From bbb590f5843bcc986929d22418519e638b45786e Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Tue, 9 Aug 2005 10:51:40 +0000
Subject: [PATCH] Move style out of feature set into features so style is
indepenent of feature_set.
---
src/include/ZMap/zmapFeature.h | 75 ++++++++++++++++++++----------
src/zmapFeature/zmapFeature.c | 14 ++++--
src/zmapFeature/zmapFeatureUtils.c | 71 ++++++++++++++++++----------
3 files changed, 106 insertions(+), 54 deletions(-)
diff --git a/src/include/ZMap/zmapFeature.h b/src/include/ZMap/zmapFeature.h
index a6e51b498..8600d38ac 100755
--- a/src/include/ZMap/zmapFeature.h
+++ b/src/include/ZMap/zmapFeature.h
@@ -25,9 +25,9 @@
* Description: Data structures describing a sequence feature.
*
* HISTORY:
- * Last edited: Jul 28 09:36 2005 (rnc)
+ * Last edited: Aug 9 11:51 2005 (edgrif)
* Created: Fri Jun 11 08:37:19 2004 (edgrif)
- * CVS info: $Id: zmapFeature.h,v 1.37 2005-07-28 08:36:38 rnc Exp $
+ * CVS info: $Id: zmapFeature.h,v 1.38 2005-08-09 10:51:40 edgrif Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_FEATURE_H
@@ -142,8 +142,12 @@ typedef struct
* QUITE A NUMBER OF ACCESS FUNCTIONS.... */
+
+/* We need some forward declarations for pointers we include in some structs. */
typedef struct ZMapFeatureAlignmentStruct_ *ZMapFeatureAlignment ;
+typedef struct ZMapFeatureTypeStyleStruct_ *ZMapFeatureTypeStyle ;
+
/* WARNING: READ THIS BEFORE CHANGING ANY FEATURE STRUCTS:
*
@@ -162,14 +166,16 @@ typedef struct ZMapFeatureAnyStruct_
{
GQuark unique_id ; /* Unique id of this feature. */
GQuark original_id ; /* Original id of this feature. */
-
-
} ZMapFeatureAnyStruct, *ZMapFeatureAny ;
-/* Holds a set of ZMapFeatureSet's.
- * Structure would usually contain a complete set of data from a server for a particular span
- * of a sequence. */
+
+/* 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_
{
GQuark unique_id ; /* Unique id of this feature. */
@@ -193,12 +199,20 @@ typedef struct ZMapFeatureContextStruct_
ZMapMapBlockStruct sequence_to_parent ; /* Shows how this sequence maps to its
ultimate parent. */
+
+ GList *feature_set_names ; /* Global list of _names_ of all requested
+ feature sets for the context,
+ _only_ these sets are loaded into
+ the context. */
+
+ GList *styles ; /* Global list of all styles, some of
+ these styles may not be used if not
+ required for the list given by
+ feature_set_names. */
+
ZMapFeatureAlignment master_align ; /* The target/master alignment out of
the below set. */
- GList *types ; /* Global list of types, _only_ these
- types are loaded into the context. */
-
GData *alignments ; /* All the alignements for this zmap
as a set of ZMapFeatureAlignment. */
@@ -237,9 +251,10 @@ typedef struct ZMapFeatureBlockStruct_
-/* Holds a set of ZMapFeature's, note that the id for the set is the same as the style name for
- * the set of features. There is duplication here and probably we should hold a pointer to the
- * the style here.... */
+/* Holds a set of ZMapFeature's, note that the id for the set is by default the same name
+ * as the style for all features in the set. BUT it may not be, the set may consist of
+ * features with many types/styles. The set id is completely independent of the style name.
