From c611e7c33e80aac22f1de28606e1eb1365eb6316 Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Fri, 24 Jun 2005 13:20:39 +0000
Subject: [PATCH] add structs/code to support alignments and blocks and better
hashing from feature context to canvas items.
---
src/include/ZMap/zmapFeature.h | 62 +++++++++++-----------
src/zmapFeature/zmapFeature.c | 58 ++++++++++++--------
src/zmapFeature/zmapFeatureTypes.c | 15 +++---
src/zmapFeature/zmapFeatureUtils.c | 85 ++++++++++++++++++++++++------
4 files changed, 144 insertions(+), 76 deletions(-)
diff --git a/src/include/ZMap/zmapFeature.h b/src/include/ZMap/zmapFeature.h
index 922b718fc..89a8e1137 100755
--- a/src/include/ZMap/zmapFeature.h
+++ b/src/include/ZMap/zmapFeature.h
@@ -22,12 +22,12 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Rob Clack (Sanger Institute, UK) rnc@sanger.ac.uk
*
- * Description: Data structures describing a genetic feature.
+ * Description: Data structures describing a sequence feature.
*
* HISTORY:
- * Last edited: Jun 23 09:37 2005 (rnc)
+ * Last edited: Jun 24 14:13 2005 (edgrif)
* Created: Fri Jun 11 08:37:19 2004 (edgrif)
- * CVS info: $Id: zmapFeature.h,v 1.28 2005-06-24 12:07:12 rnc Exp $
+ * CVS info: $Id: zmapFeature.h,v 1.29 2005-06-24 13:20:39 edgrif Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_FEATURE_H
@@ -118,7 +118,9 @@ typedef struct
typedef struct
{
int q1, q2 ; /* coords in query sequence */
+ ZMapStrand q_strand ;
int t1, t2 ; /* coords in target sequence */
+ ZMapStrand t_strand ;
} ZMapAlignBlockStruct, *ZMapAlignBlock ;
@@ -136,7 +138,8 @@ typedef struct
-/* DO THESE STRUCTS NEED TO BE EXPOSED ? PROBABLY NOT.... */
+/* DO THESE STRUCTS NEED TO BE EXPOSED ? PROBABLY NOT....TO HIDE THEM WOULD REQUIRE
+ * QUITE A NUMBER OF ACCESS FUNCTIONS.... */
typedef struct ZMapFeatureAlignmentStruct_ *ZMapFeatureAlignment ;
@@ -163,32 +166,25 @@ typedef struct ZMapFeatureContextStruct_
ZMapMapBlockStruct sequence_to_parent ; /* Shows how this sequence maps to its
ultimate parent. */
-
ZMapFeatureAlignment master_align ; /* The target/master alignment out of
the below set. */
- /* Alignments.... */
+ 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. */
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- /* Feature sets. */
- GData *feature_sets ; /* A set of ZMapFeatureSetStruct. */
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+} ZMapFeatureContextStruct, *ZMapFeatureContext ;
-} ZMapFeatureContextStruct, *ZMapFeatureContext ;
typedef struct ZMapFeatureAlignmentStruct_
{
ZMapFeatureContext parent_context ; /* Our parent context. */
GQuark unique_id ; /* Unique id this alignment. */
- GQuark original_id ; /* Original id, species ? */
-
- /* We may need some mapping data here.... */
-
- GData *types ;
+ GQuark original_id ; /* Original id of this sequence. */
GList *blocks ; /* A set of ZMapFeatureStruct. */
@@ -201,9 +197,9 @@ typedef struct ZMapFeatureBlockStruct_
ZMapFeatureAlignment parent_alignment ; /* Our parent alignment. */
GQuark unique_id ; /* Unique id for this block. */
- GQuark original_id ; /* Original id, not needed ? */
-
- ZMapMapBlockStruct features_to_sequence ; /* Shows how these features map to the
+ GQuark original_id ; /* Original id, probably not needed ? */
+
+ ZMapAlignBlockStruct block_to_sequence ; /* Shows how these features map to the
sequence, n.b. this feature set may only
span part of the sequence. */
@@ -227,7 +223,7 @@ typedef struct ZMapFeatureSetStruct_
GData *features ; /* A set of ZMapFeatureStruct. */
- GQuark style ; /* Style for these features. */
+ GQuark style_id ; /* Style for these features. */
} ZMapFeatureSetStruct, *ZMapFeatureSet ;
