diff --git a/src/include/ZMap/zmapConfigIni.h b/src/include/ZMap/zmapConfigIni.h
index 5e0020b177f0d37f1925bdc48f792480d42b8706..7b274e300db280cacb01476a40f0055fb71ab734 100755
--- a/src/include/ZMap/zmapConfigIni.h
+++ b/src/include/ZMap/zmapConfigIni.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 26 14:53 2009 (edgrif)
* Created: Thu Sep 11 10:40:13 2008 (rds)
- * CVS info: $Id: zmapConfigIni.h,v 1.10 2010-03-04 15:14:52 mh17 Exp $
+ * CVS info: $Id: zmapConfigIni.h,v 1.11 2010-03-19 08:56:41 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -68,10 +68,10 @@ gboolean zMapConfigIniContextIncludeFile(ZMapConfigIniContext context, char *fil
gchar **zMapConfigIniContextGetAllStanzaNames(ZMapConfigIniContext context);
//GList *zMapConfigIniContextGetStyleList(ZMapConfigIniContext context) ;
-gboolean zMapConfigIniContextAddGroup(ZMapConfigIniContext context,
+gboolean zMapConfigIniContextAddGroup(ZMapConfigIniContext context,
char *stanza_name, char *stanza_type,
ZMapConfigIniContextKeyEntryStruct *keys);
-gboolean zMapConfigIniContextGetValue(ZMapConfigIniContext context,
+gboolean zMapConfigIniContextGetValue(ZMapConfigIniContext context,
char *stanza_name,
char *stanza_type,
char *key_name,
@@ -120,8 +120,8 @@ ZMapConfigIniContext zMapConfigIniContextDestroy(ZMapConfigIniContext context);
GList *zMapConfigIniContextGetReferencedStanzas(ZMapConfigIniContext context,
ZMapConfigIniUserDataCreateFunc object_create_func,
- char *parent_name,
- char *parent_type,
+ char *parent_name,
+ char *parent_type,
char *parent_key,
char *child_type);
@@ -145,6 +145,7 @@ GList *zMapConfigIniContextGetNamed(ZMapConfigIniContext context, char *stanza_n
GList *zMapConfigIniContextGetStyleList(ZMapConfigIniContext context,char *styles_list_in);
gboolean zMapConfigIniGetStylesFromFile(char *styles_list, char *styles_file, GData **styles_out);
+GHashTable *zMapConfigIniGetSource2Featureset(ZMapConfigIniContext context);
void zMapConfigSourcesFreeList(GList *config_sources_list);
void zMapConfigStylesFreeList(GList *config_styles_list);
diff --git a/src/include/ZMap/zmapConfigStanzaStructs.h b/src/include/ZMap/zmapConfigStanzaStructs.h
index eb7ae4b9e638fd5d5a02ad2de5d453c0a06e283f..92b3d8c730d16a0edea3aea5a0f4e09df530fa12 100755
--- a/src/include/ZMap/zmapConfigStanzaStructs.h
+++ b/src/include/ZMap/zmapConfigStanzaStructs.h
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: Nov 13 08:58 2008 (edgrif)
* Created: Tue Aug 26 12:38:28 2008 (rds)
- * CVS info: $Id: zmapConfigStanzaStructs.h,v 1.5 2010-03-11 08:54:37 mh17 Exp $
+ * CVS info: $Id: zmapConfigStanzaStructs.h,v 1.6 2010-03-19 08:56:41 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -45,7 +45,7 @@ typedef struct _ZMapConfigSourceStruct
char *styles_list, *stylesfile ;
char *format ;
int timeout ;
- gboolean writeback, sequence, delayed ;
+ gboolean writeback, /* sequence,*/ delayed ;
} ZMapConfigSourceStruct, *ZMapConfigSource;
diff --git a/src/include/ZMap/zmapConfigStrings.h b/src/include/ZMap/zmapConfigStrings.h
index d2416bd0e75894081172961fddefd1f63394b1ef..217425b11e272fb74ee5fb8e26652b17d535109b 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 1.25 2010-03-11 08:54:37 mh17 Exp $
+ * CVS info: $Id: zmapConfigStrings.h,v 1.26 2010-03-19 08:56:41 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_CONFIG_STRINGS_H
@@ -873,4 +873,7 @@
+#define ZMAPSTANZA_FEATURESET_CONFIG "featuresets"
+
+
#endif /* !ZMAP_CONFIG_STRINGS_H */
diff --git a/src/include/ZMap/zmapFeature.h b/src/include/ZMap/zmapFeature.h
index 55b2be191db0f7b7fe11fbf9473b36015e07023c..168609dc0be08f64480256231df2cce19518dd8a 100755
--- a/src/include/ZMap/zmapFeature.h
+++ b/src/include/ZMap/zmapFeature.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: Data structures describing a sequence feature.
- *
+ *
* HISTORY:
* Last edited: Mar 3 13:40 2010 (edgrif)
* Created: Fri Jun 11 08:37:19 2004 (edgrif)
- * CVS info: $Id: zmapFeature.h,v 1.172 2010-03-04 15:25:56 mh17 Exp $
+ * CVS info: $Id: zmapFeature.h,v 1.173 2010-03-19 08:56:41 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_FEATURE_H
@@ -76,7 +76,7 @@ typedef int Coord ; /* we do need this here.... */
typedef enum {ZMAPFEATURE_STRUCT_INVALID = 0,
- ZMAPFEATURE_STRUCT_CONTEXT, ZMAPFEATURE_STRUCT_ALIGN,
+ ZMAPFEATURE_STRUCT_CONTEXT, ZMAPFEATURE_STRUCT_ALIGN,
ZMAPFEATURE_STRUCT_BLOCK, ZMAPFEATURE_STRUCT_FEATURESET,
ZMAPFEATURE_STRUCT_FEATURE} ZMapFeatureStructType ;
@@ -91,9 +91,9 @@ typedef enum {
ZMAPFEATURE_SUBPART_INVALID = 0,
ZMAPFEATURE_SUBPART_INTRON = 1 << 0,
ZMAPFEATURE_SUBPART_INTRON_CDS = 1 << 1,
- ZMAPFEATURE_SUBPART_EXON = 1 << 2,
+ ZMAPFEATURE_SUBPART_EXON = 1 << 2,
ZMAPFEATURE_SUBPART_EXON_CDS = 1 << 3,
- ZMAPFEATURE_SUBPART_GAP = 1 << 4,
+ ZMAPFEATURE_SUBPART_GAP = 1 << 4,
ZMAPFEATURE_SUBPART_MATCH = 1 << 5
} ZMapFeatureSubpartType ;
@@ -107,14 +107,14 @@ typedef enum {ZMAPPHASE_NONE = 0,
ZMAPPHASE_0, ZMAPPHASE_1, ZMAPPHASE_2} ZMapPhase ;
/* as in BLAST*, i.e. target is DNA, Protein, DNA translated */
-typedef enum {ZMAPHOMOL_NONE = 0,
+typedef enum {ZMAPHOMOL_NONE = 0,
ZMAPHOMOL_N_HOMOL, ZMAPHOMOL_X_HOMOL, ZMAPHOMOL_TX_HOMOL} ZMapHomolType ;
/* Used to specify the degree of colinearity between two alignment blocks. */
typedef enum
{
- COLINEAR_INVALID,
+ COLINEAR_INVALID,
COLINEAR_NOT, /* blocks not colinear. */
COLINEAR_IMPERFECT, /* blocks colinear but not contiguous. */
COLINEAR_PERFECT /* blocks colinear and contiguous. */
@@ -200,7 +200,7 @@ typedef struct
/*
* Sequences and Block Coordinates
*
- * In the context of displaying a single align with a single block,
+ * In the context of displaying a single align with a single block,
* given a chromosome and a sequence from that to look at *we have:
*
* 1 X chromosome bases
@@ -219,11 +219,11 @@ typedef struct
* ZMap will always be run using a sequence of 1,Y; it will never start from a coordinate not equal to 1.
* Y may be specified as 0 in various places which signifies 'the end'.
*
- * Start and end coordinates may be specified by command line args, from the main window,
+ * Start and end coordinates may be specified by command line args, from the main window,
* from a GFF file header, from other servers (eg ACEDB, DAS) and these will refer to the block
* coordinates not the sequence.
*
- * Reverse complementing is a process that applies to blocks and this involves transforming
+ * Reverse complementing is a process that applies to blocks and this involves transforming
* the coordinates S,E in the context of the containing sequence 1,Y
*/
@@ -242,18 +242,18 @@ typedef struct ZMapFeatureAlignmentStruct_ *ZMapFeatureAlignment ;
typedef struct ZMapFeatureAnyStruct_ *ZMapFeatureAny ;
-#define FEATURES_NEED_MAGIC
+#define FEATURES_NEED_MAGIC
/* WARNING: READ THIS BEFORE CHANGING ANY FEATURE STRUCTS:
- *
+ *
* This is the generalised feature struct which can be used to process any feature struct.
* It helps with certain kinds of processing, e.g. in the hash searching code which relies
* on these fields being common to all feature structs.
- *
+ *
* unique_id is used for the hash table that connects any feature struct to the canvas item
* that represents it.
- *
+ *
* original_id is used for displaying a human readable name for the struct, e.g. the feature
* name.
* */
@@ -274,10 +274,10 @@ typedef struct ZMapFeatureAnyStruct_
/* Holds a set of data that is the complete "view" of the requested sequence.
- *
+ *
* This includes all the alignments which in the case of the original "fmap" like view
* will be a single alignment containing a single block.
- *
+ *
*/
typedef struct ZMapFeatureContextStruct_
{
@@ -300,7 +300,7 @@ typedef struct ZMapFeatureContextStruct_
/* Hack...forced on us because GHash has a global destroy function per hash table, not one
* per element of the hashtable (datalists have one per node but they have their own
* problems as they are slow). There are two ways a context can be freed
- *
+ *
* See the write up for the zMapFeatureContextMerge() for how this is used.
*/
gboolean diff_context ; /* TRUE means this is a diff context. */
@@ -420,7 +420,7 @@ typedef struct ZMapFeatureSetStruct_
*
* Feature subtypes, homologies, transcripts, etc come first and then the ZMapFeatureStruct
* in which they are embedded.
- *
+ *
*/
@@ -510,7 +510,7 @@ typedef struct
/* The Feature structure itsself. Describes a single feature, the feature may be compound
* (e.g. have exons/introns * etc.) or a single span or point, e.g. an allele.
* */
-typedef struct ZMapFeatureStruct_
+typedef struct ZMapFeatureStruct_
{
/* FeatureAny section. */
#ifdef FEATURES_NEED_MAGIC
@@ -604,23 +604,23 @@ typedef struct
* very helpful, changed in favour of
* "Transcript" (could add feature_so_term) */
- char *feature_start ;
+ char *feature_start ;
char *feature_end ;
char *feature_length ;
char *feature_strand ;
char *feature_frame ;
- char *feature_query_start ;
- char *feature_query_end ;
- char *feature_query_length ;
+ char *feature_query_start ;
+ char *feature_query_end ;
+ char *feature_query_length ;
char *feature_query_strand ;
-
+
/* sub feature details (still all strings) */
- char *sub_feature_index ;
- char *sub_feature_start ;
+ char *sub_feature_index ;
+ char *sub_feature_start ;
char *sub_feature_end ;
- char *sub_feature_query_start ;
+ char *sub_feature_query_start ;
char *sub_feature_query_end ;
char *sub_feature_length ;
char *sub_feature_none_txt ; /* If no subfeature, gives reason.... */
@@ -703,30 +703,30 @@ void zMapFeatureAnyDestroy(ZMapFeatureAny feature) ;
/* ***************
- * FEATURE METHODS
+ * FEATURE METHODS
*/
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-char *zMapFeatureCreateName(ZMapFeatureType feature_type,
+char *zMapFeatureCreateName(ZMapFeatureType feature_type,
char *feature_name,
- ZMapStrand strand,
- int start, int end,
+ ZMapStrand strand,
+ int start, int end,
int query_start, int query_end) ;
-GQuark zMapFeatureCreateID(ZMapFeatureType feature_type,
+GQuark zMapFeatureCreateID(ZMapFeatureType feature_type,
char *feature_name,
- ZMapStrand strand,
+ ZMapStrand strand,
int start, int end,
int query_start, int query_end) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-char *zMapFeatureCreateName(ZMapStyleMode feature_type,
+char *zMapFeatureCreateName(ZMapStyleMode feature_type,
char *feature_name,
- ZMapStrand strand,
- int start, int end,
+ ZMapStrand strand,
+ int start, int end,
int query_start, int query_end) ;
-GQuark zMapFeatureCreateID(ZMapStyleMode feature_type,
+GQuark zMapFeatureCreateID(ZMapStyleMode feature_type,
char *feature_name,
- ZMapStrand strand,
+ ZMapStrand strand,
int start, int end,
int query_start, int query_end) ;
@@ -783,16 +783,16 @@ int zMapFeatureLength(ZMapFeature feature, ZMapFeatureLengthType length_typ
void zMapFeatureDestroy(ZMapFeature feature) ;
-/* *******************
- * FEATURE SET METHODS
+/* *******************
+ * FEATURE SET METHODS
*/
-GQuark zMapFeatureSetCreateID(char *feature_set_name) ;
+GQuark zMapFeatureSetCreateID(char *feature_set_name) ;
ZMapFeatureSet zMapFeatureSetCreate(char *source, GHashTable *features) ;
ZMapFeatureSet zMapFeatureSetIDCreate(GQuark original_id, GQuark unique_id,
ZMapFeatureTypeStyle style, GHashTable *features) ;
gboolean zMapFeatureSetAddFeature(ZMapFeatureSet feature_set, ZMapFeature feature) ;
gboolean zMapFeatureSetFindFeature(ZMapFeatureSet feature_set, ZMapFeature feature) ;
-ZMapFeature zMapFeatureSetGetFeatureByID(ZMapFeatureSet feature_set,
+ZMapFeature zMapFeatureSetGetFeatureByID(ZMapFeatureSet feature_set,
GQuark feature_id);
gboolean zMapFeatureSetRemoveFeature(ZMapFeatureSet feature_set, ZMapFeature feature) ;
void zMapFeatureSetDestroyFeatures(ZMapFeatureSet feature_set) ;
@@ -804,11 +804,11 @@ GList *zMapFeatureSetGetNamedFeatures(ZMapFeatureSet feature_set, GQuark origina
/* *********************
- * FEATURE BLOCK METHODS
+ * FEATURE BLOCK METHODS
*/
GQuark zMapFeatureBlockCreateID(int ref_start, int ref_end, ZMapStrand ref_strand,
int non_start, int non_end, ZMapStrand non_strand);
-gboolean zMapFeatureBlockDecodeID(GQuark id,
+gboolean zMapFeatureBlockDecodeID(GQuark id,
int *ref_start, int *ref_end, ZMapStrand *ref_strand,
int *non_start, int *non_end, ZMapStrand *non_strand);
ZMapFeatureBlock zMapFeatureBlockCreate(char *block_seq,
@@ -819,7 +819,7 @@ gboolean zMapFeatureBlockSetFeaturesCoords(ZMapFeatureBlock feature_block,
gboolean zMapFeatureBlockAddFeatureSet(ZMapFeatureBlock feature_block, ZMapFeatureSet feature_set) ;
gboolean zMapFeatureBlockFindFeatureSet(ZMapFeatureBlock feature_block,
ZMapFeatureSet feature_set);
-ZMapFeatureSet zMapFeatureBlockGetSetByID(ZMapFeatureBlock feature_block,
+ZMapFeatureSet zMapFeatureBlockGetSetByID(ZMapFeatureBlock feature_block,
GQuark set_id) ;
gboolean zMapFeatureBlockRemoveFeatureSet(ZMapFeatureBlock feature_block,
ZMapFeatureSet feature_set);
@@ -832,13 +832,13 @@ gboolean zMapFeatureBlockDNA(ZMapFeatureBlock block,
/* *************************
* FEATURE ALIGNMENT METHODS
*/
-GQuark zMapFeatureAlignmentCreateID(char *align_sequence, gboolean master_alignment) ;
+GQuark zMapFeatureAlignmentCreateID(char *align_sequence, gboolean master_alignment) ;
ZMapFeatureAlignment zMapFeatureAlignmentCreate(char *align_name, gboolean master_alignment) ;
-gboolean zMapFeatureAlignmentAddBlock(ZMapFeatureAlignment feature_align,
+gboolean zMapFeatureAlignmentAddBlock(ZMapFeatureAlignment feature_align,
ZMapFeatureBlock feature_block) ;
-gboolean zMapFeatureAlignmentFindBlock(ZMapFeatureAlignment feature_align,
+gboolean zMapFeatureAlignmentFindBlock(ZMapFeatureAlignment feature_align,
ZMapFeatureBlock feature_block);
-ZMapFeatureBlock zMapFeatureAlignmentGetBlockByID(ZMapFeatureAlignment feature_align,
+ZMapFeatureBlock zMapFeatureAlignmentGetBlockByID(ZMapFeatureAlignment feature_align,
GQuark block_id);
gboolean zMapFeatureAlignmentRemoveBlock(ZMapFeatureAlignment feature_align,
ZMapFeatureBlock feature_block);
@@ -860,7 +860,7 @@ gboolean zMapFeatureContextErase(ZMapFeatureContext *current_context_inout,
ZMapFeatureContext remove_context,
ZMapFeatureContext *diff_context_out);
gboolean zMapFeatureContextAddAlignment(ZMapFeatureContext feature_context,
- ZMapFeatureAlignment alignment,
+ ZMapFeatureAlignment alignment,
gboolean master) ;
gboolean zMapFeatureContextFindAlignment(ZMapFeatureContext feature_context,
ZMapFeatureAlignment feature_align);
@@ -881,32 +881,32 @@ void zMapFeatureContextDestroy(ZMapFeatureContext context, gboolean free_data) ;
GList *zMapFeatureString2QuarkList(char *string_list) ;
GList *zMapFeatureCopyQuarkList(GList *quark_list_orig) ;
-void zMapFeatureContextExecute(ZMapFeatureAny feature_any,
- ZMapFeatureStructType stop,
- ZMapGDataRecurseFunc callback,
+void zMapFeatureContextExecute(ZMapFeatureAny feature_any,
+ ZMapFeatureStructType stop,
+ ZMapGDataRecurseFunc callback,
gpointer data);
-void zMapFeatureContextExecuteFull(ZMapFeatureAny feature_any,
- ZMapFeatureStructType stop,
- ZMapGDataRecurseFunc callback,
+void zMapFeatureContextExecuteFull(ZMapFeatureAny feature_any,
+ ZMapFeatureStructType stop,
+ ZMapGDataRecurseFunc callback,
gpointer data);
-void zMapFeatureContextExecuteComplete(ZMapFeatureAny feature_any,
- ZMapFeatureStructType stop,
- ZMapGDataRecurseFunc start_callback,
- ZMapGDataRecurseFunc end_callback,
+void zMapFeatureContextExecuteComplete(ZMapFeatureAny feature_any,
+ ZMapFeatureStructType stop,
+ ZMapGDataRecurseFunc start_callback,
+ ZMapGDataRecurseFunc end_callback,
gpointer data);
-void zMapFeatureContextExecuteSubset(ZMapFeatureAny feature_any,
- ZMapFeatureStructType stop,
- ZMapGDataRecurseFunc callback,
+void zMapFeatureContextExecuteSubset(ZMapFeatureAny feature_any,
+ ZMapFeatureStructType stop,
+ ZMapGDataRecurseFunc callback,
gpointer data);
-void zMapFeatureContextExecuteRemoveSafe(ZMapFeatureAny feature_any,
- ZMapFeatureStructType stop,
- ZMapGDataRecurseFunc start_callback,
- ZMapGDataRecurseFunc end_callback,
+void zMapFeatureContextExecuteRemoveSafe(ZMapFeatureAny feature_any,
+ ZMapFeatureStructType stop,
+ ZMapGDataRecurseFunc start_callback,
+ ZMapGDataRecurseFunc end_callback,
gpointer data);
-void zMapFeatureContextExecuteStealSafe(ZMapFeatureAny feature_any,
- ZMapFeatureStructType stop,
- ZMapGDataRecurseFunc start_callback,
- ZMapGDataRecurseFunc end_callback,
+void zMapFeatureContextExecuteStealSafe(ZMapFeatureAny feature_any,
+ ZMapFeatureStructType stop,
+ ZMapGDataRecurseFunc start_callback,
+ ZMapGDataRecurseFunc end_callback,
gpointer data);
@@ -929,11 +929,12 @@ gboolean zMapFeatureAnyForceModesToStyles(ZMapFeatureAny feature_any, GData *sty
/* 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,
GIOChannel *file, GError **error_out) ;
gboolean zMapFeatureContextDumpToFile(ZMapFeatureAny feature_any,
- GData *styles,
+ GData *styles,
ZMapFeatureDumpFeatureFunc dump_func,
gpointer dump_user_data,
GIOChannel *dump_file,
@@ -946,13 +947,13 @@ gboolean zMapFeatureContextRangeDumpToFile(ZMapFeatureAny dump_set,
GIOChannel *dump_file,
GError **dump_error_out) ;
gboolean zMapFeatureListDumpToFile(GList *feature_list,
- GData *styles,
+ GData *styles,
ZMapFeatureDumpFeatureFunc dump_func,
gpointer dump_user_data,
GIOChannel *dump_file,
GError **dump_error_out);
gboolean zMapFeatureListForeachDumperCreate(ZMapFeatureDumpFeatureFunc dump_func,
- GData *styles,
+ GData *styles,
gpointer dump_user_data,
GDestroyNotify dump_user_free,
GIOChannel *dump_file,
@@ -970,7 +971,7 @@ void zMapFeature3FrameTranslationPopulate(ZMapFeatureSet feature_set);
gboolean zMapFeature3FrameTranslationCreateSet(ZMapFeatureBlock block, ZMapFeatureSet *set_out);
-gboolean zMapFeatureWorld2Transcript(ZMapFeature feature,
+gboolean zMapFeatureWorld2Transcript(ZMapFeature feature,
int w1, int w2,
int *t1, int *t2);
ZMapFrame zMapFeatureTranscriptFrame(ZMapFeature feature);
@@ -1009,19 +1010,19 @@ char *zMapFeatureDNAFeatureName(ZMapFeatureBlock block);
GQuark zMapFeatureDNAFeatureID(ZMapFeatureBlock block);
gboolean zMapFeatureDNACreateFeatureSet(ZMapFeatureBlock block, ZMapFeatureSet *feature_set_out);
void zMapFeatureDNAAddSequenceData(ZMapFeature dna_feature, char *dna_str, int sequence_length);
-ZMapFeature zMapFeatureDNACreateFeature(ZMapFeatureBlock block,
+ZMapFeature zMapFeatureDNACreateFeature(ZMapFeatureBlock block,
ZMapFeatureTypeStyle style,
- char *dna_str,
+ char *dna_str,
int sequence_length);
void zMapFeature3FrameTranslationSetCreateFeatures(ZMapFeatureSet feature_set,
ZMapFeatureTypeStyle style);
-GArray *zMapFeatureAnyAsXMLEvents(ZMapFeatureAny feature_any,
+GArray *zMapFeatureAnyAsXMLEvents(ZMapFeatureAny feature_any,
/* ZMapFeatureXMLType xml_type */
int xml_type);
-gboolean zMapFeatureAnyAsXML(ZMapFeatureAny feature_any,
+gboolean zMapFeatureAnyAsXML(ZMapFeatureAny feature_any,
ZMapXMLWriter xml_writer,
GArray **xml_events_out,
int xml_type);
@@ -1033,9 +1034,9 @@ ZMapFeatureAny zMapFeatureContextFindFeatureFromFeature(ZMapFeatureContext conte
GType zMapFeatureDataGetType(void);
-gboolean zMapFeatureGetInfo(ZMapFeatureAny feature_any,
+gboolean zMapFeatureGetInfo(ZMapFeatureAny feature_any,
ZMapFeatureSubPartSpan sub_feature,
- const gchar *first_property_name,
+ const gchar *first_property_name,
...);
diff --git a/src/include/ZMap/zmapView.h b/src/include/ZMap/zmapView.h
index 4f8fd594fa7cf5d53515935b6b5788ac4f73a96b..55f53ea64d22b1b6aa823d58ce902be4ae34fe6b 100755
--- a/src/include/ZMap/zmapView.h
+++ b/src/include/ZMap/zmapView.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.