+ */
typedef struct ZMapFeatureSetStruct_
{
GQuark unique_id ; /* Unique id for feature set used by
@@ -249,9 +264,6 @@ typedef struct ZMapFeatureSetStruct_
ZMapFeatureBlock parent_block ; /* Our parent block. */
GData *features ; /* A set of ZMapFeatureStruct. */
-
- GQuark style_id ; /* Style for these features. */
-
} ZMapFeatureSetStruct, *ZMapFeatureSet ;
@@ -302,6 +314,8 @@ typedef struct ZMapFeatureStruct_
ZMapFeatureSet parent_set ; /* Our containing set. */
+ ZMapFeatureTypeStyle style ; /* style defining how this feature is
+ drawn. */
ZMapFeatureID db_id ; /* unique DB identifier, currently
unused but will be..... */
@@ -369,7 +383,7 @@ typedef struct ZMapFeatureTypeStyleStruct_
gboolean frame_specific ;
gboolean show_rev_strand ;
-} ZMapFeatureTypeStyleStruct, *ZMapFeatureTypeStyle ;
+} ZMapFeatureTypeStyleStruct ;
@@ -398,7 +412,8 @@ ZMapFeature zMapFeatureFindFeatureInSet(ZMapFeatureSet feature_set, GQuark featu
GData *zMapFeatureFindSetInContext(ZMapFeatureContext feature_context, GQuark set_id) ;
-ZMapFeatureContext zMapFeatureContextCreate(char *sequence, int start, int end, GList *types) ;
+ZMapFeatureContext zMapFeatureContextCreate(char *sequence, int start, int end,
+ GList *styles, GList *feature_set_names) ;
gboolean zMapFeatureContextMerge(ZMapFeatureContext *current_context_inout,
ZMapFeatureContext new_context,
ZMapFeatureContext *diff_context_out) ;
@@ -419,21 +434,33 @@ void zMapFeatureBlockDestroy(ZMapFeatureBlock block, gboolean free_data) ;
ZMapFeature zmapFeatureCreateEmpty(void) ;
gboolean zmapFeatureAugmentData(ZMapFeature feature, char *feature_name_id, char *name,
- char *sequence, ZMapFeatureType feature_type,
- int start, int end, double score, ZMapStrand strand,
- ZMapPhase phase,
+ char *sequence,
+ ZMapFeatureType feature_type, ZMapFeatureTypeStyle style,
+ int start, int end, double score, ZMapStrand strand, ZMapPhase phase,
ZMapHomolType homol_type_out, int start_out, int end_out,
GArray *gaps) ;
-GQuark zMapFeatureGetStyleQuark(ZMapFeature feature) ;
+
+GList *zMapStylesGetNames(GList *styles) ;
+
+
ZMapFeatureTypeStyle zMapFeatureGetStyle(ZMapFeature feature) ;
+
+ZMapFeatureSet zMapFeatureGetSet(ZMapFeature feature) ;
+
+
void zmapFeatureDestroy(ZMapFeature feature) ;
+
+
+
ZMapFeatureSet zMapFeatureSetCreate(char *source, GData *features) ;
+
ZMapFeatureSet zMapFeatureSetIDCreate(GQuark original_id, GQuark unique_id, GData *features) ;
void zMapFeatureSetAddFeature(ZMapFeatureSet feature_set, ZMapFeature feature) ;
-ZMapFeatureTypeStyle zMapFeatureSetGetStyle(ZMapFeatureSet feature_set) ;
-void zMapFeatureSetDestroy(ZMapFeatureSet feature_set, gboolean free_data) ;
+char *zMapFeatureSetGetName(ZMapFeatureSet feature_set) ;
+
+void zMapFeatureSetDestroy(ZMapFeatureSet feature_set, gboolean free_data) ;
ZMapFeatureTypeStyle zMapFeatureTypeCreate(char *name,
char *outline, char *foreground, char *background,
diff --git a/src/zmapFeature/zmapFeature.c b/src/zmapFeature/zmapFeature.c
index aceca15b2..1b9fe5a25 100755
--- a/src/zmapFeature/zmapFeature.c
+++ b/src/zmapFeature/zmapFeature.c
@@ -27,9 +27,9 @@
*
* Exported functions: See zmapView_P.h
* HISTORY:
- * Last edited: Jul 27 13:14 2005 (edgrif)
+ * Last edited: Aug 5 16:47 2005 (edgrif)
* Created: Fri Jul 16 13:05:58 2004 (edgrif)
- * CVS info: $Id: zmapFeature.c,v 1.19 2005-07-27 12:19:53 edgrif Exp $
+ * CVS info: $Id: zmapFeature.c,v 1.20 2005-08-09 10:52:43 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -131,7 +131,8 @@ ZMapFeature zmapFeatureCreateEmpty(void)
* are different for different features.