@@ -273,12 +269,6 @@ typedef struct
* */
typedef struct ZMapFeatureStruct_
{
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- /* I think actually we want to have a pointer to our parent.... */
-
- GQuark style ; /* Style for this feature. */
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
ZMapFeatureSet parent_set ; /* Our containing set. */
@@ -293,9 +283,10 @@ typedef struct ZMapFeatureStruct_
Coord x1, x2 ; /* start, end of feature in absolute coords. */
-
ZMapStrand strand ;
+
ZMapPhase phase ;
+
float score ;
char *text ; /* needed ????? */
@@ -353,6 +344,10 @@ typedef struct ZMapFeatureTypeStyleStruct_
+GQuark zMapFeatureAlignmentCreateID(char *align_sequence, gboolean query_sequence) ;
+GQuark zMapFeatureBlockCreateID(char *align_sequence,
+ int target_start, int target_end, ZMapStrand target_strand,
+ int query_start, int query_end, ZMapStrand query_strand) ;
char *zMapFeatureCreateName(ZMapFeatureType feature_type, char *feature_name,
@@ -373,7 +368,7 @@ ZMapFeature zMapFeatureFindFeatureInSet(ZMapFeatureSet feature_set, GQuark featu
GData *zMapFeatureFindSetInContext(ZMapFeatureContext feature_context, GQuark set_id) ;
-ZMapFeatureContext zMapFeatureContextCreate(char *sequence) ;
+ZMapFeatureContext zMapFeatureContextCreate(char *sequence, int start, int end, GList *types) ;
gboolean zMapFeatureContextMerge(ZMapFeatureContext *current_context_inout,
ZMapFeatureContext new_context,
ZMapFeatureContext *diff_context_out) ;
@@ -382,11 +377,14 @@ void zMapFeatureContextAddAlignment(ZMapFeatureContext feature_context,
void zMapFeatureDump(ZMapFeatureContext feature_context, char *file) ;
void zMapFeatureContextDestroy(ZMapFeatureContext context, gboolean free_data) ;
-ZMapFeatureAlignment zMapFeatureAlignmentCreate(char *align_name, GData *types) ;
+ZMapFeatureAlignment zMapFeatureAlignmentCreate(char *align_name) ;
void zMapFeatureAlignmentAddBlock(ZMapFeatureAlignment alignment, ZMapFeatureBlock block) ;
void zMapFeatureAlignmentDestroy(ZMapFeatureAlignment alignment) ;
-ZMapFeatureBlock zMapFeatureBlockCreate(char *block_name) ;
+ZMapFeatureBlock zMapFeatureBlockCreate(char *ref_seq,
+ int ref_start, int ref_end, ZMapStrand ref_strand,
+ char *non_seq,
+ int non_start, int non_end, ZMapStrand non_strand) ;
void zMapFeatureBlockAddFeatureSet(ZMapFeatureBlock feature_block, ZMapFeatureSet feature_set) ;
void zMapFeatureBlockDestroy(ZMapFeatureBlock block, gboolean free_data) ;
@@ -417,10 +415,10 @@ char *zMapStyleCreateName(char *style_name) ;
GQuark zMapStyleCreateID(char *style_name) ;
char *zMapStyleGetName(ZMapFeatureTypeStyle style) ;
-
+ZMapFeatureTypeStyle zMapFindStyle(GList *styles, GQuark style_id) ;
ZMapFeatureTypeStyle zMapFeatureTypeCopy(ZMapFeatureTypeStyle type) ;
void zMapFeatureTypeDestroy(ZMapFeatureTypeStyle type) ;
-GData *zMapFeatureTypeGetFromFile(char *types_file) ;
+GList *zMapFeatureTypeGetFromFile(char *types_file) ;
gboolean zMapFeatureTypeSetAugment(GData **current, GData **new) ;
void zMapFeatureTypePrintAll(GData *type_set, char *user_string) ;
diff --git a/src/zmapFeature/zmapFeature.c b/src/zmapFeature/zmapFeature.c
index aceef8e95..ed9dd568a 100755
--- a/src/zmapFeature/zmapFeature.c
+++ b/src/zmapFeature/zmapFeature.c
@@ -27,9 +27,9 @@
*
* Exported functions: See zmapView_P.h
* HISTORY:
- * Last edited: Jun 23 20:02 2005 (rnc)
+ * Last edited: Jun 24 14:14 2005 (edgrif)
* Created: Fri Jul 16 13:05:58 2004 (edgrif)
- * CVS info: $Id: zmapFeature.c,v 1.15 2005-06-24 12:08:30 rnc Exp $
+ * CVS info: $Id: zmapFeature.c,v 1.16 2005-06-24 13:20:39 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -149,11 +149,6 @@ gboolean zmapFeatureAugmentData(ZMapFeature feature, char *feature_name_id, char