@@ -27,11 +27,11 @@
* collected from one or more servers. Hence the view
* interface controls both windows and connections to
* servers.
- *
+ *
* HISTORY:
* Last edited: Jun 12 14:36 2009 (edgrif)
* Created: Thu May 13 14:59:14 2004 (edgrif)
- * CVS info: $Id: zmapView.h,v 1.56 2010-03-04 15:15:27 mh17 Exp $
+ * CVS info: $Id: zmapView.h,v 1.57 2010-03-19 08:56:41 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAPVIEW_H
@@ -134,6 +134,7 @@ typedef enum {
ZMAPVIEW_LOADING, /* Loading data. */
ZMAPVIEW_LOADED, /* Full view. */
+ ZMAPVIEW_UPDATING, /* after LOADED we can request more data */
ZMAPVIEW_RESETTING, /* Returning to ZMAPVIEW_NOT_CONNECTED. */
diff --git a/src/zmapConfig/zmapConfigFile.c b/src/zmapConfig/zmapConfigFile.c
index f0794a31c7cc438710335b17dfe997bdecd7f176..af2e4fd0e6a915f9cea91e20efe331bc46b56f1d 100644
--- a/src/zmapConfig/zmapConfigFile.c
+++ b/src/zmapConfig/zmapConfigFile.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 @@
* 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:
* Created: 2009-12-09 12:09:18 (mgh)
- * CVS info: $Id: zmapConfigFile.c,v 1.3 2010-03-04 15:09:42 mh17 Exp $
+ * CVS info: $Id: zmapConfigFile.c,v 1.4 2010-03-19 08:56:41 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -113,9 +113,9 @@ gboolean zMapConfigIniReadBuffer(ZMapConfigIni config, char *buffer)
{
config->buffer_key_file = g_key_file_new();
- if(!(g_key_file_load_from_data(config->buffer_key_file,
+ if(!(g_key_file_load_from_data(config->buffer_key_file,
buffer, strlen(buffer),
- G_KEY_FILE_KEEP_COMMENTS,
+ G_KEY_FILE_KEEP_COMMENTS,
&(config->buffer_key_error))))
{
/* Do something with the error... */
@@ -227,13 +227,13 @@ gboolean zMapConfigIniSaveUser(ZMapConfigIni config)
file_contents = NULL;
}
}
-
+
return saved;
}
-gboolean zMapConfigIniHasStanza(ZMapConfigIni config,char *stanza_name)
+gboolean zMapConfigIniHasStanza(ZMapConfigIni config,char *stanza_name,GKeyFile **which)
{
GKeyFile *files[FILE_COUNT];
gboolean result = FALSE;
@@ -244,13 +244,17 @@ gboolean zMapConfigIniHasStanza(ZMapConfigIni config,char *stanza_name)
files[2] = config->user_key_file;
files[3] = config->extra_key_file;
files[4] = config->buffer_key_file;
-
- for (i = 0; result == FALSE && i < FILE_COUNT; i++)
+
+ for (i = 0;i < FILE_COUNT; i++)
{
if(files[i])
- result = g_key_file_has_group(files[i], stanza_name);
+ result = g_key_file_has_group(files[i], stanza_name);
+ if(result)
+ break;
}
-
+ if(result && which)
+ *which = files[i];
+
return result;
}
diff --git a/src/zmapConfig/zmapConfigIni_P.h b/src/zmapConfig/zmapConfigIni_P.h
index d187cc4fe52cc31099abfcf246686ee60a60c6cd..7b977899e66d172945086ebce8846a6cc1f4f72b 100644
--- a/src/zmapConfig/zmapConfigIni_P.h
+++ b/src/zmapConfig/zmapConfigIni_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.
@@ -23,12 +23,12 @@
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk,
* Rob Clack (Sanger Institute, UK) rnc@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See ZMap/ConfigIni.h
* HISTORY:
* Created: 2009-12-09 13:10:58 (mgh)
- * CVS info: $Id: zmapConfigIni_P.h,v 1.3 2010-03-04 15:09:44 mh17 Exp $
+ * CVS info: $Id: zmapConfigIni_P.h,v 1.4 2010-03-19 08:56:42 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_CONFIGINI_P_H
@@ -62,6 +62,7 @@ typedef struct _ZMapConfigIniStruct
} ZMapConfigIniStruct, *ZMapConfigIni;
+#ifdef MH17_IN_CONFIG_H
/*! @addtogroup zmapconfig
@@ -200,7 +201,7 @@ ZMapConfigStanza zMapConfigGetNextStanza(ZMapConfigStanzaSet stanzas, ZMapConfig
ZMapConfigStanzaElement zMapConfigFindElement(ZMapConfigStanza stanza, char *element_name) ;
void zMapConfigDestroyStanza(ZMapConfigStanza stanza) ;
-
+#endif
ZMapConfigIni zMapConfigIniNew(void) ;
@@ -208,7 +209,7 @@ gboolean zMapConfigIniReadAll(ZMapConfigIni config);
gboolean zMapConfigIniReadUser(ZMapConfigIni config);
gboolean zMapConfigIniReadBuffer(ZMapConfigIni config, char *buffer);
gboolean zMapConfigIniReadFile(ZMapConfigIni config, char *file);
-gboolean zMapConfigIniHasStanza(ZMapConfigIni config,char *stanza_name);
+gboolean zMapConfigIniHasStanza(ZMapConfigIni config,char *stanza_name,GKeyFile **which);
void zMapConfigIniGetStanza(ZMapConfigIni config, char *stanza_name);
void zMapConfigIniGetAllStanzas(ZMapConfigIni config);
void zMapConfigIniGetStanzaValues(ZMapConfigIni, char *stanza_name);
@@ -222,9 +223,9 @@ gboolean zMapConfigIniGetValue(ZMapConfigIni config,
char * key_name,
GValue **value_out,
GType type);
-void zMapConfigIniSetValue(ZMapConfigIni config,
- char *stanza_name,
- char *key_name,
+void zMapConfigIniSetValue(ZMapConfigIni config,
+ char *stanza_name,
+ char *key_name,
GValue *value);
gboolean zMapConfigIniSaveUser(ZMapConfigIni config);
void zMapConfigIniDestroy(ZMapConfigIni config, gboolean save_user);
diff --git a/src/zmapConfig/zmapConfigLoader.c b/src/zmapConfig/zmapConfigLoader.c
index c2d66701aecd85a5016136e2112eb50f1af50a7d..4a5f9b3df74c9b25aebfed66273e4f9e238cf5c1 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 1.8 2010-03-10 14:14:49 mh17 Exp $
+ * CVS info: $Id: zmapConfigLoader.c,v 1.9 2010-03-19 08:56:42 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -43,7 +43,7 @@
#include <ZMap/zmapConfigIni.h>
#include <ZMap/zmapConfigStrings.h>
#include <ZMap/zmapConfigStanzaStructs.h>
-
+#include <ZMap/zmapGFF.h>
static ZMapConfigIniContextKeyEntry get_app_group_data(char **stanza_name, char **stanza_type);
@@ -316,7 +316,7 @@ static void fetch_referenced_stanzas(gpointer list_data, gpointer user_data)
full_data->current_stanza_name = stanza_name;
- if (zMapConfigIniHasStanza(full_data->context->config, stanza_name) && (full_data->object_create_func))
+ if (zMapConfigIniHasStanza(full_data->context->config, stanza_name,NULL) && (full_data->object_create_func))
{
if ((full_data->current_object = (full_data->object_create_func)()))
{
@@ -655,7 +655,43 @@ gboolean zMapConfigIniGetStylesFromFile(char *styles_list, char *styles_file, GD
+/*
+ * read the [featuresets] stanza and put it in a hash table
+ * NOTE: this function operates differently from normal ConfigIni in that we do not know
+ * the names of the keys in the stanza and cannot create a struct to hold these and thier values
+ * So instead we have to use GLib directly.
+ * the strings need to be quarked first
+ */
+GHashTable *zMapConfigIniGetSource2Featureset(ZMapConfigIniContext context)
+{
+ GHashTable *hash = NULL;
+ GKeyFile *gkf;
+ gchar ** keys = NULL;
+ gsize len,n_source;
+ gchar **sources;
+ ZMapGFFSet GFFset;
+
+ if(zMapConfigIniHasStanza(context->config,ZMAPSTANZA_FEATURESET_CONFIG,&gkf))
+ {
+ hash = g_hash_table_new(NULL,NULL);
+
+ keys = g_key_file_get_keys(gkf,ZMAPSTANZA_FEATURESET_CONFIG,&len,NULL);
+ for(;len--;keys++)
+ {
+ sources = g_key_file_get_string_list(gkf,ZMAPSTANZA_FEATURESET_CONFIG,*keys,&n_source,NULL);
+
+ GFFset = g_new0(ZMapGFFSetStruct,1);
+ GFFset->feature_set_id = g_quark_from_string(*keys);
+ GFFset->description = g_strdup(*keys);
+
+ while(n_source--)
+ g_hash_table_insert(hash,GUINT_TO_POINTER(g_quark_from_string(*sources++)),GFFset);
+ }
+ }
+
+ return(hash);
+}
@@ -1016,7 +1052,7 @@ static ZMapConfigIniContextKeyEntry get_source_group_data(char **stanza_name, ch
{ ZMAPSTANZA_SOURCE_FEATURESETS, G_TYPE_STRING, source_set_property, FALSE },
{ ZMAPSTANZA_SOURCE_STYLES, G_TYPE_STRING, source_set_property, FALSE },
{ ZMAPSTANZA_SOURCE_NAVIGATORSETS, G_TYPE_STRING, source_set_property, FALSE },
- { ZMAPSTANZA_SOURCE_SEQUENCE, G_TYPE_BOOLEAN, source_set_property, FALSE },
+// { ZMAPSTANZA_SOURCE_SEQUENCE, G_TYPE_BOOLEAN, source_set_property, FALSE },
{ ZMAPSTANZA_SOURCE_WRITEBACK, G_TYPE_BOOLEAN, source_set_property, FALSE },
{ ZMAPSTANZA_SOURCE_FORMAT, G_TYPE_STRING, source_set_property, FALSE },
{ ZMAPSTANZA_SOURCE_DELAYED, G_TYPE_BOOLEAN, source_set_property, FALSE },
@@ -1058,8 +1094,8 @@ static void source_set_property(char *current_stanza_name, char *key, GType type
str_ptr = &(config_source->navigatorsets) ;
else if (g_ascii_strcasecmp(key, ZMAPSTANZA_SOURCE_TIMEOUT) == 0)
int_ptr = &(config_source->timeout) ;
- else if (g_ascii_strcasecmp(key, ZMAPSTANZA_SOURCE_SEQUENCE) == 0)
- bool_ptr = &(config_source->sequence) ;
+// else if (g_ascii_strcasecmp(key, ZMAPSTANZA_SOURCE_SEQUENCE) == 0)
+// bool_ptr = &(config_source->sequence) ;
else if (g_ascii_strcasecmp(key, ZMAPSTANZA_SOURCE_WRITEBACK) == 0)
bool_ptr = &(config_source->writeback) ;
else if (g_ascii_strcasecmp(key, ZMAPSTANZA_SOURCE_FORMAT) == 0)
diff --git a/src/zmapFeature/zmapFeature.c b/src/zmapFeature/zmapFeature.c
index 397a528a3b976da17c93201fbf7b972a3ce67009..c82811248a8a8cb5a88d7028ee52484795712422 100755
--- a/src/zmapFeature/zmapFeature.c
+++ b/src/zmapFeature/zmapFeature.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.
@@ -24,12 +24,12 @@
*
* Description: Implements feature contexts, sets and features themselves.
* Includes code to create/merge/destroy contexts and sets.
- *
+ *
* Exported functions: See zmapView_P.h
* HISTORY:
* Last edited: Dec 14 11:20 2009 (edgrif)
* Created: Fri Jul 16 13:05:58 2004 (edgrif)
- * CVS info: $Id: zmapFeature.c,v 1.122 2010-03-04 15:10:19 mh17 Exp $
+ * CVS info: $Id: zmapFeature.c,v 1.123 2010-03-19 08:56:42 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -46,9 +46,9 @@
/*! @defgroup zmapfeatures zMapFeatures: feature handling for ZMap
* @{
- *
+ *
* \brief Feature handling for ZMap.
- *
+ *
* zMapFeatures routines provide functions to create/modify/destroy individual
* features, sets of features and feature contexts (contexts are sets of sets
* of features with associated coordinate data for parent mapping etc.).
@@ -151,21 +151,21 @@ static void printDestroyDebugInfo(ZMapFeatureAny any, char *who) ;
static gboolean checkForPerfectAlign(GArray *gaps, unsigned int align_error) ;
-static ZMapFeatureContextExecuteStatus eraseContextCB(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus eraseContextCB(GQuark key,
+ gpointer data,
gpointer user_data,
char **err_out);
-static ZMapFeatureContextExecuteStatus destroyIfEmptyContextCB(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus destroyIfEmptyContextCB(GQuark key,
+ gpointer data,
gpointer user_data,
char **err_out);
-static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
+ gpointer data,
gpointer user_data,
char **err_out);
-static ZMapFeatureContextExecuteStatus addModeCB(GQuark key_id,
- gpointer data,
+static ZMapFeatureContextExecuteStatus addModeCB(GQuark key_id,
+ gpointer data,
gpointer user_data,
char **error_out) ;
static void addFeatureModeCB(gpointer key, gpointer data, gpointer user_data) ;
@@ -247,7 +247,7 @@ gboolean zMapFeatureAnyRemoveFeature(ZMapFeatureAny feature_parent, ZMapFeatureA
{
result = g_hash_table_steal(feature_parent->children, zmapFeature2HashKey(feature)) ;
feature->parent = NULL;
-
+
switch(feature->struct_type)
{
case ZMAPFEATURE_STRUCT_CONTEXT:
@@ -283,10 +283,10 @@ gboolean zMapFeatureAnyRemoveFeature(ZMapFeatureAny feature_parent, ZMapFeatureA
/* go through all the feature sets in the given AnyFeature (must be at least a feature set)
* and set the style mode from that...a bit hacky really...think about this....
- *
+ *
* Really this is all acedb methods which are not rich enough for what we want to set
* in our styles...
- *
+ *
* */
gboolean zMapFeatureAnyAddModesToStyles(ZMapFeatureAny feature_any, GData *styles)
{
@@ -297,7 +297,7 @@ gboolean zMapFeatureAnyAddModesToStyles(ZMapFeatureAny feature_any, GData *style
hack.force = FALSE ;
hack.styles = styles ;
- zMapFeatureContextExecuteSubset(feature_any,
+ zMapFeatureContextExecuteSubset(feature_any,
ZMAPFEATURE_STRUCT_FEATURESET,
addModeCB,
&hack) ;
@@ -326,7 +326,7 @@ gboolean zMapFeatureAnyForceModesToStyles(ZMapFeatureAny feature_any, GData *sty
#warning This function should be removed... and zMapFeatureAnyAddModesToStyles used instead.
- zMapFeatureContextExecuteSubset(feature_any,
+ zMapFeatureContextExecuteSubset(feature_any,
ZMAPFEATURE_STRUCT_FEATURESET,
addModeCB,
&hack) ;
@@ -409,12 +409,12 @@ ZMapFeatureAny zmapFeatureAnyCopy(ZMapFeatureAny orig_feature_any, GDestroyNotif
}
case ZMAPFEATURE_STRUCT_BLOCK:
{
- ZMapFeatureBlock new_block = (ZMapFeatureBlock)new_feature_any ;
+ ZMapFeatureBlock new_block = (ZMapFeatureBlock)new_feature_any ;
new_block->sequence.type = ZMAPSEQUENCE_NONE ;
new_block->sequence.length = 0 ;
new_block->sequence.sequence = NULL ;
-
+
break;
}
case ZMAPFEATURE_STRUCT_FEATURESET:
@@ -437,15 +437,15 @@ ZMapFeatureAny zmapFeatureAnyCopy(ZMapFeatureAny orig_feature_any, GDestroyNotif
{
int i ;
- new_feature->feature.homol.align =
- g_array_sized_new(FALSE, TRUE,
+ new_feature->feature.homol.align =
+ g_array_sized_new(FALSE, TRUE,
sizeof(ZMapAlignBlockStruct),
orig_feature->feature.homol.align->len);
for (i = 0; i < orig_feature->feature.homol.align->len; i++)
{
align = g_array_index(orig_feature->feature.homol.align, ZMapAlignBlockStruct, i);
- new_feature->feature.homol.align =
+ new_feature->feature.homol.align =
g_array_append_val(new_feature->feature.homol.align, align);
}
}
@@ -458,15 +458,15 @@ ZMapFeatureAny zmapFeatureAnyCopy(ZMapFeatureAny orig_feature_any, GDestroyNotif
if (orig_feature->feature.transcript.exons != NULL
&& orig_feature->feature.transcript.exons->len > (guint)0)
{
- new_feature->feature.transcript.exons =
- g_array_sized_new(FALSE, TRUE,
+ new_feature->feature.transcript.exons =
+ g_array_sized_new(FALSE, TRUE,
sizeof(ZMapSpanStruct),
orig_feature->feature.transcript.exons->len);
for (i = 0; i < orig_feature->feature.transcript.exons->len; i++)
{
span = g_array_index(orig_feature->feature.transcript.exons, ZMapSpanStruct, i);
- new_feature->feature.transcript.exons =
+ new_feature->feature.transcript.exons =
g_array_append_val(new_feature->feature.transcript.exons, span);
}
}
@@ -474,15 +474,15 @@ ZMapFeatureAny zmapFeatureAnyCopy(ZMapFeatureAny orig_feature_any, GDestroyNotif
if (orig_feature->feature.transcript.introns != NULL
&& orig_feature->feature.transcript.introns->len > (guint)0)
{
- new_feature->feature.transcript.introns =
- g_array_sized_new(FALSE, TRUE,
+ new_feature->feature.transcript.introns =
+ g_array_sized_new(FALSE, TRUE,
sizeof(ZMapSpanStruct),
orig_feature->feature.transcript.introns->len);
for (i = 0; i < orig_feature->feature.transcript.introns->len; i++)
{
span = g_array_index(orig_feature->feature.transcript.introns, ZMapSpanStruct, i);
- new_feature->feature.transcript.introns =
+ new_feature->feature.transcript.introns =
g_array_append_val(new_feature->feature.transcript.introns, span);
}
}
@@ -516,7 +516,7 @@ void zMapFeatureAnyDestroy(ZMapFeatureAny feature_any)
/*!
* Returns a single feature correctly intialised to be a "NULL" feature.