* */
gboolean zmapFeatureAugmentData(ZMapFeature feature, char *feature_name_id, char *name,
- char *sequence, ZMapFeatureType feature_type,
+ char *sequence,
+ ZMapFeatureType feature_type, ZMapFeatureTypeStyle style,
int start, int end, double score, ZMapStrand strand,
ZMapPhase phase,
ZMapHomolType homol_type, int query_start, int query_end,
@@ -147,6 +148,7 @@ gboolean zmapFeatureAugmentData(ZMapFeature feature, char *feature_name_id, char
feature->unique_id = g_quark_from_string(feature_name_id) ;
feature->original_id = g_quark_from_string(name) ;
feature->type = feature_type ;
+ feature->style = style ;
feature->x1 = start ;
feature->x2 = end ;
feature->strand = strand ;
@@ -437,7 +439,8 @@ void zMapFeatureBlockDestroy(ZMapFeatureBlock block, gboolean free_data)
}
-ZMapFeatureContext zMapFeatureContextCreate(char *sequence, int start, int end, GList *types)
+ZMapFeatureContext zMapFeatureContextCreate(char *sequence, int start, int end,
+ GList *types, GList *set_names)
{
ZMapFeatureContext feature_context ;
@@ -451,7 +454,8 @@ ZMapFeatureContext zMapFeatureContextCreate(char *sequence, int start, int end,
feature_context->sequence_to_parent.c2 = end ;
}
- feature_context->types = types ;
+ feature_context->styles = types ;
+ feature_context->feature_set_names = set_names ;
g_datalist_init(&(feature_context->alignments)) ;
diff --git a/src/zmapFeature/zmapFeatureUtils.c b/src/zmapFeature/zmapFeatureUtils.c
index ff0a24eda..aae9dac83 100755
--- a/src/zmapFeature/zmapFeatureUtils.c
+++ b/src/zmapFeature/zmapFeatureUtils.c
@@ -22,13 +22,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Rob Clack (Sanger Institute, UK) rnc@sanger.ac.uk
*
- * Description: Manipulates features.
- * 1
- * Exported functions: See zmapFeature.h
+ * Description: Utility routines for handling features/sets/blocks etc.