feature->type = feature_type ;
feature->x1 = start ;
feature->x2 = end ;
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- feature->style = style_id ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
feature->strand = strand ;
feature->phase = phase ;
feature->score = score ;
@@ -331,7 +326,7 @@ void zMapFeatureSetDestroy(ZMapFeatureSet feature_set, gboolean free_data)
}
-ZMapFeatureAlignment zMapFeatureAlignmentCreate(char *align_name, GData *types)
+ZMapFeatureAlignment zMapFeatureAlignmentCreate(char *align_name)
{
ZMapFeatureAlignment alignment ;
@@ -345,8 +340,6 @@ ZMapFeatureAlignment zMapFeatureAlignmentCreate(char *align_name, GData *types)
alignment->unique_id = alignment->original_id ;
}
- alignment->types = types ;
-
return alignment ;
}
@@ -373,26 +366,43 @@ void zMapFeatureAlignmentDestroy(ZMapFeatureAlignment alignment)
-ZMapFeatureBlock zMapFeatureBlockCreate(char *block_name)
+ZMapFeatureBlock zMapFeatureBlockCreate(char *ref_seq,
+ int ref_start, int ref_end, ZMapStrand ref_strand,
+ char *non_seq,
+ int non_start, int non_end, ZMapStrand non_strand)
{
ZMapFeatureBlock new_block ;
+ char *id_base ;
+
- zMapAssert(!block_name || (block_name && *block_name)) ;
+ /* need some asserts in here.... */
new_block = g_new(ZMapFeatureBlockStruct, 1) ;
- if (block_name)
- {
- new_block->original_id = g_quark_from_string(block_name) ;
- /* THIS WILL NEED CHANGING..... */
- new_block->unique_id = new_block->original_id ;
- }
+ id_base = g_strdup_printf("%s:%d-%d_vs_%s:%d-%d",
+ ref_seq, ref_start,
+ ref_end, non_seq,
+ non_start, non_end) ;
+ new_block->unique_id = g_quark_from_string(id_base) ;
+ g_free(id_base) ;
+
+ /* Use the sequence name for the original_id */
+ new_block->original_id = g_quark_from_string(non_seq) ;
+
+ new_block->block_to_sequence.t1 = ref_start ;
+ new_block->block_to_sequence.t2 = ref_end ;
+ new_block->block_to_sequence.t_strand = ref_strand ;
+
+ new_block->block_to_sequence.q1 = non_start ;
+ new_block->block_to_sequence.q2 = non_end ;
+ new_block->block_to_sequence.q_strand = non_strand ;
return new_block ;
}
+
void zMapFeatureBlockAddFeatureSet(ZMapFeatureBlock feature_block, ZMapFeatureSet feature_set)
{
@@ -427,14 +437,20 @@ void zMapFeatureBlockDestroy(ZMapFeatureBlock block, gboolean free_data)
}
-ZMapFeatureContext zMapFeatureContextCreate(char *sequence)
+ZMapFeatureContext zMapFeatureContextCreate(char *sequence, int start, int end, GList *types)
{
ZMapFeatureContext feature_context ;
feature_context = g_new0(ZMapFeatureContextStruct, 1) ;
if (sequence && *sequence)
- feature_context->sequence_name = g_quark_from_string(sequence) ;
+ {
+ feature_context->sequence_name = g_quark_from_string(sequence) ;
+ feature_context->sequence_to_parent.c1 = start ;
+ feature_context->sequence_to_parent.c2 = end ;
+ }
+
+ feature_context->types = types ;
g_datalist_init(&(feature_context->alignments)) ;
@@ -545,7 +561,7 @@ gboolean zMapFeatureContextMerge(ZMapFeatureContext *current_context_inout,
{
FeatureContextsStruct contexts ;
- diff_context = zMapFeatureContextCreate(NULL) ;
+ diff_context = zMapFeatureContextCreate(NULL, 0, 0, NULL) ;
contexts.current_feature_sets = &(current_context->feature_sets) ;
contexts.diff_feature_sets = &(diff_context->feature_sets) ;
diff --git a/src/zmapFeature/zmapFeatureTypes.c b/src/zmapFeature/zmapFeatureTypes.c
index 722ee60f8..38192ced8 100755
--- a/src/zmapFeature/zmapFeatureTypes.c
+++ b/src/zmapFeature/zmapFeatureTypes.c
@@ -27,12 +27,13 @@
*
* Exported functions: See ZMap/zmapFeature.h
* HISTORY:
- * Last edited: May 27 13:23 2005 (edgrif)
+ * Last edited: Jun 24 08:45 2005 (edgrif)