- *
+ *
* @param void None.
* @return ZMapFeature A pointer to the new ZMapFeature.
* */
@@ -558,7 +558,7 @@ ZMapFeature zMapFeatureCreateFromStandardData(char *name, char *sequence, char *
if ((feature_name_id = zMapFeatureCreateName(feature_type, name, strand,
start, end, 0, 0)) != NULL)
{
- if ((good = zMapFeatureAddStandardData(feature, feature_name_id,
+ if ((good = zMapFeatureAddStandardData(feature, feature_name_id,
name, sequence, ontology,
feature_type, style,
start, end, has_score, score,
@@ -620,7 +620,7 @@ gboolean zMapFeatureAddStandardData(ZMapFeature feature, char *feature_name_id,
/*!
* Adds data to a feature which may be empty or may already have partial features,
* e.g. transcript that does not yet have all its exons.
- *
+ *
* NOTE that really we need this to be a polymorphic function so that the arguments
* are different for different features.
* */
@@ -649,7 +649,7 @@ gboolean zMapFeatureAddKnownName(ZMapFeature feature, char *known_name)
/*!
* Adds data to a feature which may be empty or may already have partial features,
* e.g. transcript that does not yet have all its exons.
- *
+ *
* NOTE that really we need this to be a polymorphic function so that the arguments
* are different for different features.
* */
@@ -683,7 +683,7 @@ gboolean zMapFeatureAddTranscriptData(ZMapFeature feature,
/*!
* Adds data to a feature which may be empty or may already have partial features,
* e.g. transcript that does not yet have all its exons.
- *
+ *
* NOTE that really we need this to be a polymorphic function so that the arguments
* are different for different features.
* */
@@ -811,7 +811,7 @@ gboolean zMapFeatureAddAlignmentData(ZMapFeature feature,
feature->feature.homol.flags.perfect = checkForPerfectAlign(feature->feature.homol.align, align_error) ;
}
-
+
return result ;
}
@@ -833,7 +833,7 @@ gboolean zMapFeatureAddAssemblyPathData(ZMapFeature feature,
result = TRUE ;
}
-
+
return result ;
}
@@ -895,7 +895,7 @@ gboolean zMapFeatureAddText(ZMapFeature feature, GQuark source_id, char *source_
/*!
* Returns the length of a feature. For a simple feature this is just (end - start + 1),
* for transcripts and alignments the exons or blocks must be totalled up.
- *
+ *
* @param feature Feature for which length is required.
* @param length_type Length in target sequence coords or query sequence coords or spliced length.
* @return nothing.
@@ -988,7 +988,7 @@ int zMapFeatureLength(ZMapFeature feature, ZMapFeatureLengthType length_type)
/*!
* Destroys a feature, freeing up all of its resources.
- *
+ *
* @param feature The feature to be destroyed.
* @return nothing.
* */
@@ -1007,7 +1007,7 @@ void zMapFeatureDestroy(ZMapFeature feature)
-/*
+/*
* Feature Set functions.
*/
@@ -1054,7 +1054,7 @@ ZMapFeatureSet zMapFeatureSetIDCreate(GQuark original_id, GQuark unique_id,
/* Feature must not be null to be added we need at least the feature id and probably should.
* check for more.
- *
+ *
* Returns FALSE if feature is already in set.
* */
gboolean zMapFeatureSetAddFeature(ZMapFeatureSet feature_set, ZMapFeature feature)
@@ -1068,7 +1068,7 @@ gboolean zMapFeatureSetAddFeature(ZMapFeatureSet feature_set, ZMapFeature featur
/* Returns TRUE if the feature could be found in the feature_set, FALSE otherwise. */
-gboolean zMapFeatureSetFindFeature(ZMapFeatureSet feature_set,
+gboolean zMapFeatureSetFindFeature(ZMapFeatureSet feature_set,
ZMapFeature feature)
{
gboolean result = FALSE ;
@@ -1091,7 +1091,7 @@ ZMapFeature zMapFeatureSetGetFeatureByID(ZMapFeatureSet feature_set, GQuark feat
/* Feature must exist in set to be removed.
- *
+ *
* Returns FALSE if feature is not in set.
* */
gboolean zMapFeatureSetRemoveFeature(ZMapFeatureSet feature_set, ZMapFeature feature)
@@ -1192,7 +1192,7 @@ void zMapFeatureSetDestroyFeatures(ZMapFeatureSet feature_set)
-/*
+/*
* Alignment functions
*/
@@ -1207,7 +1207,7 @@ GQuark zMapFeatureAlignmentCreateID(char *align_name, gboolean master_alignment)
unique_name = g_strdup(align_name) ;
id = g_quark_from_string(unique_name) ;
-
+
g_free(unique_name);
return id;
@@ -1242,7 +1242,7 @@ gboolean zMapFeatureAlignmentAddBlock(ZMapFeatureAlignment alignment, ZMapFeatur
}
-gboolean zMapFeatureAlignmentFindBlock(ZMapFeatureAlignment feature_align,
+gboolean zMapFeatureAlignmentFindBlock(ZMapFeatureAlignment feature_align,
ZMapFeatureBlock feature_block)
{
gboolean result = FALSE;
@@ -1257,7 +1257,7 @@ gboolean zMapFeatureAlignmentFindBlock(ZMapFeatureAlignment feature_align,
ZMapFeatureBlock zMapFeatureAlignmentGetBlockByID(ZMapFeatureAlignment feature_align, GQuark block_id)
{
ZMapFeatureBlock feature_block = NULL;
-
+
feature_block = (ZMapFeatureBlock)zMapFeatureAnyGetFeatureByID((ZMapFeatureAny)feature_align, block_id) ;
return feature_block ;
@@ -1343,7 +1343,7 @@ gboolean zMapFeatureBlockSetFeaturesCoords(ZMapFeatureBlock feature_block,
}
-gboolean zMapFeatureBlockAddFeatureSet(ZMapFeatureBlock feature_block,
+gboolean zMapFeatureBlockAddFeatureSet(ZMapFeatureBlock feature_block,
ZMapFeatureSet feature_set)
{
gboolean result = FALSE ;
@@ -1379,7 +1379,7 @@ ZMapFeatureSet zMapFeatureBlockGetSetByID(ZMapFeatureBlock feature_block, GQuark
}
-gboolean zMapFeatureBlockRemoveFeatureSet(ZMapFeatureBlock feature_block,
+gboolean zMapFeatureBlockRemoveFeatureSet(ZMapFeatureBlock feature_block,
ZMapFeatureSet feature_set)
{
gboolean result = FALSE;
@@ -1451,10 +1451,10 @@ gboolean zMapFeatureContextFindAlignment(ZMapFeatureContext feature_context,
result = zMapFeatureAnyFindFeature((ZMapFeatureAny)feature_context, (ZMapFeatureAny)feature_align) ;
- return result;
+ return result;
}
-ZMapFeatureAlignment zMapFeatureContextGetAlignmentByID(ZMapFeatureContext feature_context,
+ZMapFeatureAlignment zMapFeatureContextGetAlignmentByID(ZMapFeatureContext feature_context,
GQuark align_id)
{
ZMapFeatureAlignment feature_align ;
@@ -1475,7 +1475,7 @@ gboolean zMapFeatureContextRemoveAlignment(ZMapFeatureContext feature_context,
if ((result = zMapFeatureAnyRemoveFeature((ZMapFeatureAny)feature_context, (ZMapFeatureAny)feature_alignment)))
{
if(feature_context->master_align == feature_alignment)
- feature_context->master_align = NULL;
+ feature_context->master_align = NULL;
}
return result;
@@ -1494,17 +1494,17 @@ gboolean zMapFeatureContextRemoveAlignment(ZMapFeatureContext feature_context,
* of those in the current context. Hence we end up with a context where we
* want to destroy some features (the duplicates) but not others (the ones that
* are just pointers to features in the current context).
- *
+ *
* So for the diff_context we don't set destroy functions when the context
* is created, instead we keep a separate hash of duplicate features to be destroyed.
- *
+ *
* If hashtables supported setting a destroy function for each element we
* wouldn't need to do this, but they don't (unlike g_datalists, we don't
* use those because they are too slow).
- *
+ *
* If all ok returns ZMAPFEATURE_CONTEXT_OK, merged context in merged_context_inout
* and diff context in diff_context_out. Otherwise returns a code to show what went
- * wrong, unaltered original context in merged_context_inout and diff_context_out is NULL,
+ * wrong, unaltered original context in merged_context_inout and diff_context_out is NULL,
*/
/* N.B. under new scheme, new_context_inout will be always be destroyed && NULL'd.... */
@@ -1553,7 +1553,7 @@ ZMapFeatureContextMergeCode zMapFeatureContextMerge(ZMapFeatureContext *merged_c
merge_data.diff_context = diff_context ;
merge_data.status = ZMAP_CONTEXT_EXEC_STATUS_OK ;
merge_data.new_features = FALSE ;
-
+
/* THIS LOOKS SUSPECT...WHY ISN'T THE NAMES LIST COPIED FROM NEW_CONTEXT....*/
copy_features = g_list_copy(new_context->feature_set_names) ;
@@ -1595,12 +1595,19 @@ ZMapFeatureContextMergeCode zMapFeatureContextMerge(ZMapFeatureContext *merged_c
{
/* Debug stuff... */
GError *err = NULL ;
-
+
printf("(Merge) full context:\n") ;
zMapFeatureDumpStdOutFeatures(current_context, current_context->styles, &err) ;
}
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+#ifndef MH17_NEVER
+ {
+ GError *err = NULL;
+ zMapFeatureDumpToFileName(diff_context,"features.txt","(Merge) diff context:\n", NULL, &err) ;
+ zMapFeatureDumpToFileName(current_context,"features.txt","(Merge) full context:\n", NULL, &err) ;
+ }
+#endif
status = ZMAPFEATURE_CONTEXT_OK ;
}
else
@@ -1652,7 +1659,7 @@ gboolean zMapFeatureContextErase(ZMapFeatureContext *current_context_inout,
zMapAssert(current_context_inout && remove_context && diff_context_out) ;
current_context = *current_context_inout ;
-
+
diff_context = zMapFeatureContextCreate(NULL, 0, 0, NULL);
diff_context->diff_context = TRUE;
diff_context->elements_to_destroy = g_hash_table_new_full(NULL, NULL, NULL, destroyFeatureAny);
@@ -1671,7 +1678,7 @@ gboolean zMapFeatureContextErase(ZMapFeatureContext *current_context_inout,
merge_data.iteration_context = remove_context;
merge_data.diff_context = diff_context;
merge_data.status = ZMAP_CONTEXT_EXEC_STATUS_OK;
-
+
/* LOOKS SUSPECT...SHOULD BE COPIED....*/
diff_context->feature_set_names = g_list_copy(remove_context->feature_set_names) ;
@@ -1679,19 +1686,19 @@ gboolean zMapFeatureContextErase(ZMapFeatureContext *current_context_inout,
copy_list = g_list_copy(remove_context->feature_set_names) ;
current_context->feature_set_names = g_list_concat(current_context->feature_set_names,
copy_list) ;
-
+
/* Set the original and unique ids so that the context passes the feature validity checks */
- diff_context_string = g_strdup_printf("%s vs %s\n",
+ diff_context_string = g_strdup_printf("%s vs %s\n",
g_quark_to_string(current_context->unique_id),
g_quark_to_string(remove_context->unique_id));
- diff_context->original_id =
+ diff_context->original_id =
diff_context->unique_id = g_quark_from_string(diff_context_string);
g_free(diff_context_string);
-
+
zMapFeatureContextExecuteRemoveSafe((ZMapFeatureAny)remove_context, ZMAPFEATURE_STRUCT_FEATURE,
eraseContextCB, destroyIfEmptyContextCB, &merge_data);
-
+
if(merge_data.status == ZMAP_CONTEXT_EXEC_STATUS_OK)
{
@@ -1705,13 +1712,13 @@ gboolean zMapFeatureContextErase(ZMapFeatureContext *current_context_inout,
if(merge_erase_dump_context_G)
{
GError *err = NULL;
-
+
printf("(Erase) diff context:\n") ;
zMapFeatureDumpStdOutFeatures(diff_context, diff_context->styles, &err) ;
-
+
printf("(Erase) full context:\n") ;
zMapFeatureDumpStdOutFeatures(current_context, current_context->styles, &err) ;
-
+
}
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
@@ -1745,8 +1752,8 @@ void zMapFeatureContextDestroy(ZMapFeatureContext feature_context, gboolean free
-/*
- * Internal routines.
+/*
+ * Internal routines.
*/
@@ -1892,11 +1899,11 @@ static gboolean withdrawFeatureAny(gpointer key, gpointer value, gpointer user_d
/* Returns TRUE if the target blocks match coords are within align_error bases of each other, if
* there are less than two blocks then FALSE is returned.
- *
+ *
* Sometimes, for reasons I don't understand, its possible to have two butting matches, i.e. they
* should really be one continuous match. It may be that this happens at a clone boundary, I don't
* try to correct this because really its a data entry problem.
- *
+ *
* */
static gboolean checkForPerfectAlign(GArray *gaps, unsigned int align_error)
{
@@ -1947,8 +1954,8 @@ static gboolean checkForPerfectAlign(GArray *gaps, unsigned int align_error)
return perfect_align ;
}
-static ZMapFeatureContextExecuteStatus eraseContextCB(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus eraseContextCB(GQuark key,
+ gpointer data,
gpointer user_data,
char **err_out)
{
@@ -1967,18 +1974,18 @@ static ZMapFeatureContextExecuteStatus eraseContextCB(GQuark key,
case ZMAPFEATURE_STRUCT_CONTEXT:
break;
case ZMAPFEATURE_STRUCT_ALIGN:
- merge_data->current_view_align =
- (ZMapFeatureAny)(zMapFeatureContextGetAlignmentByID(merge_data->view_context,
+ merge_data->current_view_align =
+ (ZMapFeatureAny)(zMapFeatureContextGetAlignmentByID(merge_data->view_context,
key));
break;
case ZMAPFEATURE_STRUCT_BLOCK:
- merge_data->current_view_block = zMapFeatureAnyGetFeatureByID(merge_data->current_view_align,
+ merge_data->current_view_block = zMapFeatureAnyGetFeatureByID(merge_data->current_view_align,
key);
break;
case ZMAPFEATURE_STRUCT_FEATURESET:
- merge_data->current_view_set = zMapFeatureAnyGetFeatureByID(merge_data->current_view_block,
+ merge_data->current_view_set = zMapFeatureAnyGetFeatureByID(merge_data->current_view_block,
key);
- break;
+ break;
case ZMAPFEATURE_STRUCT_FEATURE:
/* look up in the current */
@@ -1990,10 +1997,10 @@ static ZMapFeatureContextExecuteStatus eraseContextCB(GQuark key,
if(merge_debug_G)
zMapLogWarning("%s","\tFeature in erase and current contexts...");
- /* insert into the diff context.
+ /* insert into the diff context.
* BUT, need to check if the parents exist in the diff context first.
*/
- if (!merge_data->current_diff_align)
+ if (!merge_data->current_diff_align)
{
if(merge_debug_G)
zMapLogWarning("%s","\tno parent align... creating align in diff");
@@ -2001,12 +2008,12 @@ static ZMapFeatureContextExecuteStatus eraseContextCB(GQuark key,
merge_data->current_diff_align
= featureAnyCreateFeature(merge_data->current_view_align->struct_type,
NULL,
- merge_data->current_view_align->original_id,
+ merge_data->current_view_align->original_id,
merge_data->current_view_align->unique_id,
NULL) ;
-
- zMapFeatureContextAddAlignment(merge_data->diff_context,
- (ZMapFeatureAlignment)merge_data->current_diff_align,
+
+ zMapFeatureContextAddAlignment(merge_data->diff_context,
+ (ZMapFeatureAlignment)merge_data->current_diff_align,
FALSE);
}
if (!merge_data->current_diff_block)
@@ -2021,7 +2028,7 @@ static ZMapFeatureContextExecuteStatus eraseContextCB(GQuark key,
merge_data->current_view_block->unique_id,
NULL) ;
- zMapFeatureAlignmentAddBlock((ZMapFeatureAlignment)merge_data->current_diff_align,
+ zMapFeatureAlignmentAddBlock((ZMapFeatureAlignment)merge_data->current_diff_align,
(ZMapFeatureBlock)merge_data->current_diff_block);
}
if(!merge_data->current_diff_set)
@@ -2036,19 +2043,19 @@ static ZMapFeatureContextExecuteStatus eraseContextCB(GQuark key,
merge_data->current_view_set->unique_id,
NULL) ;
- zMapFeatureBlockAddFeatureSet((ZMapFeatureBlock)merge_data->current_diff_block,
- (ZMapFeatureSet)merge_data->current_diff_set);
+ zMapFeatureBlockAddFeatureSet((ZMapFeatureBlock)merge_data->current_diff_block,
+ (ZMapFeatureSet)merge_data->current_diff_set);
}
if(merge_debug_G)
zMapLogWarning("%s","\tmoving feature from current to diff context ... removing ... and inserting.");
/* remove from the current context.*/
- remove_status = zMapFeatureSetRemoveFeature((ZMapFeatureSet)merge_data->current_view_set,
+ remove_status = zMapFeatureSetRemoveFeature((ZMapFeatureSet)merge_data->current_view_set,
erased_feature);
zMapAssert(remove_status);
- zMapFeatureSetAddFeature((ZMapFeatureSet)merge_data->current_diff_set,
+ zMapFeatureSetAddFeature((ZMapFeatureSet)merge_data->current_diff_set,
erased_feature);
#ifdef MESSES_UP_HASH
@@ -2066,7 +2073,7 @@ static ZMapFeatureContextExecuteStatus eraseContextCB(GQuark key,
if(merge_debug_G)
zMapLogWarning("%s","\tFeature absent from current context, nothing to do...");
/* no ...
- * leave in the erase context.
+ * leave in the erase context.
*/
}
break;
@@ -2077,8 +2084,8 @@ static ZMapFeatureContextExecuteStatus eraseContextCB(GQuark key,
return status ;
}
-static ZMapFeatureContextExecuteStatus destroyIfEmptyContextCB(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus destroyIfEmptyContextCB(GQuark key,
+ gpointer data,
gpointer user_data,
char **err_out)
{
@@ -2107,7 +2114,7 @@ static ZMapFeatureContextExecuteStatus destroyIfEmptyContextCB(GQuark key,
#endif /* MESSES_UP_HASH */
status = ZMAP_CONTEXT_EXEC_STATUS_OK_DELETE;
}
- merge_data->current_diff_align =
+ merge_data->current_diff_align =
merge_data->current_view_align = NULL;
break;
case ZMAPFEATURE_STRUCT_BLOCK:
@@ -2152,8 +2159,8 @@ static ZMapFeatureContextExecuteStatus destroyIfEmptyContextCB(GQuark key,
/* It's very important to note that the diff context hash tables _do_not_ have destroy functions,
* this is what prevents them from freeing their children. */
-static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
+ gpointer data,
gpointer user_data,
char **err_out)
{
@@ -2199,7 +2206,7 @@ static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
default:
zMapAssertNotReached();
}
-
+
switch(feature_any->struct_type)
{
@@ -2249,7 +2256,7 @@ static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
merge_data->new_features = new = TRUE; /* This is a NEW feature. */
- /* We would use featureAnyAddFeature, but it does another
+ /* We would use featureAnyAddFeature, but it does another
* g_hash_table_lookup... */
g_hash_table_insert((*view_path_parent_ptr)->children,
zmapFeature2HashKey(feature_any),
@@ -2259,7 +2266,7 @@ static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
/* update the path */
*view_path_ptr = feature_any;
-
+
diff_feature_any = feature_any;
diff_feature_any->parent = *view_path_parent_ptr;
@@ -2275,7 +2282,7 @@ static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
featureAnyAddToDestroyList(merge_data->diff_context, diff_feature_any);
}
- // mh17:
+ // mh17:
// 1) featureAnyAddFeature checks to see if it's there first, which we just did :-(
// 2) look at the comment 25 lines above about not using featureAnyAddFeature
featureAnyAddFeature(*diff_path_parent_ptr, diff_feature_any);
@@ -2297,7 +2304,7 @@ static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
}
/* general code stop */
-
+
#ifdef NO_IDEA_WHAT_SHOULD_HAPPEN_HERE
/* possibly nothing... unsure where the master alignment status [will] comes from. */
@@ -2305,7 +2312,7 @@ static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
if(is_master_align && feature_any->struct_type == ZMAPFEATURE_STRUCT_ALIGN)
{
merge_data->diff_context->master_align = (ZMapFeatureAlignment)diff_feature_any;
- }
+ }
#endif /* NO_IDEA_WHAT_SHOULD_HAPPEN_HERE */
}
break;
@@ -2313,14 +2320,14 @@ static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
{
zMapAssert(view_path_parent_ptr && *view_path_parent_ptr &&
diff_path_parent_ptr && *diff_path_parent_ptr);
-
+
feature_any->parent = NULL;
status = ZMAP_CONTEXT_EXEC_STATUS_OK_DELETE;
if (!(zMapFeatureAnyGetFeatureByID(*view_path_parent_ptr, feature_any->unique_id)))
{
merge_data->new_features = new = TRUE;
-
+
featureAnyAddFeature(*diff_path_parent_ptr, feature_any);
featureAnyAddFeature(*view_path_parent_ptr, feature_any);
@@ -2381,7 +2388,7 @@ static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
/* but we need to reset parent pointer....*/
diff_align->parent = (ZMapFeatureAny)(merge_data->view_context) ;
-
+
status = ZMAP_CONTEXT_EXEC_STATUS_DONT_DESCEND ;
}
else
@@ -2435,7 +2442,7 @@ static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
/* add to the full context align */
zMapFeatureAlignmentAddBlock(merge_data->current_view_align, feature_block);
merge_data->current_view_block = feature_block ;
-
+
merge_data->new_features = new = TRUE ;
/* If its new we can simply copy a pointer over to the diff context
@@ -2444,7 +2451,7 @@ static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
/* but we need to reset parent pointer....*/
diff_block->parent = (ZMapFeatureAny)(merge_data->current_view_align) ;
-
+
status = ZMAP_CONTEXT_EXEC_STATUS_DONT_DESCEND ;
}
@@ -2497,10 +2504,10 @@ static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
/* If its new we can simply copy a pointer over to the diff context
* and stop recursing.... */
diff_set = (ZMapFeatureAny)feature_set ;
-
+
/* but we need to reset parent pointer....*/
diff_set->parent = (ZMapFeatureAny)(merge_data->current_view_block) ;
-
+
status = ZMAP_CONTEXT_EXEC_STATUS_DONT_DESCEND ;
}
@@ -2549,7 +2556,7 @@ static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
* and stop recursing.... */
diff_feature = (ZMapFeatureAny)feature ;
-
+
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
/* I don't think we need to do this because features do not have children. */
@@ -2557,7 +2564,7 @@ static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
status = ZMAP_CONTEXT_EXEC_STATUS_DONT_DESCEND ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
- /* We need to reset parent pointer....and the style pointer....
