmapWindow, FooCanvasItem *item) ;
ZMapWindowFeatureShow zmapWindowFeatureShow(ZMapWindow zmapWindow, FooCanvasItem *item) ;
GtkTreeModel *zmapWindowFeatureListCreateStore(ZMapWindowListType list_type) ;
@@ -1066,8 +1066,8 @@ ZMapGUIMenuItem zmapWindowMakeMenuMarkDumpOps(int *start_index_inout,
ZMapGUIMenuItemCallbackFunc callback_func,
gpointer callback_data) ;
-gboolean zmapWindowUpdateXRemoteData(ZMapWindow window,
- ZMapFeatureAny feature_any,
+gboolean zmapWindowUpdateXRemoteData(ZMapWindow window,
+ ZMapFeatureAny feature_any,
char *action,
FooCanvasItem *real_item);
gboolean zmapWindowUpdateXRemoteDataFull(ZMapWindow window, ZMapFeatureAny feature_any,
@@ -1084,7 +1084,7 @@ void zmapWindowZoomControlHandleResize(ZMapWindow window);
double zmapWindowZoomControlLimitSpan(ZMapWindow window, double y1, double y2) ;
void zmapWindowZoomControlCopyTo(ZMapWindowZoomControl orig, ZMapWindowZoomControl new) ;
void zmapWindowZoomControlGetScrollRegion(ZMapWindow window,
- double *x1_out, double *y1_out,
+ double *x1_out, double *y1_out,
double *x2_out, double *y2_out);
@@ -1103,7 +1103,7 @@ char *zmapWindowFeatureDescription(ZMapFeature feature) ;
void zmapWindowFeatureHighlightDNA(ZMapWindow window, ZMapFeature Feature, FooCanvasItem *item);
char *zmapWindowFeatureTranscriptFASTA(ZMapFeature feature, gboolean spliced, gboolean cds_only);
-/*
+/*
void zmapWindowzoomControlClampSpan(ZMapWindow window, double *top_inout, double *bot_inout) ;
*/
void zmapWindowDebugWindowCopy(ZMapWindow window);
@@ -1115,7 +1115,7 @@ void zmapWindowDrawScaleBar(ZMapWindow window, double start, double end) ;
/*!-------------------------------------------------------------------!
*| Checks to see if the item really is visible. In order to do this |
- *| all the item's parent groups need to be examined. |
+ *| all the item's parent groups need to be examined. |
*!-------------------------------------------------------------------!*/
gboolean zmapWindowItemIsVisible(FooCanvasItem *item) ;
/*!-------------------------------------------------------------------!
@@ -1190,7 +1190,7 @@ void zmapWindowMarkItem(ZMapWindow window, FooCanvasItem *item, gboolean mark) ;
#ifdef RDS_BREAKING_STUFF
ZMapWindowItemHighlighter zmapWindowItemTextHighlightCreateData(FooCanvasGroup *group);
ZMapWindowItemHighlighter zmapWindowItemTextHighlightRetrieve(FooCanvasGroup *group);
-gboolean zmapWindowItemTextHighlightGetIndices(ZMapWindowItemHighlighter select_control,
+gboolean zmapWindowItemTextHighlightGetIndices(ZMapWindowItemHighlighter select_control,
int *firstIdx, int *lastIdx);
void zmapWindowItemTextHighlightFinish(ZMapWindowItemHighlighter select_control);
gboolean zmapWindowItemTextHighlightValidForMotion(ZMapWindowItemHighlighter select_control);
@@ -1200,7 +1200,7 @@ gboolean zmapWindowItemTextHighlightBegin(ZMapWindowItemHighlighter select_contr
FooCanvasGroup *group_under_control,
FooCanvasItem *item_receiving_event);
void zmapWindowItemTextHighlightUpdateCoords(ZMapWindowItemHighlighter select_control,
- double event_x_coord,
+ double event_x_coord,
double event_y_coord);