* Created: Tue Dec 14 13:15:11 2004 (edgrif)
- * CVS info: $Id: zmapFeatureTypes.c,v 1.6 2005-05-27 15:14:31 edgrif Exp $
+ * CVS info: $Id: zmapFeatureTypes.c,v 1.7 2005-06-24 13:20:39 edgrif Exp $
*-------------------------------------------------------------------
*/
+#include <stdio.h>
#include <ZMap/zmapUtils.h>
#include <ZMap/zmapConfig.h>
#include <zmapFeature_P.h>
@@ -211,9 +212,9 @@ gboolean zMapFeatureTypeSetAugment(GData **current, GData **new)
/* Read the type/method/source (call it what you will) information from the given file
* which currently must reside in the users $HOME/.ZMap directory. */
-GData *zMapFeatureTypeGetFromFile(char *types_file_name)
+GList *zMapFeatureTypeGetFromFile(char *types_file_name)
{
- GData *types = NULL ;
+ GList *types = NULL ;
gboolean result = FALSE ;
ZMapConfigStanzaSet types_list = NULL ;
ZMapConfig config ;
@@ -251,7 +252,7 @@ GData *zMapFeatureTypeGetFromFile(char *types_file_name)
int num_types = 0 ;
ZMapConfigStanza next_types ;
- g_datalist_init(&types) ;
+ types = NULL ;
/* Current error handling policy is to connect to servers that we can and
* report errors for those where we fail but to carry on and set up the ZMap
@@ -280,7 +281,9 @@ GData *zMapFeatureTypeGetFromFile(char *types_file_name)
zMapConfigGetElementBool(next_types, "frame_specific"),
zMapConfigGetElementBool(next_types, "show_reverse")) ;
- g_datalist_id_set_data(&types, new_type->unique_id, new_type) ;
+
+ types = g_list_append(types, new_type) ;
+
num_types++ ;
}
else
diff --git a/src/zmapFeature/zmapFeatureUtils.c b/src/zmapFeature/zmapFeatureUtils.c
index 6a29b1cb7..18a0f35a8 100755
--- a/src/zmapFeature/zmapFeatureUtils.c
+++ b/src/zmapFeature/zmapFeatureUtils.c
@@ -26,9 +26,9 @@
* 1
* Exported functions: See zmapFeature.h
* HISTORY:
- * Last edited: May 23 11:53 2005 (edgrif)
+ * Last edited: Jun 24 11:58 2005 (edgrif)
* Created: Tue Nov 2 2004 (rnc)
- * CVS info: $Id: zmapFeatureUtils.c,v 1.10 2005-05-27 15:15:06 edgrif Exp $
+ * CVS info: $Id: zmapFeatureUtils.c,v 1.11 2005-06-24 13:20:39 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -52,6 +52,8 @@ static void printFeatureBlock(gpointer data, gpointer user_data) ;
static void printFeatureSet(GQuark key_id, gpointer data, gpointer user_data) ;
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) ;
+
/* This function creates a unique id for a feature. This is essential if we are to use the
@@ -135,7 +137,7 @@ GQuark zMapFeatureGetStyleQuark(ZMapFeature feature)
{
GQuark style_quark ;
- style_quark = feature->parent_set->style ;
+ style_quark = feature->parent_set->style_id ;
return style_quark ;
}
@@ -144,14 +146,29 @@ GQuark zMapFeatureGetStyleQuark(ZMapFeature feature)
ZMapFeatureTypeStyle zMapFeatureGetStyle(ZMapFeature feature)
{
ZMapFeatureTypeStyle style ;
- GData *types = feature->parent_set->parent_block->parent_alignment->types ;
+ GList *styles = feature->parent_set->parent_block->parent_alignment->parent_context->types ;
+
+ style = zMapFindStyle(styles, feature->parent_set->style_id) ;
+
+ return style ;
+}
+
+
+
+ZMapFeatureTypeStyle zMapFindStyle(GList *styles, GQuark style_id)
+{
+ ZMapFeatureTypeStyle style ;
+ GList *list ;
+
+ list = g_list_find_custom(styles, GUINT_TO_POINTER(style_id), findStyle) ;
- style = (ZMapFeatureTypeStyle)g_datalist_id_get_data(&(types),
- feature->parent_set->style) ;
+ style = list->data ;
return style ;
}
+
+
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
/* WE MAY STILL WANT A FUNCTION LIKE THIS BUT IT WILL NEED MORE ARGS, E.G. ALIGNMENT... */
ZMapFeature zMapFeatureFindFeatureInContext(ZMapFeatureContext feature_context,