+ /* We need to reset parent pointer....and the style pointer....
* order is critical here since featureany call resets parent... */
featureAnyAddFeature((ZMapFeatureAny)merge_data->current_diff_set, diff_feature) ;
@@ -2569,7 +2576,7 @@ static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
zMapLogWarning("feature(%p)->parent = %p. current_view_set = %p",
feature, feature->parent, merge_data->current_view_set);
}
-
+
break;
}
#endif /* GENERALISING */
@@ -2595,7 +2602,7 @@ static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
-/*
+/*
* Following functions all operate on any feature type,
* they were written to reduce duplication of code.
*/
@@ -2708,7 +2715,7 @@ static gboolean destroyFeatureAnyWithChildren(ZMapFeatureAny feature_any, gboole
zMapAssert(g_hash_table_size(feature_any->children) == 0) ;
result = TRUE ;
}
- }
+ }
/* Now destroy the feature. */
if (result)
@@ -2732,8 +2739,8 @@ static void featureAnyAddToDestroyList(ZMapFeatureContext context, ZMapFeatureAn
}
-static ZMapFeatureContextExecuteStatus addModeCB(GQuark key_id,
- gpointer data,
+static ZMapFeatureContextExecuteStatus addModeCB(GQuark key_id,
+ gpointer data,
gpointer user_data,
char **error_out)
{
@@ -2755,7 +2762,7 @@ static ZMapFeatureContextExecuteStatus addModeCB(GQuark key_id,
case ZMAPFEATURE_STRUCT_FEATURESET:
{
hack->feature_set = (ZMapFeatureSet)feature_any ;
-
+
g_hash_table_foreach(hack->feature_set->features, addFeatureModeCB, hack) ;
break;
@@ -2779,10 +2786,10 @@ static ZMapFeatureContextExecuteStatus addModeCB(GQuark key_id,
* 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.
- *
+ *
* Note that I'm setting some other style data here because we need different default bumping
* modes etc for different feature types....
- *
+ *
* */
static void addFeatureModeCB(gpointer key, gpointer data, gpointer user_data)
{
@@ -2806,7 +2813,7 @@ static void addFeatureModeCB(gpointer key, gpointer data, gpointer user_data)
else
g_warning("Force=TRUE and style '%s' has no mode (Could have used zMapFeatureAnyAddModesToStyles)", g_quark_to_string(feature->style_id));
}
-
+
if (force || !zMapStyleHasMode(style))
{
ZMapStyleMode mode ;
diff --git a/src/zmapFeature/zmapFeatureOutput.c b/src/zmapFeature/zmapFeatureOutput.c
index 07ca72a122f96ecc17fc92b2b2792c5451759564..0957c41a8458f08b9640d503aefdd5b2b8053710 100755
--- a/src/zmapFeature/zmapFeatureOutput.c
+++ b/src/zmapFeature/zmapFeatureOutput.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.
@@ -23,17 +23,19 @@
* 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 1 11:32 2009 (edgrif)
* Created: Tue Oct 28 16:20:33 2008 (rds)
- * CVS info: $Id: zmapFeatureOutput.c,v 1.8 2010-03-04 15:10:26 mh17 Exp $
+ * CVS info: $Id: zmapFeatureOutput.c,v 1.9 2010-03-19 08:56:42 mh17 Exp $
*-------------------------------------------------------------------
*/
#include <unistd.h> /* STDOUT_FILENO */
+#include <string.h>
+
#include <ZMap/zmapFeature.h>
typedef enum
@@ -72,18 +74,18 @@ typedef struct
} DumpWithinRangeStruct, *DumpWithinRange;
/* Internal functions */
-static ZMapFeatureContextExecuteStatus dump_features_cb(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus dump_features_cb(GQuark key,
+ gpointer data,
gpointer user_data,
char **err_out);
static void invoke_dump_features_cb(gpointer list_data, gpointer user_data);
-static gboolean simple_context_print_cb(ZMapFeatureAny feature_any,
+static gboolean simple_context_print_cb(ZMapFeatureAny feature_any,
GData *styles,
GString *dump_string_in_out,
GError **error,
gpointer user_data);
-static ZMapFeatureContextExecuteStatus range_invoke_dump_features_cb(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus range_invoke_dump_features_cb(GQuark key,
+ gpointer data,
gpointer user_data,
char **err_out);
@@ -137,6 +139,28 @@ gboolean zMapFeatureDumpStdOutFeatures(ZMapFeatureContext feature_context, GData
}
+gboolean zMapFeatureDumpToFileName(ZMapFeatureContext feature_context,char *filename, char *header, GData *styles, GError **error_out)
+{
+ gboolean result = FALSE ;
+ GIOChannel *file ;
+ gssize len;
+
+ file = g_io_channel_new_file(filename,"a",error_out) ;
+
+ g_io_channel_write_chars(file,header,strlen(header),&len,error_out);
+
+ result = zMapFeatureContextDump(feature_context, styles, file, error_out) ;
+
+ if (g_io_channel_flush(file, error_out) != G_IO_STATUS_NORMAL)
+ printf("cannot flush stdout\n") ;
+
+ if (g_io_channel_shutdown(file, TRUE, error_out) != G_IO_STATUS_NORMAL)
+ result = FALSE ;
+
+ return result ;
+}
+
+
/*!
@@ -179,13 +203,13 @@ gboolean zMapFeatureListForeachDumperCreate(ZMapFeatureDumpFeatureFunc dump_func
dump_data->dump_data = dump_any ;
dump_data->dump_free = dump_user_free ;
dump_data->dump_string = g_string_sized_new(2000);
-
+
*dumper_func_out = invoke_dump_features_cb;
*dumper_data_out = dump_data;
result = dump_data->status;
}
-
+
return result;
}
@@ -207,7 +231,7 @@ gboolean zMapFeatureListForeachDumperDestroy(gpointer dumper_data)
if (g_io_channel_flush(dump_data->channel, dump_data->dump_error) != G_IO_STATUS_NORMAL)
result = FALSE;
}
-
+
if(dump_data->dump_free && dump_data->dump_data->user_data)
(dump_data->dump_free)(dump_data->dump_data->user_data);
@@ -300,7 +324,7 @@ gboolean zMapFeatureContextDumpToFile(ZMapFeatureAny dump_set,
dump_data.dump_data = &dump_any ;
dump_data.dump_string = g_string_sized_new(2000);
- zMapFeatureContextExecuteSubset(dump_set, ZMAPFEATURE_STRUCT_FEATURE,
+ zMapFeatureContextExecuteSubset(dump_set, ZMAPFEATURE_STRUCT_FEATURESET,
dump_features_cb, &dump_data);
g_string_free(dump_data.dump_string, TRUE);
@@ -383,8 +407,8 @@ GQuark zMapFeatureContextDumpErrorDomain(void)
-static ZMapFeatureContextExecuteStatus dump_features_cb(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus dump_features_cb(GQuark key,
+ gpointer data,
gpointer user_data,
char **err_out)
{
@@ -462,7 +486,7 @@ static ZMapFeatureContextExecuteStatus dump_features_cb(GQuark key,
{
/* what does this mean? We'll probably get round to the
* data again, do we need to g_string_erase? */
-
+
if(bytes_written != 0)
dump_data->dump_string = g_string_erase(dump_data->dump_string, 0, bytes_written);
}
@@ -505,7 +529,7 @@ static gboolean simple_context_print_cb(ZMapFeatureAny feature_any,
gpointer user_data)
{
gboolean result = TRUE;
-
+
switch(feature_any->struct_type)
{
case ZMAPFEATURE_STRUCT_CONTEXT:
@@ -514,7 +538,7 @@ static gboolean simple_context_print_cb(ZMapFeatureAny feature_any,
feature_context = (ZMapFeatureContext)feature_any;
g_string_append_printf(dump_string_in_out,
- "Feature Context:\t%s\t%s\t%s\t%s\t%d\t%d\t%d\t%d\t%d\t%d\n",
+ "Feature Context:\t%s\t%s\t%s\t%s\t%d\t%d\t%d\t%d\t%d\t%d\n",
g_quark_to_string(feature_context->unique_id),
g_quark_to_string(feature_context->original_id),
g_quark_to_string(feature_context->sequence_name),
@@ -530,12 +554,12 @@ static gboolean simple_context_print_cb(ZMapFeatureAny feature_any,
case ZMAPFEATURE_STRUCT_ALIGN:
{
ZMapFeatureAlignment feature_align;
-
+
feature_align = (ZMapFeatureAlignment)feature_any;
g_string_append_printf(dump_string_in_out,
- "\tAlignment:\t%s\n",
+ "\tAlignment:\t%s\n",
g_quark_to_string(feature_align->unique_id)) ;
-
+
}
break;
case ZMAPFEATURE_STRUCT_BLOCK:
@@ -543,7 +567,7 @@ static gboolean simple_context_print_cb(ZMapFeatureAny feature_any,
ZMapFeatureBlock feature_block;
feature_block = (ZMapFeatureBlock)feature_any;
g_string_append_printf(dump_string_in_out,
- "\tBlock:\t%s\t%d\t%d\t%d\t%d\n",
+ "\tBlock:\t%s\t%d\t%d\t%d\t%d\n",
g_quark_to_string(feature_block->unique_id),
feature_block->block_to_sequence.t1,
feature_block->block_to_sequence.t2,
@@ -564,19 +588,21 @@ static gboolean simple_context_print_cb(ZMapFeatureAny feature_any,
case ZMAPFEATURE_STRUCT_FEATURE:
{
ZMapFeature feature;
- char *type, *strand, *phase;
+ char *type = "(type)", *strand, *phase;
ZMapFeatureTypeStyle style ;
feature = (ZMapFeature)feature_any;
- style = zMapFindStyle(styles, feature->style_id) ;
- type = (char *)zMapStyleMode2ExactStr(zMapStyleGetMode(style)) ;
-
+ if(styles)
+ {
+ style = zMapFindStyle(styles, feature->style_id) ;
+ type = (char *)zMapStyleMode2ExactStr(zMapStyleGetMode(style)) ;
+ }
strand = zMapFeatureStrand2Str(feature->strand) ;
phase = zMapFeaturePhase2Str(feature->phase) ;
g_string_append_printf(dump_string_in_out,
- "\t\t%s\t%d\t%s\t%s\t%d\t%d\t%s\t%s\t%f",
+ "\t\t%s\t%d\t%s\t%s\t%d\t%d\t%s\t%s\t%f",
(char *)g_quark_to_string(feature->unique_id),
feature->db_id,
(char *)g_quark_to_string(feature->original_id),
@@ -605,7 +631,7 @@ static gboolean simple_context_print_cb(ZMapFeatureAny feature_any,
}
static ZMapFeatureContextExecuteStatus range_invoke_dump_features_cb(GQuark key,
- gpointer data,
+ gpointer data,
gpointer user_data,
char **err_out)
{
@@ -621,7 +647,7 @@ static ZMapFeatureContextExecuteStatus range_invoke_dump_features_cb(GQuark ke
case ZMAPFEATURE_STRUCT_FEATURESET:
if(dump_data->status)
{
- status = dump_features_cb(key, data, user_data, err_out);
+ status = dump_features_cb(key, data, user_data, err_out);
}
break;
case ZMAPFEATURE_STRUCT_FEATURE:
diff --git a/src/zmapServer/zmapServerProtocolHandler.c b/src/zmapServer/zmapServerProtocolHandler.c
index 87b383107928c24482888841978ab79ac92bd896..77c61b8effe74be70286bb5b2263d578f1706469 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 1.57 2010-03-15 11:00:39 mh17 Exp $
+ * CVS info: $Id: zmapServerProtocolHandler.c,v 1.58 2010-03-19 08:56:42 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -740,11 +740,15 @@ 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)
{
gboolean result = FALSE ;
FindStylesStruct find_data = {NULL} ;
+ if(!required_styles) // MH17: semantics -> don't need styles therefore have those that are required
+ return(TRUE);
+
find_data.all_styles = all_styles ;
g_list_foreach(required_styles, findStyleCB, &find_data) ;
@@ -767,7 +771,7 @@ static void findStyleCB(gpointer data, gpointer user_data)
style_id = zMapStyleCreateID((char *)g_quark_to_string(style_id)) ;
if ((zMapFindStyle(find_data->all_styles, style_id)))
- find_data->found_style = TRUE ;
+ find_data->found_style = TRUE;
else
{
if (!(find_data->missing_styles))
@@ -894,6 +898,7 @@ ZMapThreadReturnCode getStyles(ZMapServer server, ZMapServerReqStyles styles, ch
/* Make sure that all the styles that are required for the feature sets were found.
* (This check should be controlled from analysing the number of feature servers or
* flags set for servers.....) */
+
if (thread_rc == ZMAPTHREAD_RETURNCODE_OK
&& !haveRequiredStyles(tmp_styles, styles->required_styles_in, &missing_styles))
{
@@ -904,7 +909,7 @@ ZMapThreadReturnCode getStyles(ZMapServer server, ZMapServerReqStyles styles, ch
}
else if(missing_styles)
{
- g_free(missing_styles); /* haveRequiredStyles return == TRUE doesn't mean missing_styles == NULL */
+ g_free(missing_styles); /* haveRequiredStyles return == TRUE doesn't mean missing_styles == NULL */
}
/* Find out if the styles will need to have their mode set from the features.
diff --git a/src/zmapThreads/zmapThreads.c b/src/zmapThreads/zmapThreads.c
index 4f438183e13cbf9d99e6e4adedcd2edf472e10c4..15d9d4c4a3fd7e7e5cf3e2ec64220658e60de6af 100755
--- a/src/zmapThreads/zmapThreads.c
+++ b/src/zmapThreads/zmapThreads.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.
@@ -26,12 +26,12 @@
* thread and a slave thread. This code knows nothing
* about what it is passing, it just handles the passing
* and returning of data.
- *
+ *
* Exported functions: See ZMap/zmapThread.h
* HISTORY:
* Last edited: Mar 20 12:09 2009 (edgrif)
* Created: Thu Jan 27 11:25:37 2005 (edgrif)
- * CVS info: $Id: zmapThreads.c,v 1.8 2010-03-04 15:10:53 mh17 Exp $
+ * CVS info: $Id: zmapThreads.c,v 1.9 2010-03-19 08:56:42 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -52,9 +52,9 @@ static void destroyThread(ZMapThread thread) ;
/*! @defgroup zmapthreads zMapThreads: creating, controlling and destroying slave threads
* @{
- *
+ *
* \brief Slave Threads
- *
+ *
* zMapThreads routines create, issue requests to, and destroy slave threads.