void zmapWindowItemTextHighlightRegion(ZMapWindowItemHighlighter select_control,
FooCanvasItem *feature_parent,
@@ -1210,33 +1210,33 @@ void zmapWindowItemTextHighlightSetFullText(ZMapWindowItemHighlighter select_con
char *zmapWindowItemTextHighlightGetFullText(ZMapWindowItemHighlighter select_control);
void zmapWindowItemTextHighlightReset(ZMapWindowItemHighlighter select_control);
#endif
-gboolean zmapWindowCreateSetColumns(ZMapWindow window,
- ZMapWindowContainerFeatures forward_strand_group,
+gboolean zmapWindowCreateSetColumns(ZMapWindow window,
+ ZMapWindowContainerFeatures forward_strand_group,
ZMapWindowContainerFeatures reverse_strand_group,
- ZMapFeatureBlock block,
+ ZMapFeatureBlock block,
ZMapFeatureSet feature_set,
- GData *styles,
+ GHashTable *styles,
ZMapFrame frame,
- FooCanvasGroup **forward_col_out,
+ FooCanvasGroup **forward_col_out,
FooCanvasGroup **reverse_col_out,
FooCanvasGroup **separator_col_out);
void zmapWindowDrawFeatureSet(ZMapWindow window,
- GData *styles,
+ GHashTable *styles,
ZMapFeatureSet feature_set,
- FooCanvasGroup *forward_col,
+ FooCanvasGroup *forward_col,
FooCanvasGroup *reverse_col,
ZMapFrame frame) ;
void zmapWindowRemoveEmptyColumns(ZMapWindow window,
FooCanvasGroup *forward_group, FooCanvasGroup *reverse_group) ;
gboolean zmapWindowRemoveIfEmptyCol(FooCanvasGroup **col_group) ;
-void zmapWindowDrawSeparatorFeatures(ZMapWindow window,
+void zmapWindowDrawSeparatorFeatures(ZMapWindow window,
ZMapFeatureBlock block,
ZMapFeatureSet feature_set,
ZMapFeatureTypeStyle style);
-gboolean zmapWindowUpdateStyles(ZMapWindow window, GData **read_only_styles, GData **display_styles) ;
-gboolean zmapWindowGetMarkedSequenceRangeFwd(ZMapWindow window,
+gboolean zmapWindowUpdateStyles(ZMapWindow window, GHashTable *read_only_styles, GHashTable *display_styles) ;
+gboolean zmapWindowGetMarkedSequenceRangeFwd(ZMapWindow window,
ZMapFeatureBlock block,
int *start, int *end);
@@ -1246,7 +1246,7 @@ ZMapFeatureTypeStyle zmapWindowStyleTableFind(GHashTable *style_table, GQuark st
void zmapWindowStyleTableForEach(GHashTable *style_table,
ZMapWindowStyleTableCallback app_func, gpointer app_data) ;
void zmapWindowStyleTableDestroy(GHashTable *style_table) ;
-GList *zmapWindowFeatureSetStyles(ZMapWindow window, GData *all_styles, GQuark feature_set_id);
+GList *zmapWindowFeatureSetStyles(ZMapWindow window, GHashTable *all_styles, GQuark feature_set_id);
/* Ruler Functions */
ZMapWindowRulerCanvas zmapWindowRulerCanvasCreate(ZMapWindowRulerCanvasCallbackList callbacks);
@@ -1261,7 +1261,7 @@ void zmapWindowRulerCanvasSetVAdjustment(ZMapWindowRulerCanvas obj, GtkAdjustmen
void zmapWindowRulerCanvasSetPixelsPerUnit(ZMapWindowRulerCanvas obj, double x, double y);
void zmapWindowRulerCanvasSetLineHeight(ZMapWindowRulerCanvas obj,
double border);
-void zmapWindowRulerGroupDraw(FooCanvasGroup *parent, double project_at,
+void zmapWindowRulerGroupDraw(FooCanvasGroup *parent, double project_at,
double origin, double start, double end);
/* Stats functions. */
--
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