+ *
+ * Exported functions: See ZMap/zmapFeature.h
* HISTORY:
- * Last edited: Jul 28 09:37 2005 (rnc)
+ * Last edited: Aug 9 11:55 2005 (edgrif)
* Created: Tue Nov 2 2004 (rnc)
- * CVS info: $Id: zmapFeatureUtils.c,v 1.20 2005-07-28 08:38:22 rnc Exp $
+ * CVS info: $Id: zmapFeatureUtils.c,v 1.21 2005-08-09 10:55:30 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -54,6 +54,7 @@ static void printFeature(GQuark key_id, gpointer data, gpointer user_data) ;
static gboolean printLine(GIOChannel *channel, gchar *line) ;
static gint findStyle(gconstpointer list_data, gconstpointer user_data) ;
static gint findStyleName(gconstpointer list_data, gconstpointer user_data) ;
+static void addTypeQuark(gpointer data, gpointer user_data) ;
/* This function creates a unique id for a feature. This is essential if we are to use the
@@ -151,43 +152,38 @@ gboolean zMapFeatureSetCoords(ZMapStrand strand, int *start, int *end, int *quer
}
-GQuark zMapFeatureGetStyleQuark(ZMapFeature feature)
+
+ZMapFeatureSet zMapFeatureGetSet(ZMapFeature feature)
{
- GQuark style_quark ;
+ ZMapFeatureSet feature_set ;
- style_quark = feature->parent_set->style_id ;
+ feature_set = feature->parent_set ;
- return style_quark ;
+ return feature_set ;
}
-
ZMapFeatureTypeStyle zMapFeatureGetStyle(ZMapFeature feature)
{
ZMapFeatureTypeStyle style ;
- GList *styles = feature->parent_set->parent_block->parent_alignment->parent_context->types ;
- style = zMapFindStyle(styles, feature->parent_set->style_id) ;
- zMapAssert(style) ;
+ style = feature->style ;
return style ;
}
-ZMapFeatureTypeStyle zMapFeatureSetGetStyle(ZMapFeatureSet feature_set)
+char *zMapFeatureSetGetName(ZMapFeatureSet feature_set)
{
- ZMapFeatureTypeStyle style ;
- GList *styles = feature_set->parent_block->parent_alignment->parent_context->types ;
+ char *set_name ;
- style = zMapFindStyle(styles, feature_set->style_id) ;
- zMapAssert(style) ;
+ set_name = (char *)g_quark_to_string(feature_set->original_id) ;
- return style ;
+ return set_name ;
}
-
/* Retrieve a style struct for the given style id. */
ZMapFeatureTypeStyle zMapFindStyle(GList *styles, GQuark style_id)
{
@@ -218,7 +214,32 @@ gboolean zMapStyleNameExists(GList *style_name_list, char *style_name)
+/* Retrieve a Glist of the names of all the styles... */
+GList *zMapStylesGetNames(GList *styles)
+{
+ GList *quark_list = NULL ;
+
+ zMapAssert(styles) ;
+ g_list_foreach(styles, addTypeQuark, (void *)&quark_list) ;
+
+ return quark_list ;
+}
+
+/* GFunc() callback function, appends style names to a string, its called for lists
+ * of either style name GQuarks or lists of style structs. */
+static void addTypeQuark(gpointer data, gpointer user_data)
+{
+ ZMapFeatureTypeStyle style = (ZMapFeatureTypeStyle)data ;
+ GList **quarks_out = (GList **)user_data ;
+ GList *quark_list = *quarks_out ;
+
+ quark_list = g_list_append(quark_list, GUINT_TO_POINTER(style->unique_id)) ;
+
+ *quarks_out = quark_list ;
+
+ return ;
+}
@@ -402,14 +423,14 @@ gboolean zMapFeatureStr2Strand(char *string, ZMapStrand *strand)
gboolean zMapFeatureValidatePhase(char *value, ZMapPhase *phase)
{
- gboolean status = TRUE;
+ gboolean status = TRUE ;
- *phase = ZMAPPHASE_NONE;
+ *phase = ZMAPPHASE_NONE ;
if (zMapStr2Int(value, phase) != TRUE || *phase < 0 || *phase > 3)
- status = FALSE;
+ status = FALSE ;
- return status;
+ return status ;
}
@@ -603,7 +624,7 @@ static void printFeatureSet(GQuark key_id, gpointer data, gpointer user_data)
line = g_strdup_printf("\tFeature Set:\t%s\t%s\n",
g_quark_to_string(feature_set->unique_id),
- (char *)g_quark_to_string(feature_set->style_id)) ;
+ (char *)g_quark_to_string(feature_set->original_id)) ;
/* Only proceed if there's no problem printing the line */
if ((dump_features->status = printLine(dump_features->channel, line)))
--
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