* On creation slave threads are given a routine that they will call whenever
* they receive a request. This routine handles the request and returns the
@@ -146,9 +146,9 @@ void zMapThreadRequest(ZMapThread thread, void *request)
gboolean zMapThreadGetReply(ZMapThread thread, ZMapThreadReply *state)
{
gboolean got_value ;
-
+
got_value = zmapVarGetValue(&(thread->reply), state) ;
-
+
return got_value ;
}
@@ -166,9 +166,9 @@ gboolean zMapThreadGetReplyWithData(ZMapThread thread, ZMapThreadReply *state,
void **data, char **err_msg)
{
gboolean got_value ;
-
+
got_value = zmapVarGetValueWithData(&(thread->reply), state, data, err_msg) ;
-
+
return got_value ;
}
@@ -222,8 +222,9 @@ void zMapThreadKill(ZMapThread thread)
int status ;
ZMAPTHREAD_DEBUG(("GUI: killing and destroying thread for thread %s\n", zMapThreadGetThreadID(thread))) ;
+zMapLogWarning("GUI: killing and destroying thread for thread %s\n", zMapThreadGetThreadID(thread)) ;
- /* we could signal an exit here by setting a condvar of EXIT...but that might lead to
+ /* we could signal an exit here by setting a condvar of EXIT...but that might lead to
* deadlocks, think about this bit.. */
/* Signal the thread to cancel it */
@@ -254,7 +255,7 @@ void zMapThreadDestroy(ZMapThread thread)
-/*
+/*
* --------------------- Internal routines ------------------------------
*/
diff --git a/src/zmapView/zmapView.c b/src/zmapView/zmapView.c
index b87773238bb42082e3edca7f9118103ea562df05..d86f7bdf723c253f466f42d8584dc39117571326 100755
--- a/src/zmapView/zmapView.c
+++ b/src/zmapView/zmapView.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Mar 11 14:55 2010 (edgrif)
* Created: Thu May 13 15:28:26 2004 (edgrif)
- * CVS info: $Id: zmapView.c,v 1.183 2010-03-15 11:17:15 mh17 Exp $
+ * CVS info: $Id: zmapView.c,v 1.184 2010-03-19 08:56:42 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -79,7 +79,7 @@ typedef struct
GData *curr_styles ; /* Styles for this context. */
ZMapFeatureContext curr_context ;
- ZMapServerReqType last_request ;
+ ZMapServerReqType display_after ;
} ConnectionDataStruct, *ConnectionData ;
@@ -141,7 +141,7 @@ static ZMapViewConnection createConnection(ZMapView zmap_view,
GList *req_featuresets,
gboolean dna_requested, gboolean writeback_server,
gboolean terminate);
-static void destroyConnection(ZMapViewConnection *view_conn) ;
+static void destroyConnection(ZMapView view, ZMapViewConnection view_conn) ;
static void killGUI(ZMapView zmap_view) ;
static void killConnections(ZMapView zmap_view) ;
@@ -322,6 +322,7 @@ 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();
+
/* Set up sequence to be fetched, in this case server defaults to whatever is set in config. file. */
sequence_fetch = g_new0(ZMapViewSequenceMapStruct, 1) ;
sequence_fetch->sequence = g_strdup(sequence) ;
@@ -366,6 +367,26 @@ void zMapViewSetupNavigator(ZMapViewWindow view_window, GtkWidget *canvas_widget
+static GHashTable *zmapViewGetIniFeaturesets(char *config_str)
+{
+ ZMapConfigIniContext context ;
+ GHashTable *hash = NULL;
+
+ if ((context = zMapConfigIniContextProvide()))
+ {
+ if(config_str)
+ zMapConfigIniContextIncludeBuffer(context, config_str);
+
+ hash = zMapConfigIniGetSource2Featureset(context);
+
+ zMapConfigIniContextDestroy(context);
+ }
+
+ return(hash);
+}
+
+
+
/* Connect a View to its databases via threads, at this point the View is blank and waiting
* to be called to load some data. */
gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
@@ -403,23 +424,11 @@ gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
/* There are a number of predefined methods that we require so add these in as well
* as the mapping for "feature set" -> style for these. */
addPredefined(&(zmap_view->orig_styles), &(zmap_view->featureset_2_stylelist)) ;
-
-#ifdef MH17_NOT_NEEDED
- if(stylesfile)
- {
- // each server will either return styles or read in the ones on styles file
- // so no need to do this here and merge them in
- GData *styles;
-
- if(zMapConfigIniGetStylesFromFile(NULL,stylesfile,&styles))
- {
- zmap_view->orig_styles =
- zMapStyleMergeStyles(zmap_view->orig_styles,styles,ZMAPSTYLE_MERGE_MERGE) ;
- }
- }
-#endif
}
+ // as we have not connected yet we just assign this mapping if it's there, no need to merge
+ zmap_view->source_2_featureset = zmapViewGetIniFeaturesets(config_str);
+
/* Set up connections to the named servers. */
if (settings_list)
{
@@ -482,7 +491,7 @@ gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
#ifdef NOT_REQUIRED_ATM
- /* This will become redundant with step stuff..... */
+ /* Thvmrna ; tris will become redundant with step stuff..... */
else if (!checkSequenceToServerMatch(zmap_view->sequence_2_server, &tmp_seq))
{
@@ -531,21 +540,23 @@ gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
(char *)current_server->styles_list,
(char *)stylesfile,
req_featuresets,
- dna_requested, // current_server->sequence,
+ dna_requested, // current_server->sequence,
current_server->writeback,
- FALSE ))) // (has to be) current_server->delayed,
+ FALSE ))) // (has to be) current_server->delayed,
{
- connections++ ;
+ connections++ ;
/* If at least one connection succeeded then we are up and running, if not then the zmap
* returns to the init state. */
zmap_view->state = ZMAPVIEW_LOADING ;
/* THESE NEED TO GO WHEN STEP LIST STUFF IS DONE PROPERLY.... */
- if (current_server->sequence)
- zmap_view->sequence_server = view_con ;
+ // this is an optimisation: the server supports DNA so no point in searching for it
+ // if we implement multiple sources then we can remove this
+ if (dna_requested)
+ zmap_view->sequence_server = view_con ;
if (current_server->writeback)
- zmap_view->writeback_server = view_con ;
+ zmap_view->writeback_server = view_con ;
}
}
@@ -951,8 +962,6 @@ gboolean zMapViewReset(ZMapView zmap_view)
sequence. */
killConnections(zmap_view) ;
- zmap_view->connections_loaded = 0 ;
-
result = TRUE ;
}
@@ -1093,7 +1102,7 @@ char *zMapViewGetStatusStr(ZMapViewState state)
/* Array must be kept in synch with ZmapState enum in zmapView.h */
static char *zmapStates[] = {"",
"Connecting", "Connected",
- "Data loading", "Data loaded",
+ "Data loading", "Data loaded","Columns loading",
"Resetting", "Dying"} ;
char *state_str ;
@@ -1250,9 +1259,9 @@ char *zmapViewGetStatusAsStr(ZMapViewState state)
{
/* Array must be kept in synch with ZmapState enum in ZMap.h */
static char *zmapStates[] = {"ZMAPVIEW_INIT",
- "ZMAPVIEW_NOT_CONNECTED", "ZMAPVIEW_NO_WINDOW",
+// "ZMAPVIEW_NOT_CONNECTED", "ZMAPVIEW_NO_WINDOW",
"ZMAPVIEW_CONNECTING", "ZMAPVIEW_CONNECTED",
- "ZMAPVIEW_LOADING", "ZMAPVIEW_LOADED",
+ "ZMAPVIEW_LOADING", "ZMAPVIEW_LOADED", "ZMAPVIEW_UPDATING",
"ZMAPVIEW_RESETTING", "ZMAPVIEW_DYING"} ;
char *state_str ;
@@ -1309,17 +1318,22 @@ static GHashTable *zmapViewGetFeatureSourceHash(GList *sources)
src = sources->data;
if(!src->featuresets)
continue;
- features = g_strsplit_set(src->featuresets,"; \t",0); // this will give null entries eg 'aaa ; bbbb' -> 5 strings
+ features = g_strsplit(src->featuresets,";",0); // this will give null entries eg 'aaa ; bbbb' -> 5 strings
if(!features)
continue;
-
for(feats = features;*feats;feats++)
{
GQuark q;
// the data we want to lookup happens to have been quarked
if(**feats)
{
- q = g_quark_from_string(*feats);
+ gchar *feature;
+
+ feature = *feats;
+ feature = g_strstrip(feature);
+ if(!feature)
+ continue;
+ q = zMapFeatureSetCreateID(feature);
g_hash_table_insert(hash,GUINT_TO_POINTER(q), (gpointer) src);
}
}
@@ -1348,82 +1362,114 @@ static GHashTable *zmapViewGetFeatureSourceHash(GList *sources)
void zmapViewLoadFeatures(ZMapView view, ZMapFeatureBlock block_orig, GList *req_sources,
int features_start, int features_end)
{
- ZMapFeatureContext orig_context, context ;
+ ZMapFeatureContext context ;
ZMapFeatureBlock block ;
- GList *req_featuresets ;
GHashTable *hash = NULL;
- GList * sources;
+ GList * sources = NULL;
ZMapConfigSource server;
- char *stylesfile;
+ char *stylesfile = NULL;
gboolean requested = FALSE;
sources = zmapViewGetIniSources(NULL,&stylesfile);
hash = zmapViewGetFeatureSourceHash(sources);
- orig_context = (ZMapFeatureContext)zMapFeatureGetParentGroup((ZMapFeatureAny)block_orig,
- ZMAPFEATURE_STRUCT_CONTEXT) ;
+// orig_context = (ZMapFeatureContext)zMapFeatureGetParentGroup((ZMapFeatureAny)block_orig,
+// ZMAPFEATURE_STRUCT_CONTEXT) ;
/* Copy the original context from the target block upwards setting feature set names
* and the range of features to be copied. */
- context = zMapFeatureContextCopyWithParents((ZMapFeatureAny)block_orig) ;
+// context = zMapFeatureContextCopyWithParents((ZMapFeatureAny)block_orig) ;
/* ok...need to look up col here.... */
- req_featuresets = zmapViewSrc2FSetGetList(view->source_2_featureset, req_sources) ;
- context->feature_set_names = req_featuresets ;
+// req_featuresets = zmapViewSrc2FSetGetList(view->source_2_featureset, req_sources) ;
- block = zMapFeatureAlignmentGetBlockByID(context->master_align, block_orig->unique_id) ;
+// block = zMapFeatureAlignmentGetBlockByID(context->master_align, block_orig->unique_id) ;
- zMapFeatureBlockSetFeaturesCoords(block, features_start, features_end) ;
+// zMapFeatureBlockSetFeaturesCoords(block, features_start, features_end) ;
for(;req_sources;req_sources = g_list_next(req_sources))
{
- GQuark featureset = GPOINTER_TO_INT(req_sources->data);
+ GQuark featureset = GPOINTER_TO_UINT(req_sources->data);
- // MH17: a question: we are requesting source not featuresets: is this right?
server = zmapViewGetSourceFromFeatureset(hash,featureset);
+
if(server)
{
- GList *req_feature = NULL;
+ GList *req_featuresets = NULL;
int existing = FALSE;
ZMapViewConnection view_conn = NULL;
- GList *view_con_list;
+// GList *view_con_list;
+#warning include this when thread cleanup debugged
// make a list of one feature only
- req_feature = g_list_append(req_feature,req_sources->data);
-
+ req_featuresets = g_list_append(req_featuresets,GUINT_TO_POINTER(featureset));
+#ifdef MH17_ONLY_WHEN_THREAD_CLEANUP_IS_DEBUGGED
// look for server in view->connections list
for(view_con_list = view->connection_list;view_con_list;view_con_list = g_list_next(view_con_list))
{
view_conn = (ZMapViewConnection) view_con_list->data;
if(!strcmp(view_conn->url,server->url))
+ {
+ existing = TRUE;
break;
+ }
}
- if(!view_con_list)
- view_conn = NULL; // (not found)
+#endif
+ /* Copy the original context from the target block upwards setting feature set names
+ * and the range of features to be copied.
+ * We need one for each featureset/ request
+ */
+#if 1
+ // This loads but does not display appear in stats or in columns list, but it does get merged into the view
+ // using this as it may be necessaru for Blixem
+ context = zMapFeatureContextCopyWithParents((ZMapFeatureAny)block_orig) ;
+ context->feature_set_names = req_featuresets ;
+
+ block = zMapFeatureAlignmentGetBlockByID(context->master_align, block_orig->unique_id) ;
+ zMapFeatureBlockSetFeaturesCoords(block, features_start, features_end) ;
+
+#else
+/*
+ try the exact stuff fron startup that works
+ it's a lot simpler and fails in exactly the same way
+*/
+ context = createContext(view->sequence, view->start, view->end, req_featuresets) ;
+#endif
+ // make the windows have the same list of featuresets so that they display
+ g_list_foreach(view->window_list, invoke_merge_in_names, req_featuresets);
-printf("request featureset %s from %s\n",g_quark_to_string(GPOINTER_TO_UINT(req_feature->data)),server->url);
+
+printf("request featureset %s from %s\n",g_quark_to_string(GPOINTER_TO_UINT(req_featuresets->data)),server->url);
// start a new server connection
// can optionally use an existing one -> pass in second arg
- createConnection(view, view_conn, context, server->url,
+ if(createConnection(view, existing ? view_conn : NULL,
+ context, server->url,
(char *)server->format,
server->timeout,
(char *)server->version,
(char *)server->styles_list,
stylesfile,
- req_feature,
+ req_featuresets,
FALSE,
server->writeback,
- !existing );
- g_list_free(req_feature);
- requested = TRUE; // set even if create fails: wiil get unset in check connection state
+ !existing ))
+ {
+ requested = TRUE;
+ }
+ // g_list_free(req_featuresets); no! this list gets used by threads
+ req_featuresets = NULL;
}
}
if(requested)
+ {
zmapViewBusy(view, TRUE) ; // gets unset when all step lists finish
+ view->state = ZMAPVIEW_UPDATING;
+ (*(view_cbs_G->state_change))(view, view->app_data, NULL) ;
+ }
if(sources)
zMapConfigSourcesFreeList(sources);
@@ -1517,7 +1563,7 @@ static void scrollCB(ZMapWindow window, void *caller_data, void *window_data)
printf("In View, in window scroll callback\n") ;
-
+//
return ;
}
@@ -1880,7 +1926,8 @@ static gboolean checkStateConnections(ZMapView zmap_view)
{
gboolean call_again = TRUE ; /* Normally we want to called continuously. */
gboolean state_change = TRUE ; /* Has view state changed ?. */
- gboolean has_step_list = FALSE; // any requests still active?
+ gboolean reqs_finished = FALSE;
+ int has_step_list = 0; // any requests still active?
if (zmap_view->connection_list)
{
@@ -1983,10 +2030,9 @@ static gboolean checkStateConnections(ZMapView zmap_view)
}
else
{
- threadDebugMsg(thread, "GUI: thread %s, got data\n", NULL) ;
+ // threadDebugMsg(thread, "GUI: thread %s, got data\n", NULL) ;
- /* Really we should only be loading stuff if we are LOADING.... */
- if (zmap_view->state != ZMAPVIEW_LOADING && zmap_view->state != ZMAPVIEW_LOADED)
+ if (zmap_view->state != ZMAPVIEW_LOADING && zmap_view->state != ZMAPVIEW_UPDATING)
{
threadDebugMsg(thread, "GUI: thread %s, got data but ZMap state is - %s\n",
zmapViewGetStatusAsStr(zMapViewGetStatus(zmap_view))) ;
@@ -2015,7 +2061,7 @@ static gboolean checkStateConnections(ZMapView zmap_view)
/* Warn the user ! */
zMapWarning("Source \"%s\" is being cancelled, check log for details.", view_con->url) ;
- zMapLogCritical("Source \"%s\" is being cancelled"
+ zMapLogCritical("Source \"%s\" is being cancelled"//
" because a request to it has failed,"
" error was: %s", view_con->url, err_msg) ;
@@ -2053,7 +2099,7 @@ static gboolean checkStateConnections(ZMapView zmap_view)
}
default:
{
- zMapLogFatalLogicErr("switch(), unknown value: %d", reply) ;
+ zMapLogFatalLogicErr("switch(), unknown value: %d", reply) ;
break ;
}
@@ -2061,32 +2107,46 @@ static gboolean checkStateConnections(ZMapView zmap_view)
}
- /* Check for more connection steps and dispatch them or clear up if finished. */
+
+ /* If the thread has died then remove it's connection. */
+ // do this before counting up the number of step lists
+ if (thread_has_died)
+ {
+ /* We are going to remove an item from the list so better move on from
+ * this item. */
+
+ list_item = g_list_next(list_item) ;
+ zmap_view->connection_list = g_list_remove(zmap_view->connection_list, view_con) ;
+printf("thread died %s -> %d %x\n", view_con->url,g_list_length(zmap_view->connection_list), GPOINTER_TO_INT(zmap_view->connection_list));
+zMapLogWarning("thread died %s -> %d %x\n", view_con->url,g_list_length(zmap_view->connection_list), GPOINTER_TO_INT(zmap_view->connection_list));
+
+ if(view_con->step_list)
+ reqs_finished = TRUE;
+
+ destroyConnection(zmap_view,view_con) ;
+
+ }
+
+ /* Check for more connection steps and dispatch them or clear up if finished. */
if ((view_con->step_list))
{
/* If there were errors then all connections may have been removed from
* step list or if we have finished then destroy step_list. */
if (zmapViewStepListIsNext(view_con->step_list))
{
+
zmapViewStepListIter(view_con) ;
- has_step_list = TRUE;
+ has_step_list++;
}
else
{
zmapViewStepListDestroy(view_con) ;
+ reqs_finished = TRUE;
+printf("step list %s finished\n",view_con->url);
+zMapLogWarning("step list %s finished\n",view_con->url);
}
}
- /* If the thread has died then remove it's connection. */
- if (thread_has_died)
- {
- /* We are going to remove an item from the list so better move on from
- * this item. */
- list_item = g_list_next(list_item) ;
- zmap_view->connection_list = g_list_remove(zmap_view->connection_list, view_con) ;
-
- destroyConnection(&view_con) ;
- }
if (err_msg)
g_free(err_msg) ;
@@ -2095,22 +2155,28 @@ static gboolean checkStateConnections(ZMapView zmap_view)
}
+ /* Try this here..... */
+ if(!has_step_list && reqs_finished)
+ {
+ zmapViewBusy(zmap_view, FALSE) ;
+ /*
+ * rather than count up the number loaded we say 'LOADED' if there's no LOADING active
+ * This accounts for failures as well as completed loads
+ */
+ zmap_view->state = ZMAPVIEW_LOADED ;
+ state_change = TRUE;
+printf("state set to loaded\n");
+ }
+
+ if (state_change)
+ (*(view_cbs_G->state_change))(zmap_view, zmap_view->app_data, NULL) ;
/* At this point if we have connections then we carry on looping looking for
* replies from the views. If there are no threads left then we need to examine
* our state and take action depending on whether we are dying or threads
* have died or whatever.... */
- if (zmap_view->connection_list)
- {
- /* Signal layer above us if view has changed state. */
- if (state_change)
- (*(view_cbs_G->state_change))(zmap_view, zmap_view->app_data, NULL) ;
- /* Try this here..... */
- if(!has_step_list)
- zmapViewBusy(zmap_view, FALSE) ;
- }
- else
+ if (!zmap_view->connection_list)
{
/* Decide if we need to be called again or if everythings dead. */
call_again = checkContinue(zmap_view) ;
@@ -2145,7 +2211,7 @@ static gboolean dispatchContextRequests(ZMapViewConnection connection, ZMapServe
ZMapServerReqFeatureSets feature_sets = (ZMapServerReqFeatureSets)req_any ;
feature_sets->featureset_2_stylelist_out = connect_data->featureset_2_stylelist ;
-
+// MH17: if this is an output parameter why do we set it on dispatch?
break ;
}
@@ -2223,6 +2289,9 @@ static gboolean processDataRequests(ZMapViewConnection view_con, ZMapServerReqAn
ZMapView zmap_view = view_con->parent_view ;
/* Process the different types of data coming back. */
+printf("%s: response to %d was %d\n",view_con->url,req_any->type,req_any->response);
+zMapLogWarning("%s: response to %d was %d\n",view_con->url,req_any->type,req_any->response);
+
switch (req_any->type)
{
case ZMAP_SERVERREQ_CREATE:
@@ -2247,6 +2316,7 @@ static gboolean processDataRequests(ZMapViewConnection view_con, ZMapServerReqAn
break ;
}
+
case ZMAP_SERVERREQ_FEATURESETS:
{
ZMapServerReqFeatureSets feature_sets = (ZMapServerReqFeatureSets)req_any ;
@@ -2315,12 +2385,17 @@ static gboolean processDataRequests(ZMapViewConnection view_con, ZMapServerReqAn
feature_sets->featureset_2_stylelist_out = NULL;
}
- /* Hack, stick the source to featureset mapping in the first time only for now...should be merged in
- * the end....and also the data one.... */
+ /* merge these in, the base mapping is defined in config ZMap [featuresets] */
+ // NB these are not supplied by pipeServers and we assume a 1-1 mapping
+ // of source to display featureset and source to style.
+ // See zmapViewRemoteReceive.c/xml_featureset_start_cb()
+// needs sorting; not implemented, we just get the first one
+
if (!(zmap_view->source_2_featureset))
zmap_view->source_2_featureset = feature_sets->source_2_featureset_out ;
if (!(zmap_view->source_2_sourcedata))
+
zmap_view->source_2_sourcedata = feature_sets->source_2_sourcedata_out ;
@@ -2406,19 +2481,13 @@ static gboolean processDataRequests(ZMapViewConnection view_con, ZMapServerReqAn
}
/* ok...once we are here we can display stuff.... */
- if (result && req_any->type == connect_data->last_request)
+ if (result && req_any->type == connect_data->display_after)
{
/* Isn't there a problem here...which bit of info goes with which server ???? */
zmapViewSessionAddServerInfo(zmap_view->session_data, connect_data->database_path) ;
getFeatures(zmap_view, get_features, connect_data->curr_styles) ;
- zmap_view->connections_loaded++ ;
-
- /* This will need to be more sophisticated, we will need to time
- * connections out. */
- if (zmap_view->connections_loaded == g_list_length(zmap_view->connection_list))
- zmap_view->state = ZMAPVIEW_LOADED ;
}
break ;
@@ -2472,6 +2541,7 @@ static gboolean processGetSeqRequests(ZMapViewConnection view_con, ZMapServerReq
get_sequence->sequences,
get_sequence->flags,
&blixem_pid,
+
&(zmap_view->kill_blixems))))
zmap_view->spawned_processes = g_list_append(zmap_view->spawned_processes,
GINT_TO_POINTER(blixem_pid)) ;
@@ -2510,7 +2580,8 @@ static void killConnections(ZMapView zmap_view)
{
GList* list_item ;
- zMapAssert(zmap_view->connection_list) ;
+ if(!(zmap_view->connection_list))
+ return;
list_item = g_list_first(zmap_view->connection_list) ;
do
@@ -2569,6 +2640,14 @@ static ZMapViewConnection createConnection(ZMapView zmap_view,
int url_parse_error ;
ZMapURL urlObj;
+ /* Parse the url and create connection. */
+ if (!(urlObj = url_parse(server_url, &url_parse_error)))
+ {
+ zMapLogWarning("GUI: url %s did not parse. Parse error < %s >\n",
+ server_url, url_error(url_parse_error)) ;
+ return(NULL);
+ }
+
if(view_con)
{
// use existing connection if not busy
@@ -2581,13 +2660,6 @@ if(existing) printf("using existing connection %s\n",view_con->url);
if(!view_con)
{
- /* Parse the url and create connection. */
- if (!(urlObj = url_parse(server_url, &url_parse_error)))
- {
- zMapLogWarning("GUI: url %s did not parse. Parse error < %s >\n",
- server_url, url_error(url_parse_error)) ;
- return(NULL);
- }
/* Create the thread to service the connection requests, we give it a function that it will call
* to decode the requests we send it and a terminate function. */
if ((thread = zMapThreadCreate(zMapServerRequestHandler,
@@ -2597,7 +2669,7 @@ if(existing) printf("using existing connection %s\n",view_con->url);
view_con = g_new0(ZMapViewConnectionStruct, 1) ;
view_con->parent_view = zmap_view ;
view_con->thread = thread ;
- view_con->url = g_strdup(urlObj->url) ;
+ view_con->url = g_strdup(server_url) ;
printf("create thread for %s\n",view_con->url);
}
else
@@ -2614,8 +2686,9 @@ printf("create thread for %s\n",view_con->url);
connect_data = g_new0(ConnectionDataStruct, 1) ;
connect_data->curr_context = context ;
- if(terminate) // ie server->delayed
- connect_data->dynamic_loading = TRUE ;
+ if(terminate) // ie server->delayed -> called after startup
+ connect_data->dynamic_loading = TRUE ;
+
connect_data->featureset_2_stylelist = zMap_g_hashlist_create() ;
view_con->request_data = connect_data ;
@@ -2629,7 +2702,7 @@ printf("create thread for %s\n",view_con->url);
/* Record info. for this session. */
zmapViewSessionAddServer(zmap_view->session_data,urlObj,format) ;
- connect_data->last_request = ZMAP_SERVERREQ_INVALID;
+ connect_data->display_after = ZMAP_SERVERREQ_FEATURES;
/* Set up this connection in the step list. */
if(!existing)
@@ -2640,8 +2713,6 @@ printf("create thread for %s\n",view_con->url);
zmapViewStepListAddServerReq(view_con->step_list, view_con, ZMAP_SERVERREQ_OPEN, req_any) ;
req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_GETSERVERINFO) ;
zmapViewStepListAddServerReq(view_con->step_list, view_con, ZMAP_SERVERREQ_GETSERVERINFO, req_any) ;
- // how can this be? maybe we want to connect and req data later on. Right now not likely
- connect_data->last_request = ZMAP_SERVERREQ_GETSERVERINFO ;
}
if(req_featuresets)
@@ -2654,27 +2725,24 @@ printf("create thread for %s\n",view_con->url);
zmapViewStepListAddServerReq(view_con->step_list, view_con, ZMAP_SERVERREQ_NEWCONTEXT, req_any) ;
req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_FEATURES) ;
zmapViewStepListAddServerReq(view_con->step_list, view_con, ZMAP_SERVERREQ_FEATURES, req_any) ;
- connect_data->last_request = ZMAP_SERVERREQ_FEATURES ;
}
if (dna_requested)
{
req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_SEQUENCE) ;
zmapViewStepListAddServerReq(view_con->step_list, view_con, ZMAP_SERVERREQ_SEQUENCE, req_any) ;
- connect_data->last_request = ZMAP_SERVERREQ_SEQUENCE ;
+ connect_data->display_after = ZMAP_SERVERREQ_SEQUENCE ;
}
if(terminate)
-
{
req_any = zMapServerRequestCreate(ZMAP_SERVERREQ_TERMINATE) ;
zmapViewStepListAddServerReq(view_con->step_list, view_con, ZMAP_SERVERREQ_TERMINATE, req_any) ;
- connect_data->last_request = ZMAP_SERVERREQ_TERMINATE ;
}
if(!existing)
- zmap_view->connection_list = g_list_append(zmap_view->connection_list, view_con) ;
-
+ zmap_view->connection_list = g_list_append(zmap_view->connection_list, view_con) ;
+printf("view_con: %s -> %d %x\n", view_con->url,g_list_length(zmap_view->connection_list), GPOINTER_TO_INT(zmap_view->connection_list));
/* Start the connection to the source. */
zmapViewStepListIter(view_con) ;
}
@@ -2692,9 +2760,15 @@ printf("create thread for %s\n",view_con->url);
-static void destroyConnection(ZMapViewConnection *view_conn_ptr)
+static void destroyConnection(ZMapView view, ZMapViewConnection view_conn)
{
- ZMapViewConnection view_conn = *view_conn_ptr ;
+
+ zMapLogWarning("destroyConnection\n",NULL);
+
+ if(view->sequence_server == view_conn)
+ view->sequence_server = NULL;
+ if(view->writeback_server == view_conn)
+ view->writeback_server = NULL;
zMapThreadDestroy(view_conn->thread) ;
@@ -2707,8 +2781,6 @@ static void destroyConnection(ZMapViewConnection *view_conn_ptr)
g_free(view_conn) ;
- *view_conn_ptr = NULL ;
-
return ;
}
@@ -2918,6 +2990,15 @@ static gboolean justMergeContext(ZMapView view, ZMapFeatureContext *context_inou
}
merge = zMapFeatureContextMerge(&(view->features), &new_features, &diff_context) ;
+#ifndef MH17_NEVER
+ {
+ GError *err = NULL;
+
+ zMapFeatureDumpToFileName(diff_context,"features.txt","(justMerge) diff context:\n", NULL, &err) ;
+ zMapFeatureDumpToFileName(view->features,"features.txt","(justMerge) view->Features:\n", NULL, &err) ;
+
+ }
+#endif
if (merge == ZMAPFEATURE_CONTEXT_OK)
{
@@ -3022,7 +3103,7 @@ static void commandCB(ZMapWindow window, void *caller_data, void *window_data)
view_con = view->sequence_server ;
- if (!view_con || !view_con->sequence_server)
+ if (!view_con) // || !view_con->sequence_server)
{
zMapWarning("%s", "Sequence server incorrectly specified in config file"
" so cannot fetch local sequences for blixem.") ;
@@ -3034,6 +3115,8 @@ static void commandCB(ZMapWindow window, void *caller_data, void *window_data)
}
else
{
+ zmapViewBusy(view, TRUE) ;
+
/* Create the step list that will be used to fetch the sequences. */
view_con->step_list = zmapViewStepListCreate(NULL, processGetSeqRequests, NULL) ;
zmapViewStepListAddStep(view_con->step_list, ZMAP_SERVERREQ_GETSEQUENCE,
@@ -3459,7 +3542,8 @@ static void threadDebugMsg(ZMapThread thread, char *format_str, char *msg)
thread_id = zMapThreadGetThreadID(thread) ;
full_msg = g_strdup_printf(format_str, thread_id, msg ? msg : "") ;
- zMapDebug("%s", full_msg) ;
+// zMapDebug("%s", full_msg) ;
+ zMapLogWarning("%s",full_msg);
g_free(full_msg) ;
g_free(thread_id) ;
@@ -3478,6 +3562,7 @@ static gboolean checkContinue(ZMapView zmap_view)
{
case ZMAPVIEW_INIT:
case ZMAPVIEW_LOADED: // delayed servers get cleared up, we do not need connections to run
+
{
/* Nothing to do here I think.... */
connections = TRUE ;
@@ -3520,6 +3605,19 @@ static gboolean checkContinue(ZMapView zmap_view)
break ;
}
+ case ZMAPVIEW_UPDATING:
+ {
+ /* zmap is ok but a new column didn't come through */
+ zmap_view->state = ZMAPVIEW_LOADED;
+
+ /* Signal layer above us because the view has stopped loading. */
+ (*(view_cbs_G->state_change))(zmap_view, zmap_view->app_data, NULL) ;
+printf("check continue thread died while updating\n");
+zMapLogWarning("check continue thread died while updating\n",NULL);
+ connections = TRUE ;
+
+ break;
+ }
case ZMAPVIEW_RESETTING:
{
/* zmap is ok but user has reset it and all threads have died so we need to stop
@@ -3562,7 +3660,7 @@ static gboolean checkContinue(ZMapView zmap_view)
break ;
}
}
-
+if(!connections) printf("checkContinue returns FALSE\n");
return connections ;
}
diff --git a/src/zmapView/zmapViewRemoteReceive.c b/src/zmapView/zmapViewRemoteReceive.c
index 80e73330e5d1721e68b3c97028dec1c4c932e16e..9f372d0c649c0dc9940bc51d4c969b15a9d02142 100755
--- a/src/zmapView/zmapViewRemoteReceive.c
+++ b/src/zmapView/zmapViewRemoteReceive.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.
@@ -27,11 +27,11 @@
* a peer application set up to interact with zmap.
*
* Exported functions: See zmapView_P.h
- *
+ *
* HISTORY:
* Last edited: Jan 27 15:46 2010 (edgrif)
* Created: Tue Jul 10 21:02:42 2007 (rds)
- * CVS info: $Id: zmapViewRemoteReceive.c,v 1.41 2010-03-04 15:11:36 mh17 Exp $
+ * CVS info: $Id: zmapViewRemoteReceive.c,v 1.42 2010-03-19 08:56:42 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -80,7 +80,7 @@ typedef enum
typedef struct
{
ZMapViewValidXRemoteActions action ;
- gboolean edit_action ; /*
+ gboolean edit_action ; /*
Does this action edit the feature context ? */
@@ -169,8 +169,8 @@ static ZMapFeatureContextExecuteStatus mark_matching_invalid(GQuark key, gpointe
static ZMapFeatureContextExecuteStatus sanity_check_context(GQuark key, gpointer data, gpointer user_data, char **error_out);
static void zoomWindowToFeature(ZMapView view, RequestData input_data, ResponseData output_data) ;
-static ZMapFeatureContextExecuteStatus zoomToFeatureCB(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus zoomToFeatureCB(GQuark key,
+ gpointer data,
gpointer user_data,
char **error_out) ;
@@ -203,10 +203,10 @@ static void copyAddFeature(gpointer key, gpointer value, gpointer user_data) ;
/* Descriptor table of action attributes */
static ActionDescriptorStruct action_table_G[] =
{
-
- {ZMAPVIEW_REMOTE_INVALID}
+
+ {ZMAPVIEW_REMOTE_INVALID}
} ;
#endif
@@ -260,11 +260,11 @@ static char *actions_G[ZMAPVIEW_REMOTE_UNKNOWN + 1] =
/* Where is all starts from. Everything else should be static */
void zmapViewSetupXRemote(ZMapView view, GtkWidget *widget)
{
- zMapXRemoteInitialiseWidgetFull(widget, PACKAGE_NAME,
- ZMAP_DEFAULT_REQUEST_ATOM_NAME,
- ZMAP_DEFAULT_RESPONSE_ATOM_NAME,
- view_execute_command,
- view_post_execute,
+ zMapXRemoteInitialiseWidgetFull(widget, PACKAGE_NAME,
+ ZMAP_DEFAULT_REQUEST_ATOM_NAME,
+ ZMAP_DEFAULT_RESPONSE_ATOM_NAME,
+ view_execute_command,
+ view_post_execute,
view);
return ;
}
@@ -273,8 +273,8 @@ char *zMapViewRemoteReceiveAccepts(ZMapView view)
{
char *xml = NULL;
- xml = zMapXRemoteClientAcceptsActionsXML(zMapXRemoteWidgetGetXID(view->xremote_widget),
- &actions_G[ZMAPVIEW_REMOTE_INVALID + 1],
+ xml = zMapXRemoteClientAcceptsActionsXML(zMapXRemoteWidgetGetXID(view->xremote_widget),
+ &actions_G[ZMAPVIEW_REMOTE_INVALID + 1],
ZMAPVIEW_REMOTE_UNKNOWN - 1);
return xml;
@@ -283,7 +283,7 @@ char *zMapViewRemoteReceiveAccepts(ZMapView view)
-/*
+/*
* Internal functions.
*/
@@ -363,7 +363,7 @@ static char *view_execute_command(char *command_text, gpointer user_data, int *s
g_quark_to_string(input_data.feature->original_id)) ;
output_data.code = ZMAPXREMOTE_FAILED ;
}
- else
+ else
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
if (drawNewFeatures(view, &input_data, &output_data)
@@ -375,8 +375,8 @@ static char *view_execute_command(char *command_text, gpointer user_data, int *s
post_data->action = input.common.action;
post_data->edit_context = input_data.edit_context;
- g_object_set_data(G_OBJECT(view->xremote_widget),
- VIEW_POST_EXECUTE_DATA,
+ g_object_set_data(G_OBJECT(view->xremote_widget),
+ VIEW_POST_EXECUTE_DATA,
post_data);
}
@@ -406,7 +406,7 @@ static char *view_execute_command(char *command_text, gpointer user_data, int *s
output_data.code = ZMAPXREMOTE_UNKNOWNCMD;
break;
}
-
+
*statusCode = output_data.code;
response = g_string_free(output_data.messages, FALSE);
}
@@ -430,14 +430,14 @@ static char *view_execute_command(char *command_text, gpointer user_data, int *s
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.") ;
}
-
+
return response;
}
@@ -459,10 +459,10 @@ static char *view_post_execute(char *command_text, gpointer user_data, int *stat
case ZMAPVIEW_REMOTE_CREATE_FEATURE:
{
status = zmapViewDrawDiffContext(view, &(post_data->edit_context));
-
+
if(!status)
post_data->edit_context = NULL; /* So the view->features context doesn't get destroyed */
-
+
if(post_data->edit_context)
zMapFeatureContextDestroy(post_data->edit_context, TRUE);
}
@@ -657,12 +657,12 @@ static gboolean drawNewFeatures(ZMapView view, RequestData input_data, ResponseD
}
else
{
- zMapFeatureContextExecute((ZMapFeatureAny)(input_data->edit_context),
+ zMapFeatureContextExecute((ZMapFeatureAny)(input_data->edit_context),
ZMAPFEATURE_STRUCT_FEATURE,
delete_from_list,
&(input_data->feature_list));
- zMapFeatureContextExecute((ZMapFeatureAny)(view->features),
+ zMapFeatureContextExecute((ZMapFeatureAny)(view->features),
ZMAPFEATURE_STRUCT_FEATURE,
mark_matching_invalid,
&(input_data->feature_list));
@@ -703,7 +703,7 @@ static void draw_failed_make_message(gpointer list_data, gpointer user_data)
g_string_append_printf(response_data->messages,
"Failed to draw feature '%s' [%s]. Unknown reason.\n",
(char *)g_quark_to_string(feature_any->original_id),
- (char *)g_quark_to_string(feature_any->unique_id));
+ (char *)g_quark_to_string(feature_any->unique_id));
}
return ;
@@ -732,13 +732,13 @@ static gint matching_unique_id(gconstpointer list_data, gconstpointer user_data)
ZMapFeatureAny a = (ZMapFeatureAny)list_data, b = (ZMapFeatureAny)user_data ;
match = !(a->unique_id == b->unique_id);
-
+
return match;
}
-static ZMapFeatureContextExecuteStatus delete_from_list(GQuark key,
- gpointer data,
- gpointer user_data,
+static ZMapFeatureContextExecuteStatus delete_from_list(GQuark key,
+ gpointer data,
+ gpointer user_data,
char **error_out)
{
ZMapFeatureAny any = (ZMapFeatureAny)data;
@@ -755,8 +755,8 @@ static ZMapFeatureContextExecuteStatus delete_from_list(GQuark key,
return ZMAP_CONTEXT_EXEC_STATUS_OK;
}
-static ZMapFeatureContextExecuteStatus mark_matching_invalid(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus mark_matching_invalid(GQuark key,
+ gpointer data,
gpointer user_data,
char **error_out)
{
@@ -775,8 +775,8 @@ static ZMapFeatureContextExecuteStatus mark_matching_invalid(GQuark key,
return ZMAP_CONTEXT_EXEC_STATUS_OK;
}
-static ZMapFeatureContextExecuteStatus sanity_check_context(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus sanity_check_context(GQuark key,
+ gpointer data,
gpointer user_data,
char **error_out)
{
@@ -800,7 +800,7 @@ static ZMapFeatureContextExecuteStatus sanity_check_context(GQuark key,
static void populate_data_from_view(ZMapView view, RequestData xml_data)
{
xml_data->orig_context = zMapViewGetFeatures(view) ;
-
+
/* Copy basics of original context. */
xml_data->edit_context = (ZMapFeatureContext)zMapFeatureAnyCopy((ZMapFeatureAny)(xml_data->orig_context)) ;
@@ -808,15 +808,15 @@ static void populate_data_from_view(ZMapView view, RequestData xml_data)
xml_data->edit_context->styles = NULL ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
+
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
xml_data->styles = xml_data->orig_context->styles ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
xml_data->styles = view->orig_styles ;
-
-
+
+
return ;
}
@@ -827,7 +827,7 @@ static void populate_data_from_view(ZMapView view, RequestData xml_data)
/* XML_TAG_HANDLERS */
/* ====================================================== */
-/*
+/*
*
* <zmap action="create_feature">
* <featureset name="Coding">
@@ -924,7 +924,7 @@ static gboolean xml_request_start_cb(gpointer user_data, ZMapXMLElement set_elem
{
GQuark load_id ;
RequestData request_data = (RequestData)(xml_data->user_data);
-
+
load_id = zMapXMLAttributeGetValue(attr) ;
if (zMapLogQuarkIsStr(load_id, "mark"))
@@ -942,7 +942,7 @@ static gboolean xml_request_start_cb(gpointer user_data, ZMapXMLElement set_elem
}
result = TRUE ;
-
+
break;
}
@@ -1007,7 +1007,7 @@ static gboolean xml_align_start_cb(gpointer user_data, ZMapXMLElement set_elemen
err_msg = g_strdup_printf("Unknown Align \"%s\": not found in original_context", align_name) ;
zMapXMLParserRaiseParsingError(parser, err_msg) ;
g_free(err_msg) ;
-
+
result = FALSE ;
}
else
@@ -1076,7 +1076,7 @@ static gboolean xml_block_start_cb(gpointer user_data, ZMapXMLElement set_elemen
err_msg = g_strdup_printf("Bad Format Block name: \"%s\"", block_name) ;
zMapXMLParserRaiseParsingError(parser, err_msg) ;
g_free(err_msg) ;
-
+
result = FALSE ;
}
else
@@ -1090,7 +1090,7 @@ static gboolean xml_block_start_cb(gpointer user_data, ZMapXMLElement set_elemen
err_msg = g_strdup_printf("Unknown Block \"%s\": not found in original_context", block_name) ;
zMapXMLParserRaiseParsingError(parser, err_msg) ;
g_free(err_msg) ;
-
+
result = FALSE ;
}
else
@@ -1157,17 +1157,25 @@ static gboolean xml_featureset_start_cb(gpointer user_data, ZMapXMLElement set_e
request_data->source_id = set_id ;
/* Check to see if we can find this source name in any of the featuresets. */
- if (!(set_data = g_hash_table_lookup(request_data->view->source_2_featureset,
+ if (!request_data->view->source_2_featureset ||
+ !(set_data = g_hash_table_lookup(request_data->view->source_2_featureset,
GINT_TO_POINTER(set_id))))
- {
- char *err_msg ;
+ {
+ // if not defined assume featureset name = source name
- err_msg = g_strdup_printf("Source %s not found in view->source_2_feature_set",
- g_quark_to_string(set_id)) ;
+ featureset_id = set_id;
+ featureset_name = set_name;
+
+#if MH17_NOT_NEEDED
+ char *err_msg ;
+
+ err_msg = g_strdup_printf("Source %s not found in view->source_2_feature_set",
+ g_quark_to_string(set_id)) ;
zMapXMLParserRaiseParsingError(parser, err_msg) ;
g_free(err_msg) ;
-
+
result = FALSE ;
+#endif
}
else
{
@@ -1197,7 +1205,7 @@ static gboolean xml_featureset_start_cb(gpointer user_data, ZMapXMLElement set_e
request_data->orig_feature_set = zMap_g_hash_table_nth(request_data->orig_block->feature_sets, 0) ;
request_data->feature_set
= (ZMapFeatureSet)zMapFeatureAnyCopy((ZMapFeatureAny)(request_data->orig_feature_set)) ;
-
+
result = TRUE ;
}
@@ -1207,33 +1215,40 @@ static gboolean xml_featureset_start_cb(gpointer user_data, ZMapXMLElement set_e
{
ZMapGFFSource source_data ;
- if (!(source_data = g_hash_table_lookup(request_data->view->source_2_sourcedata,
+ if (!request_data->view->source_2_sourcedata ||
+ !(source_data = g_hash_table_lookup(request_data->view->source_2_sourcedata,
GINT_TO_POINTER(set_id))))
{
+ // if not defined assume style name = source name
+
+ request_data->style_id = request_data->source_id;
+
+#if MH17_NOT_NEEDED
char *err_msg ;
err_msg = g_strdup_printf("Source %s not found in view->source_2_sourcedata",
g_quark_to_string(set_id)) ;
zMapXMLParserRaiseParsingError(parser, err_msg) ;
g_free(err_msg) ;
-
+
result = FALSE ;
- }
+#endif
+ }
else
{
request_data->style_id = source_data->style_id ;
+ }
- if (!(request_data->style = zMapFindStyle(request_data->view->orig_styles, request_data->style_id)))
- {
- char *err_msg ;
+ if (!(request_data->style = zMapFindStyle(request_data->view->orig_styles, request_data->style_id)))
+ {
+ char *err_msg ;
- err_msg = g_strdup_printf("Style %s not found in view->orig_styles",
- g_quark_to_string(request_data->style_id)) ;
- zMapXMLParserRaiseParsingError(parser, err_msg) ;
- g_free(err_msg) ;
+ err_msg = g_strdup_printf("Style %s not found in view->orig_styles",
+ g_quark_to_string(request_data->style_id)) ;
+ zMapXMLParserRaiseParsingError(parser, err_msg) ;
+ g_free(err_msg) ;
- result = FALSE ;
- }
+ result = FALSE ;
}
}
@@ -1260,7 +1275,7 @@ static gboolean xml_featureset_start_cb(gpointer user_data, ZMapXMLElement set_e
if (result && (attr = zMapXMLElementGetAttributeByName(set_element, "start")))
{
- request_data->start = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
+ request_data->start = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
(char **)NULL, 10);
}
else
@@ -1268,10 +1283,10 @@ static gboolean xml_featureset_start_cb(gpointer user_data, ZMapXMLElement set_e
zMapXMLParserRaiseParsingError(parser, "start is a required attribute for feature.");
result = FALSE ;
}
-
+
if (result && (attr = zMapXMLElementGetAttributeByName(set_element, "end")))
{
- request_data->end = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
+ request_data->end = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
(char **)NULL, 10);
}
else
@@ -1290,12 +1305,12 @@ static gboolean xml_featureset_start_cb(gpointer user_data, ZMapXMLElement set_e
{
/* If we can't find the featureset it's a serious error and we can't carry on. */
char *err_msg ;
-
+
err_msg = g_strdup_printf("Unknown FeatureSet \"%s\": not found in original_block",
featureset_name) ;
zMapXMLParserRaiseParsingError(parser, err_msg) ;
g_free(err_msg) ;
-
+
result = FALSE ;
}
@@ -1375,9 +1390,9 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
result = TRUE ;
zMapXMLParserCheckIfTrueErrorReturn(request_data->block == NULL,
- parser,
+ parser,
"feature tag not contained within featureset tag");
-
+
if (result && (attr = zMapXMLElementGetAttributeByName(feature_element, "name")))
{
feature_name_q = zMapXMLAttributeGetValue(attr);
@@ -1387,11 +1402,11 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
zMapXMLParserRaiseParsingError(parser, "name is a required attribute for feature.");
result = FALSE ;
}
-
+
if (result && (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
@@ -1399,10 +1414,10 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
zMapXMLParserRaiseParsingError(parser, "start is a required attribute for feature.");
result = FALSE ;
}
-
+
if (result && (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
@@ -1418,7 +1433,7 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
zMapFeatureFormatStrand((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
&(strand));
}
-
+
if((attr = zMapXMLElementGetAttributeByName(feature_element, "score")))
{
score = zMapXMLAttributeValueToDouble(attr);
@@ -1427,7 +1442,7 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
if ((attr = zMapXMLElementGetAttributeByName(feature_element, "start_not_found")))
{
- start_phase = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
+ start_phase = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
(char **)NULL, 10);
start_not_found = TRUE;
@@ -1463,13 +1478,13 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
zMapXMLAttributeGetValue(attr);
}
}
-
+
if (result && !zMapXMLParserLastErrorMsg(parser))
{
feature_name = (char *)g_quark_to_string(feature_name_q);
if (result
- && (request_data->feature = zMapFeatureCreateFromStandardData(feature_name, NULL, "",
+ && (request_data->feature = zMapFeatureCreateFromStandardData(feature_name, NULL, "",
ZMAPSTYLE_MODE_BASIC,
request_data->style,
start, end, has_score,
@@ -1488,7 +1503,7 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
zMapFeatureAddTranscriptStartEnd(request_data->feature, start_not_found,
start_phase, end_not_found);
}
-
+
if ((attr = zMapXMLElementGetAttributeByName(feature_element, "locus")))
{
ZMapFeatureSet locus_feature_set = NULL;
@@ -1498,7 +1513,7 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
GQuark locus_set_id = zMapStyleCreateID(ZMAP_FIXED_STYLE_LOCUS_NAME);
char *new_locus_name = (char *)g_quark_to_string(new_locus_id);
ZMapFeatureTypeStyle locus_style ;
-
+
if (!(locus_style
= zMapFindStyle(request_data->styles, zMapStyleCreateID(ZMAP_FIXED_STYLE_LOCUS_NAME))))
{
@@ -1515,7 +1530,7 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
locus_feature_set = zMapFeatureSetCreate(ZMAP_FIXED_STYLE_LOCUS_NAME, NULL);
zMapFeatureBlockAddFeatureSet(request_data->block, locus_feature_set);
}
-
+
/* For some reason lace passes over odd xml here...
<zmap action="delete_feature">
<featureset>
@@ -1529,10 +1544,10 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
i.e. deleting the locus name it's creating!
*/
- old_feature =
+ old_feature =
(ZMapFeature)zMapFeatureContextFindFeatureFromFeature(request_data->orig_context,
(ZMapFeatureAny)request_data->feature);
-
+
if ((old_feature) && (old_feature->type == ZMAPSTYLE_MODE_TRANSCRIPT)
&& (old_feature->locus_id != 0) && (old_feature->locus_id != new_locus_id))
{
@@ -1547,22 +1562,22 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
* 2 - We are modifying an existing feature.
* 3 - Lace has passed a locus="name" which does not = existing feature locus name.
* 4 - Locus start and end are based on feature start end.
- * If they are the extent of the locus as they should be...
- * The unique_id will be different and therefore the next
+ * If they are the extent of the locus as they should be...
+ * The unique_id will be different and therefore the next
* zMapFeatureContextFindFeatureFromFeature will fail.
* This means the locus won't be deleted as it should be.
*/
zMapLogMessage("loci '%s' & '%s' don't match will delete '%s'",
old_locus_name, new_locus_name, old_locus_name);
-
+
tmp_locus_feature = zMapFeatureCreateFromStandardData(old_locus_name,
NULL, "",
ZMAPSTYLE_MODE_BASIC, locus_style,
- start, end, FALSE, 0.0,
+ start, end, FALSE, 0.0,
ZMAPSTRAND_NONE,
ZMAPPHASE_NONE);
zMapFeatureSetAddFeature(locus_feature_set, tmp_locus_feature);
-
+
if ((old_locus_feature
= zMapFeatureContextFindFeatureFromFeature(request_data->orig_context,
(ZMapFeatureAny)tmp_locus_feature)))
@@ -1577,11 +1592,11 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
locus_feature = zMapFeatureCreateFromStandardData(old_locus_name,
NULL, "",
ZMAPSTYLE_MODE_BASIC, locus_style,
- start, end, FALSE, 0.0,
+ start, end, FALSE, 0.0,
ZMAPSTRAND_NONE,
ZMAPPHASE_NONE);
}
-
+
zMapFeatureDestroy(tmp_locus_feature);
}
else
@@ -1590,27 +1605,27 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
locus_feature = zMapFeatureCreateFromStandardData(new_locus_name,
NULL, "",
ZMAPSTYLE_MODE_BASIC, locus_style,
- start, end, FALSE, 0.0,
+ start, end, FALSE, 0.0,
ZMAPSTRAND_NONE,
ZMAPPHASE_NONE);
-
- }
-
+
+ }
+
/* The feature set and feature need to have their styles set... */
-
- /* managed to get the styles set up. Add the feature to
+
+ /* managed to get the styles set up. Add the feature to
* feature set and finish up the locus. */
- zMapFeatureSetAddFeature(locus_feature_set,
+ zMapFeatureSetAddFeature(locus_feature_set,
locus_feature);
zMapFeatureAddLocus(locus_feature, new_locus_id);
-
+
/* We'll still add the locus to the transcript
* feature so at least this information is
* preserved whatever went on with the styles */
zMapFeatureAddLocus(request_data->feature, new_locus_id);
}
}
-
+
/* THIS DOESN'T DO A DEEP ENOUGH COPY, WE FAIL LATER FOR SOME ACTIONS
* BECAUSE STUFF LIKE THE HOMOL DATA IS NOT COPIED SO WE CAN'T FIND
@@ -1657,7 +1672,7 @@ static gboolean xml_export_start_cb(gpointer user_data, ZMapXMLElement export_el
}
-static gboolean xml_subfeature_end_cb(gpointer user_data, ZMapXMLElement sub_element,
+static gboolean xml_subfeature_end_cb(gpointer user_data, ZMapXMLElement sub_element,
ZMapXMLParser parser)
{
ZMapXMLAttribute attr = NULL;
@@ -1668,8 +1683,8 @@ static gboolean xml_subfeature_end_cb(gpointer user_data, ZMapXMLElement sub_ele
if(xml_data->common.action == ZMAPVIEW_REMOTE_INVALID)
return FALSE;
- zMapXMLParserCheckIfTrueErrorReturn(request_data->feature == NULL,
- parser,
+ zMapXMLParserCheckIfTrueErrorReturn(request_data->feature == NULL,
+ parser,
"a feature end tag without a created feature.");
feature = request_data->feature;
@@ -1678,12 +1693,12 @@ static gboolean xml_subfeature_end_cb(gpointer user_data, ZMapXMLElement sub_ele
GQuark ontology = zMapXMLAttributeGetValue(attr);
ZMapSpanStruct span = {0,0};
ZMapSpan exon_ptr = NULL, intron_ptr = NULL;
-
+
feature->type = ZMAPSTYLE_MODE_TRANSCRIPT;
if((attr = zMapXMLElementGetAttributeByName(sub_element, "start")))
{
- span.x1 = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
+ span.x1 = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
(char **)NULL, 10);
}
else
@@ -1691,7 +1706,7 @@ static gboolean xml_subfeature_end_cb(gpointer user_data, ZMapXMLElement sub_ele
if((attr = zMapXMLElementGetAttributeByName(sub_element, "end")))
{
- span.x2 = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
+ span.x2 = strtol((char *)g_quark_to_string(zMapXMLAttributeGetValue(attr)),
(char **)NULL, 10);
}
else
@@ -1713,8 +1728,8 @@ static gboolean xml_subfeature_end_cb(gpointer user_data, ZMapXMLElement sub_ele
return TRUE; /* tell caller to clean us up. */
}
-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;
@@ -1765,18 +1780,18 @@ static void zoomWindowToFeature(ZMapView view, RequestData input_data, ResponseD
span = (ZMapSpan)(list->data);
- zMapWindowZoomToWorldPosition(view_window->window, FALSE,
+ zMapWindowZoomToWorldPosition(view_window->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[ZMAPVIEW_REMOTE_ZOOM_TO]);
output_data->code = ZMAPXREMOTE_BADREQUEST;
@@ -1786,8 +1801,8 @@ static void zoomWindowToFeature(ZMapView view, RequestData input_data, ResponseD
}
-static ZMapFeatureContextExecuteStatus zoomToFeatureCB(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus zoomToFeatureCB(GQuark key,
+ gpointer data,
gpointer user_data,
char **error_out)
{
diff --git a/src/zmapView/zmapViewUtils.c b/src/zmapView/zmapViewUtils.c
index 367b2b8f977c9e1e38d2306466d6b13b122ce473..d5b80d8acba3be0162ec497a288022403c8a7e8d 100755
--- a/src/zmapView/zmapViewUtils.c
+++ b/src/zmapView/zmapViewUtils.c
@@ -30,7 +30,7 @@
* HISTORY:
* Last edited: Mar 11 13:27 2010 (edgrif)
* Created: Mon Sep 20 10:29:15 2004 (edgrif)
- * CVS info: $Id: zmapViewUtils.c,v 1.19 2010-03-15 11:00:39 mh17 Exp $
+ * CVS info: $Id: zmapViewUtils.c,v 1.20 2010-03-19 08:56:42 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -75,20 +75,8 @@ typedef struct
static void cwh_destroy_key(gpointer cwh_data) ;
static void cwh_destroy_value(gpointer cwh_data) ;
-
-//static void stepDispatch(gpointer data, gpointer user_data) ;
-//static void stepFinished(gpointer data, gpointer user_data) ;
static ZMapViewConnectionStep stepListFindStep(ZMapViewConnectionStepList step_list, ZMapServerReqType request_type) ;
-//static void stepFind(gpointer data, gpointer user_data) ;
-//static void reqFind(gpointer data, gpointer user_data) ;
-//static void connectionRemove(gpointer data, gpointer user_data) ;
static void stepDestroy(gpointer data, gpointer user_data) ;
-//static void requestDestroy(gpointer data, gpointer user_data) ;
-//static void isConnection(gpointer data, gpointer user_data) ;
-//static void removeFailedConnections(ZMapViewConnectionStepList step_list, ZMapViewConnectionStep step) ;
-//static GList *findFailedRequests(ZMapViewConnectionStep step) ;
-//static void findFailed(gpointer data, gpointer user_data) ;
-//static void removeFailed(gpointer data, gpointer user_data) ;
static void getSetCB(void *data, void *user_data) ;
@@ -772,13 +760,15 @@ GQuark zmapViewSrc2FSetGetID(GHashTable *source_2_featureset, char *source_name)
GQuark source_id ;
ZMapGFFSet set_data ;
- source_id = zMapFeatureSetCreateID(source_name) ;
-
- if ((set_data = g_hash_table_lookup(source_2_featureset, GINT_TO_POINTER(set_id))))
- {
- set_id = set_data->feature_set_id ;
- }
+ if(source_2_featureset)
+ {
+ source_id = zMapFeatureSetCreateID(source_name) ;
+ if ((set_data = g_hash_table_lookup(source_2_featureset, GINT_TO_POINTER(set_id))))
+ {
+ set_id = set_data->feature_set_id ;
+ }
+ }
return set_id ;
}
@@ -863,6 +853,8 @@ static void getSetCB(void *data, void *user_data)
GList *set_list = set_data_cb->set_list ;
ZMapGFFSet set_data ;
+ if(!set_data_cb->source_2_featureset)
+ return;
if ((set_data = g_hash_table_lookup(set_data_cb->source_2_featureset, GINT_TO_POINTER(source_id))))
{
diff --git a/src/zmapView/zmapView_P.h b/src/zmapView/zmapView_P.h
index b45435d8b9e21ee27d9a0086b117695f786f4fc4..161e714ed884df580512e2be3086cea5be124480 100755
--- a/src/zmapView/zmapView_P.h
+++ b/src/zmapView/zmapView_P.h
@@ -26,7 +26,7 @@
* HISTORY:
* Last edited: Mar 11 13:27 2010 (edgrif)
* Created: Thu May 13 15:06:21 2004 (edgrif)
- * CVS info: $Id: zmapView_P.h,v 1.57 2010-03-15 11:00:39 mh17 Exp $
+ * CVS info: $Id: zmapView_P.h,v 1.58 2010-03-19 08:56:42 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_VIEW_P_H
@@ -176,8 +176,8 @@ typedef struct _ZMapViewConnectionStruct
/* THESE SHOULD GO, THEY NEED TO BE REPLACED BY THE NEW STEP STRUCT STUFF....... */
/* Record whether this connection will serve up raw sequence or deal with feature edits. */
- gboolean sequence_server ;
- gboolean writeback_server ;
+// gboolean sequence_server ;
+// gboolean writeback_server ;
/* */
ZMapView parent_view ;
@@ -198,7 +198,7 @@ typedef struct _ZMapViewConnectionStruct
/* A "View" is a set of one or more windows that display data retrieved from one or
* more servers. Note that the "View" windows are _not_ top level windows, they are panes
* within a container widget that is supplied as a parent of the View then the View
- * is first created.
+ * is first created.zMapFeatureSetCreateID
* Each View has lists of windows and lists of connections, the view handles these lists
* using zmapWindow and zmapConnection calls.
* */
@@ -248,15 +248,11 @@ typedef struct _ZMapViewStruct
#endif /* NOT_REQUIRED_ATM */
- int connections_loaded ; /* Record of number of connections
- * loaded so for each reload. */
GList *connection_list ; /* Of ZMapViewConnection. */
ZMapViewConnection sequence_server ; /* Which connection to get raw
sequence from. */
ZMapViewConnection writeback_server ; /* Which connection to send edits to. */
-// ZMapViewConnectionStepList step_list ; /* List of steps required to get data from server. */
-
/* The features....needs thought as to how this updated/constructed..... */
ZMapFeatureContext features ;
@@ -266,11 +262,11 @@ typedef struct _ZMapViewStruct
GData *orig_styles ;
GHashTable *featureset_2_stylelist ; /* Mapping of each feature_set to all
- the styles it requires. */
+ the styles it requires. using a GHashTable of GLists of style quark id's.*/
- GHashTable *source_2_featureset ; /* Mapping of a feature source to a featureset. */
+ GHashTable *source_2_featureset ; /* Mapping of a feature source to a featureset using ZMapGFFSet */
- GHashTable *source_2_sourcedata ; /* Mapping of a feature source to its data. */
+ GHashTable *source_2_sourcedata ; /* Mapping of a feature source to its data.using ZMapGFFSource */
/* We need to know if the user has done a revcomp for a few reasons to do with coord
* transforms and the way annotation is done....*/
diff --git a/src/zmapWindow/zmapWindowItem.c b/src/zmapWindow/zmapWindowItem.c
index 66fe12f3b490d780d838733ac9ed52007627593d..13079e87fef505ac67f575ad339999346a44ac53 100755
--- a/src/zmapWindow/zmapWindowItem.c
+++ b/src/zmapWindow/zmapWindowItem.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: Feb 15 14:06 2010 (edgrif)
* Created: Thu Sep 8 10:37:24 2005 (edgrif)
- * CVS info: $Id: zmapWindowItem.c,v 1.128 2010-03-04 15:13:00 mh17 Exp $
+ * CVS info: $Id: zmapWindowItem.c,v 1.129 2010-03-19 08:56:42 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -81,8 +81,8 @@ typedef struct
#if NOT_USED
-static gboolean simple_highlight_region(FooCanvasPoints **points_out,
- FooCanvasItem *subject,
+static gboolean simple_highlight_region(FooCanvasPoints **points_out,
+ FooCanvasItem *subject,
gpointer user_data);
#endif
static void highlightCB(gpointer data, gpointer user_data) ;
@@ -98,11 +98,11 @@ static void getVisibleCanvas(ZMapWindow window,
double *screenx1_out, double *screeny1_out,
double *screenx2_out, double *screeny2_out) ;
-static FooCanvasItem *translation_item_from_block_frame(ZMapWindow window, char *column_name,
+static FooCanvasItem *translation_item_from_block_frame(ZMapWindow window, char *column_name,
gboolean require_visible,
ZMapFeatureBlock block, ZMapFrame frame) ;
-static void fill_workaround_struct(ZMapWindowContainerGroup container,
+static void fill_workaround_struct(ZMapWindowContainerGroup container,
FooCanvasPoints *points,
ZMapContainerLevelType level,
gpointer user_data);
@@ -129,7 +129,7 @@ GList *zmapWindowItemSortByPostion(GList *feature_item_list)
gboolean zmapWindowItemGetStrandFrame(FooCanvasItem *item, ZMapStrand *set_strand, ZMapFrame *set_frame)
-{
+{
ZMapWindowContainerFeatureSet container;
ZMapFeature feature ;
gboolean result = FALSE ;
@@ -158,7 +158,7 @@ GList *zmapWindowItemListToFeatureList(GList *item_list)
}
-/*
+/*
(TYPE)zmapWindowItemGetFeatureAny(ITEM, STRUCT_TYPE)
#define zmapWindowItemGetFeatureSet(ITEM) (ZMapFeatureContext)zmapWindowItemGetFeatureAnyType((ITEM), ZMAPFEATURE_STRUCT_CONTEXT)
@@ -210,16 +210,16 @@ ZMapFeatureAny zmapWindowItemGetFeatureAnyType(FooCanvasItem *item, ZMapFeatureS
}
/*
- * Feature Item highlighting....
+ * Feature Item highlighting....
*/
/* Highlight a feature or list of related features (e.g. all hits for same query sequence).
- *
+ *
* */
void zMapWindowHighlightObject(ZMapWindow window, FooCanvasItem *item,
gboolean replace_highlight_item, gboolean highlight_same_names)
-{
+{
zmapWindowHighlightObject(window, item, replace_highlight_item, highlight_same_names) ;
return ;
@@ -240,24 +240,24 @@ static ZMapFeatureContextExecuteStatus highlight_feature(GQuark key, gpointer da
if(highlight_data->multiple_select || highlight_data->highlighted == 0)
{
replace_highlight = !(highlight_data->multiple_select);
-
+
if((feature_item = zmapWindowFToIFindFeatureItem(highlight_data->window->context_to_item,
feature_in->strand, ZMAPFRAME_NONE,
feature_in)))
{
if(highlight_data->multiple_select)
replace_highlight = !(zmapWindowFocusIsItemInHotColumn(highlight_data->window->focus, feature_item));
-
+
feature_current = zmapWindowItemGetFeature(feature_item);
zMapAssert(feature_current);
- if(feature_in->type == ZMAPSTYLE_MODE_TRANSCRIPT &&
+ if(feature_in->type == ZMAPSTYLE_MODE_TRANSCRIPT &&
feature_in->feature.transcript.exons->len > 0 &&
feature_in->feature.transcript.exons->len != feature_current->feature.transcript.exons->len)
{
ZMapSpan span;
int i;
-
+
/* need to do something to find sub feature items??? */
for(i = 0; i < feature_in->feature.transcript.exons->len; i++)
{
@@ -288,7 +288,7 @@ static ZMapFeatureContextExecuteStatus highlight_feature(GQuark key, gpointer da
else
/* we need to highlight the full feature */
zmapWindowHighlightObject(highlight_data->window, feature_item, replace_highlight, TRUE);
-
+
if(replace_highlight)
highlight_data->highlighted = 0;
else
@@ -307,7 +307,7 @@ void zMapWindowHighlightObjects(ZMapWindow window, ZMapFeatureContext context, g
highlight_data.window = window;
highlight_data.multiple_select = multiple_select;
- highlight_data.highlighted =
+ highlight_data.highlighted =
highlight_data.feature_count = 0;
zMapFeatureContextExecute((ZMapFeatureAny)context, ZMAPFEATURE_STRUCT_FEATURE,
@@ -318,7 +318,7 @@ void zMapWindowHighlightObjects(ZMapWindow window, ZMapFeatureContext context, g
void zmapWindowHighlightObject(ZMapWindow window, FooCanvasItem *item,
gboolean replace_highlight_item, gboolean highlight_same_names)
-{
+{
ZMapWindowCanvasItem canvas_item ;
ZMapFeature feature ;
GList *set_items ;
@@ -346,7 +346,7 @@ void zmapWindowHighlightObject(ZMapWindow window, FooCanvasItem *item,
if (highlight_same_names)
{
char *set_strand, *set_frame ;
-
+
set_strand = set_frame = "*" ;
set_items = zmapWindowFToIFindSameNameItems(window->context_to_item, set_strand, set_frame, feature) ;
@@ -386,11 +386,11 @@ void zmapWindowHighlightObject(ZMapWindow window, FooCanvasItem *item,
FOO_CANVAS_ITEM(canvas_item), frame_itr)))
{
FooCanvasGroup *container;
-
+
container = (FooCanvasGroup *)zmapWindowContainerCanvasItemGetContainer(framed_3ft);
-
+
}
-
+
}
}
@@ -400,7 +400,7 @@ void zmapWindowHighlightObject(ZMapWindow window, FooCanvasItem *item,
}
void zMapWindowHighlightFocusItems(ZMapWindow window)
-{
+{
FooCanvasItem *hot_item ;
FooCanvasGroup *hot_column = NULL;
@@ -417,7 +417,7 @@ void zMapWindowHighlightFocusItems(ZMapWindow window)
void zMapWindowUnHighlightFocusItems(ZMapWindow window)
-{
+{
FooCanvasItem *hot_item ;
FooCanvasGroup *hot_column ;
@@ -429,7 +429,7 @@ void zMapWindowUnHighlightFocusItems(ZMapWindow window)
zmapWindowFocusForEachFocusItem(window->focus, unhighlightCB, window) ;
if (hot_column || hot_item)
- zmapWindowFocusReset(window->focus) ;
+ zmapWindowFocusReset(window->focus) ;
return ;
}
@@ -482,7 +482,7 @@ FooCanvasItem *zmapWindowItemGetNthChild(FooCanvasGroup *compound_item, int chil
}
/* Need to test whether this works for groups...it should do....
- *
+ *
* For simple features or the parent of a compound feature the raise is done on the item
* directly, for compound objects we want to raise the parent so that the whole item
* is still raised.
@@ -524,18 +524,18 @@ FooCanvasItem *zmapWindowItemGetDNAParentItem(ZMapWindow window, FooCanvasItem *
if((feature = zmapWindowItemGetFeature(item)))
{
- if((block = (ZMapFeatureBlock)(zMapFeatureGetParentGroup((ZMapFeatureAny)feature, ZMAPFEATURE_STRUCT_BLOCK))) &&
+ if((block = (ZMapFeatureBlock)(zMapFeatureGetParentGroup((ZMapFeatureAny)feature, ZMAPFEATURE_STRUCT_BLOCK))) &&
(feature_name = zMapFeatureDNAFeatureName(block)))
{
- dna_id = zMapFeatureCreateID(ZMAPSTYLE_MODE_RAW_SEQUENCE,
- feature_name,
+ dna_id = zMapFeatureCreateID(ZMAPSTYLE_MODE_RAW_SEQUENCE,
+ feature_name,
ZMAPSTRAND_FORWARD, /* ALWAYS FORWARD */
block->block_to_sequence.q1,
block->block_to_sequence.q2,
0,0);
g_free(feature_name);
}
-
+
if((dna_item = zmapWindowFToIFindItemFull(window->context_to_item,
block->parent->unique_id,
block->unique_id,
@@ -604,9 +604,9 @@ FooCanvasItem *zmapWindowItemGetDNATextItem(ZMapWindow window, FooCanvasItem *it
/* highlights the dna given any foocanvasitem (with a feature) and a start and end */
/* This _only_ highlights in the current window! */
-void zmapWindowItemHighlightDNARegion(ZMapWindow window,
- FooCanvasItem *item,
- int region_start,
+void zmapWindowItemHighlightDNARegion(ZMapWindow window,
+ FooCanvasItem *item,
+ int region_start,
int region_end)
{
ZMapWindowSequenceFeature sequence_feature;
@@ -652,7 +652,7 @@ FooCanvasItem *zmapWindowItemGetTranslationItemFromItemFrame(ZMapWindow window,
{
/* First go up to block... */
block = (ZMapFeatureBlock)
- (zMapFeatureGetParentGroup((ZMapFeatureAny)(feature),
+ (zMapFeatureGetParentGroup((ZMapFeatureAny)(feature),
ZMAPFEATURE_STRUCT_BLOCK));
zMapAssert(block);
@@ -667,7 +667,7 @@ FooCanvasItem *zmapWindowItemGetTranslationItemFromItemFrame(ZMapWindow window,
return translation;
}
-void zmapWindowItemHighlightRegionTranslations(ZMapWindow window, FooCanvasItem *item,
+void zmapWindowItemHighlightRegionTranslations(ZMapWindow window, FooCanvasItem *item,
int region_start, int region_end)
{
int frame;
@@ -683,7 +683,7 @@ void zmapWindowItemHighlightRegionTranslations(ZMapWindow window, FooCanvasItem
/* highlights the translation given any foocanvasitem (with a
* feature), frame and a start and end (protein seq coords) */
/* This _only_ highlights in the current window! */
-void zmapWindowItemHighlightTranslationRegion(ZMapWindow window, FooCanvasItem *item,
+void zmapWindowItemHighlightTranslationRegion(ZMapWindow window, FooCanvasItem *item,
ZMapFrame required_frame,
int region_start, int region_end)
{
@@ -692,7 +692,7 @@ void zmapWindowItemHighlightTranslationRegion(ZMapWindow window, FooCanvasItem *
if((translation_item = zmapWindowItemGetTranslationItemFromItemFrame(window, item, required_frame)))
{
FooCanvasGroup *container;
-
+
container = (FooCanvasGroup *)zmapWindowContainerCanvasItemGetContainer(translation_item);
/* we just want to call sequenceSelect() */
@@ -755,7 +755,7 @@ FooCanvasGroup *zmapWindowItemGetTranslationColumnFromBlock(ZMapWindow window, Z
feature_set,
ZMAPSTRAND_FORWARD, /* STILL ALWAYS FORWARD */
ZMAPFRAME_NONE);
-
+
return FOO_CANVAS_GROUP(translation);
}
@@ -793,7 +793,7 @@ FooCanvasItem *zmapWindowItemGetShowTranslationColumn(ZMapWindow window, FooCanv
//feature_set->style = style;
zMapFeatureBlockAddFeatureSet(block, feature_set);
}
-
+
if (feature_set)
{
ZMapWindowContainerGroup parent_container;
@@ -812,12 +812,12 @@ FooCanvasItem *zmapWindowItemGetShowTranslationColumn(ZMapWindow window, FooCanv
#endif /* SIMPLIER */
parent_container = zmapWindowContainerUtilsItemGetParentLevel(item, ZMAPCONTAINER_LEVEL_BLOCK);
-
+
/* Get the Forward Group Parent Container... */
forward_container = zmapWindowContainerBlockGetContainerStrand((ZMapWindowContainerBlock)parent_container, ZMAPSTRAND_FORWARD);
/* zmapWindowCreateSetColumns needs the Features not the Parent. */
forward_features = zmapWindowContainerGetFeatures((ZMapWindowContainerGroup)forward_container);
-
+
/* make the column... */
if (zmapWindowCreateSetColumns(window,
forward_features,
@@ -840,7 +840,7 @@ FooCanvasItem *zmapWindowItemGetShowTranslationColumn(ZMapWindow window, FooCanv
return translation;
}
-static FooCanvasItem *translation_item_from_block_frame(ZMapWindow window, char *column_name,
+static FooCanvasItem *translation_item_from_block_frame(ZMapWindow window, char *column_name,
gboolean require_visible,
ZMapFeatureBlock block, ZMapFrame frame)
{
@@ -891,7 +891,7 @@ FooCanvasItem *zmapWindowItemGetTranslationItemFromItem(ZMapWindow window, FooCa
{
/* First go up to block... */
block = (ZMapFeatureBlock)
- (zMapFeatureGetParentGroup((ZMapFeatureAny)(feature),
+ (zMapFeatureGetParentGroup((ZMapFeatureAny)(feature),
ZMAPFEATURE_STRUCT_BLOCK));
zMapAssert(block);
@@ -915,7 +915,7 @@ ZMapFeatureTypeStyle zmapWindowItemGetStyle(ZMapWindow window, FooCanvasItem *it
ZMapFeature feature = NULL;
canvas_item = zMapWindowCanvasItemIntervalGetTopLevelObject(item);
-
+
if((canvas_item != NULL) &&
(feature = zMapWindowCanvasItemGetFeature(canvas_item)))
{
@@ -931,10 +931,10 @@ ZMapFeatureTypeStyle zmapWindowItemGetStyle(ZMapWindow window, FooCanvasItem *it
/* Finds the feature item in a window corresponding to the supplied feature item..which is
* usually one from a different window....
- *
+ *
* This routine can return NULL if the user has two different sequences displayed and hence
* there will be items in one window that are not present in another.
- *
+ *
* */
FooCanvasItem *zMapWindowFindFeatureItemByItem(ZMapWindow window, FooCanvasItem *item)
{
@@ -1035,7 +1035,7 @@ gboolean zmapWindowItemIsOnScreen(ZMapWindow window, FooCanvasItem *item, gboole
/* Scrolls to an item if that item is not visible on the scren.
- *
+ *
* NOTE: scrolling is only done in the axis in which the item is completely
* invisible, the other axis is left unscrolled so that the visible portion
* of the feature remains unaltered.
@@ -1117,7 +1117,7 @@ gboolean zmapWindowItemRegionIsVisible(ZMapWindow window, FooCanvasItem *item)
feature = (ZMapFeature) zmapWindowItemGetFeatureAnyType(item, -1) ;
zMapAssert(feature) ;
-
+
/* Get the features canvas coords (may be very different for align block features... */
zMapFeature2MasterCoords(feature, &feature_x1, &feature_x2);
@@ -1130,7 +1130,7 @@ gboolean zmapWindowItemRegionIsVisible(ZMapWindow window, FooCanvasItem *item)
{
visible = TRUE;
}
-
+
return visible;
}
@@ -1154,7 +1154,7 @@ void zmapWindowItemCentreOnItemSubPart(ZMapWindow window, FooCanvasItem *item,
{
double ix1, ix2, iy1, iy2;
int cx1, cx2, cy1, cy2;
- int final_canvasx, final_canvasy,
+ int final_canvasx, final_canvasy,
tmpx, tmpy, cheight, cwidth;
gboolean debug = FALSE;
@@ -1252,8 +1252,8 @@ void zmapWindowItemCentreOnItemSubPart(ZMapWindow window, FooCanvasItem *item,
/* get canvas coords to work with */
- foo_canvas_w2c(item->canvas, ix1, iy1, &cx1, &cy1);
- foo_canvas_w2c(item->canvas, ix2, iy2, &cx2, &cy2);
+ foo_canvas_w2c(item->canvas, ix1, iy1, &cx1, &cy1);
+ foo_canvas_w2c(item->canvas, ix2, iy2, &cx2, &cy2);
if(debug)
{
@@ -1269,7 +1269,7 @@ void zmapWindowItemCentreOnItemSubPart(ZMapWindow window, FooCanvasItem *item,
tmpy += 1;
final_canvasx = cx1 + (tmpx / 2);
final_canvasy = cy1 + (tmpy / 2);
-
+
tmpx = GTK_WIDGET(window->canvas)->allocation.width;
tmpy = GTK_WIDGET(window->canvas)->allocation.height;
if(tmpx & 1)
@@ -1277,14 +1277,14 @@ void zmapWindowItemCentreOnItemSubPart(ZMapWindow window, FooCanvasItem *item,
if(tmpy & 1)
tmpy -= 1;
cwidth = tmpx / 2; cheight = tmpy / 2;
- final_canvasx -= cwidth;
+ final_canvasx -= cwidth;
final_canvasy -= cheight;
if(debug)
{
printf("[zmapWindowItemCentreOnItem] cwidth=%d cheight=%d\n", cwidth, cheight);
printf("[zmapWindowItemCentreOnItem] scrolling to"
- " canvas x=%d y=%d\n",
+ " canvas x=%d y=%d\n",
final_canvasx, final_canvasy);
}
@@ -1391,7 +1391,7 @@ void zmapWindowPrintI2W(FooCanvasItem *item, char *text, double x1_in, double y1
/* moves a feature to new coordinates */
-void zMapWindowMoveItem(ZMapWindow window, ZMapFeature origFeature,
+void zMapWindowMoveItem(ZMapWindow window, ZMapFeature origFeature,
ZMapFeature modFeature, FooCanvasItem *item)
{
double top, bottom, offset;
@@ -1402,11 +1402,11 @@ void zMapWindowMoveItem(ZMapWindow window, ZMapFeature origFeature,
top = modFeature->x1;
bottom = modFeature->x2;
zmapWindowSeq2CanOffset(&top, &bottom, offset);
-
+
if (modFeature->type == ZMAPSTYLE_MODE_TRANSCRIPT)
{
zMapAssert(origFeature);
-
+
foo_canvas_item_set(item->parent, "y", top, NULL);
}
else
@@ -1421,7 +1421,7 @@ void zMapWindowMoveItem(ZMapWindow window, ZMapFeature origFeature,
/* Returns the sequence coords that correspond to the given _world_ foocanvas coords.
- *
+ *
* NOTE that although we only return y coords, we need the world x coords as input
* in order to find the right foocanvas item from which to get the sequence coords. */
gboolean zmapWindowWorld2SeqCoords(ZMapWindow window,
@@ -1436,8 +1436,7 @@ gboolean zmapWindowWorld2SeqCoords(ZMapWindow window,
{
FooCanvasGroup *block_container ;
ZMapFeatureBlock block ;
-
-zMapLogWarning("got foo item at %f %f %f %f",wx1,wy1,wx2,wy2);
+
/* Getting the block struct as well is a bit belt and braces...we could return it but
* its redundant info. really. */
if ((block_container = FOO_CANVAS_GROUP(zmapWindowContainerUtilsItemGetParentLevel(item, ZMAPCONTAINER_LEVEL_BLOCK)))
@@ -1448,7 +1447,7 @@ zMapLogWarning("got foo item at %f %f %f %f",wx1,wy1,wx2,wy2);
offset = (double)(block->block_to_sequence.q1 - 1) ; /* - 1 for 1 based coord system. */
my_foo_canvas_world_bounds_to_item(FOO_CANVAS_ITEM(block_container), &wx1, &wy1, &wx2, &wy2) ;
-zMapLogWarning("%s","got block");
+
if (block_grp_out)
*block_grp_out = block_container ;
@@ -1462,7 +1461,7 @@ zMapLogWarning("%s","got block");
else
zMapLogWarning("%s", "No Block Container");
}
- else
+ else
{
get_item_at_workaround_struct workaround_struct = {NULL};
double scroll_x2;
@@ -1471,7 +1470,6 @@ zMapLogWarning("%s","got block");
workaround_struct.wx2 = wx2;
workaround_struct.wy1 = wy1;
workaround_struct.wy2 = wy2;
-zMapLogWarning("Workaround %f %f %f %f",wx1,wy1,wx2,wy2);
/* For some reason foo_canvas_get_item_at() fails to find items
* a lot of the time even when it shouldn't and so we need a solution. */
@@ -1530,8 +1528,8 @@ gboolean zmapWindowItem2SeqCoords(FooCanvasItem *item, int *y1, int *y2)
#if NOT_USED
-static gboolean simple_highlight_region(FooCanvasPoints **points_out,
- FooCanvasItem *subject,
+static gboolean simple_highlight_region(FooCanvasPoints **points_out,
+ FooCanvasItem *subject,
gpointer user_data)
{
StartEndTextHighlight high_data = (StartEndTextHighlight)user_data;
@@ -1540,7 +1538,7 @@ static gboolean simple_highlight_region(FooCanvasPoints **points_out,
int index1, index2;
gboolean first_found, last_found;
gboolean redraw = FALSE;
-
+
points = foo_canvas_points_new(8);
index1 = high_data->start;
@@ -1786,7 +1784,7 @@ void my_foo_canvas_item_goto(FooCanvasItem *item, double *x, double *y)
if (x || y)
{
- x1 = y1 = x2 = y2 = 0.0 ;
+ x1 = y1 = x2 = y2 = 0.0 ;
dx = dy = 0.0 ;
foo_canvas_item_get_bounds(item, &x1, &y1, &x2, &y2) ;
@@ -1820,7 +1818,7 @@ gboolean zmapWindowItemIsVisible(FooCanvasItem *item) // mh17:not called from a
{
visible = zmapWindowItemIsShown(FOO_CANVAS_ITEM(parent));
/* how many parents we got? */
- parent = FOO_CANVAS_GROUP(FOO_CANVAS_ITEM(parent)->parent);
+ parent = FOO_CANVAS_GROUP(FOO_CANVAS_ITEM(parent)->parent);
}
}
#endif
@@ -1831,17 +1829,17 @@ gboolean zmapWindowItemIsVisible(FooCanvasItem *item) // mh17:not called from a
gboolean zmapWindowItemIsShown(FooCanvasItem *item)
{
gboolean visible = FALSE;
-
+
zMapAssert(FOO_IS_CANVAS_ITEM(item)) ;
- g_object_get(G_OBJECT(item),
+ g_object_get(G_OBJECT(item),
"visible", &visible,
NULL);
return visible;
}
-void zmapWindowItemGetVisibleCanvas(ZMapWindow window,
+void zmapWindowItemGetVisibleCanvas(ZMapWindow window,
double *wx1, double *wy1,
double *wx2, double *wy2)
{
@@ -1853,7 +1851,7 @@ void zmapWindowItemGetVisibleCanvas(ZMapWindow window,
-/*
+/*
* Internal routines.
*/
@@ -1905,7 +1903,7 @@ static void highlightItem(ZMapWindow window, FooCanvasItem *item, gboolean highl
if(highlight)
{
if(window->highlights_set.item)
- zMapWindowCanvasItemSetIntervalColours(item, ZMAPSTYLE_COLOURTYPE_SELECTED,
+ zMapWindowCanvasItemSetIntervalColours(item, ZMAPSTYLE_COLOURTYPE_SELECTED,
&(window->colour_item_highlight));
else
zMapWindowCanvasItemSetIntervalColours(item, ZMAPSTYLE_COLOURTYPE_SELECTED, NULL);
@@ -1926,10 +1924,10 @@ static gint sortByPositionCB(gconstpointer a, gconstpointer b)
FooCanvasItem *item_b = (FooCanvasItem *)b ;
ZMapFeature feat_a ;
ZMapFeature feat_b ;
-
+
feat_a = zmapWindowItemGetFeature(item_a);
zMapAssert(feat_a) ;
-
+
feat_b = zmapWindowItemGetFeature(item_b);
zMapAssert(feat_b) ;
@@ -1987,7 +1985,7 @@ static void getVisibleCanvas(ZMapWindow window,
}
/* workaround for a failing foo_canvas_item_at(). Actually only looks for blocks! */
-static void fill_workaround_struct(ZMapWindowContainerGroup container,
+static void fill_workaround_struct(ZMapWindowContainerGroup container,
FooCanvasPoints *points,
ZMapContainerLevelType level,
gpointer user_data)
@@ -2008,10 +2006,10 @@ if(!container) return;
if((cont_backgrd = (FooCanvasItem *)zmapWindowContainerGetBackground(container)))
{
double offset;
- AreaStruct area_src = {workaround->wx1, workaround->wy1, workaround->wx2, workaround->wy2},
+ AreaStruct area_src = {workaround->wx1, workaround->wy1, workaround->wx2, workaround->wy2},
area_block = {};
foo_canvas_item_get_bounds(cont_backgrd,
- &(area_block.x1), &(area_block.y1),
+ &(area_block.x1), &(area_block.y1),
&(area_block.x2), &(area_block.y2));
/* The original size of the block needs to be used, not the longitem resized size. */
@@ -2019,7 +2017,7 @@ if(!container) return;
{
double long_y1, long_y2;
/* Get the original size of the block's background, see caller & RT #75034 */
- if(zmapWindowLongItemCoords(workaround->window->long_items, cont_backgrd,
+ if(zmapWindowLongItemCoords(workaround->window->long_items, cont_backgrd,
&long_y1, &long_y2))
{
area_block.y1 = long_y1;
@@ -2028,7 +2026,7 @@ if(!container) return;
}
if((workaround->wx1 >= area_block.x1 && workaround->wx2 <= area_block.x2 &&
- workaround->wy1 >= area_block.y1 && workaround->wy2 <= area_block.y2) ||
+ workaround->wy1 >= area_block.y1 && workaround->wy2 <= area_block.y2) ||
areas_intersect_gt_threshold(&area_src, &area_block, 0.55))
{
/* We're inside */
@@ -2037,8 +2035,8 @@ if(!container) return;
offset = (double)(block->block_to_sequence.q1 - 1) ; /* - 1 for 1 based coord system. */
- my_foo_canvas_world_bounds_to_item(FOO_CANVAS_ITEM(cont_backgrd),
- &(workaround->wx1), &(workaround->wy1),
+ my_foo_canvas_world_bounds_to_item(FOO_CANVAS_ITEM(cont_backgrd),
+ &(workaround->wx1), &(workaround->wy1),
&(workaround->wx2), &(workaround->wy2)) ;
workaround->seq_x = floor(workaround->wy1 - offset + 0.5) ;
@@ -2055,7 +2053,7 @@ if(!container) return;
workaround->wx2, workaround->wy2);
}
}
-
+
}
break;
default:
@@ -2084,7 +2082,7 @@ static gboolean areas_intersection(AreaStruct *area_1, AreaStruct *area_2, AreaS
overlap = TRUE;
}
else
- intersect->x1 = intersect->y1 =
+ intersect->x1 = intersect->y1 =
intersect->x2 = intersect->y2 = 0.0;
return overlap;
@@ -2102,7 +2100,7 @@ static gboolean areas_intersect_gt_threshold(AreaStruct *area_1, AreaStruct *are
{
aI = (inter.x2 - inter.x1 + 1.0) * (inter.y2 - inter.y1 + 1.0);
a1 = (area_1->x2 - area_1->x1 + 1.0) * (area_1->y2 - area_1->y1 + 1.0);
-
+
if(threshold > 0.0 && threshold < 1.0)
threshold = 1.0 - threshold;
else
@@ -2131,17 +2129,17 @@ static gboolean areas_intersect_gt_threshold(AreaStruct *area_1, AreaStruct *are
static gboolean foo_canvas_items_get_intersect(FooCanvasItem *i1, FooCanvasItem *i2, FooCanvasPoints **points_out)
{
gboolean intersect = FALSE;
-
+
if(points_out)
{
AreaStruct a1 = {};
AreaStruct a2 = {};
AreaStruct i = {};
-
- foo_canvas_item_get_bounds(i1,
+
+ foo_canvas_item_get_bounds(i1,
&(a1.x1), (&a1.y1),
&(a1.x2), (&a1.y2));
- foo_canvas_item_get_bounds(i2,
+ foo_canvas_item_get_bounds(i2,
&(a2.x1), (&a2.y1),
&(a2.x2), (&a2.y2));
@@ -2166,10 +2164,10 @@ static gboolean foo_canvas_items_intersect(FooCanvasItem *i1, FooCanvasItem *i2,
AreaStruct a2 = {};
gboolean intersect = FALSE;
- foo_canvas_item_get_bounds(i1,
+ foo_canvas_item_get_bounds(i1,
&(a1.x1), (&a1.y1),
&(a1.x2), (&a1.y2));
- foo_canvas_item_get_bounds(i2,
+ foo_canvas_item_get_bounds(i2,
&(a2.x1), (&a2.y1),
&(a2.x2), (&a2.y2));