@@ -197,10 +214,6 @@ GData *zMapFeatureFindSetInBlock(ZMapFeatureBlock feature_block, GQuark set_id)
}
-
-
-
-
/* Dump out a feature context, if file is NULL then goes to stdout. */
void zMapFeatureDump(ZMapFeatureContext feature_context, char *file)
{
@@ -238,8 +251,12 @@ void zMapFeatureDump(ZMapFeatureContext feature_context, char *file)
if (!channel)
{
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
zMapShowMsg(ZMAP_MSG_WARNING, "Can't open output file \"%s\": %s",
filepath, channel_error->message) ;
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
g_error_free(channel_error) ;
}
else
@@ -253,12 +270,20 @@ void zMapFeatureDump(ZMapFeatureContext feature_context, char *file)
/* close output file */
if (g_io_channel_shutdown(channel, TRUE, &channel_error) != G_IO_STATUS_NORMAL)
{
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
zMapShowMsg(ZMAP_MSG_WARNING, "Error closing output file \"%s\": %s",
filepath, channel_error->message) ;
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
g_error_free(channel_error) ;
}
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
else
zMapShowMsg(ZMAP_MSG_INFORMATION, "Feature Context dumped to \"%s\"", filepath) ;
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
}
g_free(filepath) ;
@@ -311,8 +336,8 @@ static void printFeatureContext(ZMapFeatureContext feature_context, DumpFeatures
char *line ;
line = g_strdup_printf("Feature Context:\t%s\t%s\t%d\t%d\t%d\t%d\t%d\t%d\n",
- feature_context->sequence_name,
- feature_context->parent_name,
+ g_quark_to_string(feature_context->sequence_name),
+ g_quark_to_string(feature_context->parent_name),
feature_context->parent_span.x1,
feature_context->parent_span.x2,
feature_context->sequence_to_parent.p1,
@@ -361,15 +386,22 @@ static void printFeatureBlock(gpointer data, gpointer user_data)
char *line ;
line = g_strdup_printf("\tBlock:\t%s\t%d\t%d\t%d\t%d\n", g_quark_to_string(block->unique_id),
- block->features_to_sequence.p1,
- block->features_to_sequence.p2,
- block->features_to_sequence.c1,
- block->features_to_sequence.c2) ;
+ block->block_to_sequence.t1,
+ block->block_to_sequence.t2,
+ block->block_to_sequence.q1,
+ block->block_to_sequence.q2) ;
/* Only proceed if there's no problem printing the line */
+
+ /* JUST FOR NOW.... */
+ dump_features->status = printLine(dump_features->channel, line) ;
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
if ((dump_features->status = printLine(dump_features->channel, line)))
g_datalist_foreach(&(block->feature_sets), printFeatureSet, dump_features) ;
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
g_free(line) ;
@@ -390,7 +422,7 @@ 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)) ;
+ (char *)g_quark_to_string(feature_set->style_id)) ;
/* Only proceed if there's no problem printing the line */
if ((dump_features->status = printLine(dump_features->channel, line)))
@@ -499,8 +531,12 @@ static gboolean printLine(GIOChannel *channel, gchar *line)
if (g_io_channel_write_chars(channel, line, -1, &bytes_written, &channel_error) != G_IO_STATUS_NORMAL)
{
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
zMapShowMsg(ZMAP_MSG_WARNING, "Error writing to output file: %50s... : %s",
line, channel_error->message) ;
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
g_error_free(channel_error) ;
status = FALSE ;
}
@@ -509,3 +545,18 @@ static gboolean printLine(GIOChannel *channel, gchar *line)
}
+/* GCompareFunc function, called for each member of a list of styles to see if the supplied
+ * style id matches the that in the style. */
+static gint findStyle(gconstpointer list_data, gconstpointer user_data)
+{
+ gint result = -1 ;
+ ZMapFeatureTypeStyle style = (ZMapFeatureTypeStyle)list_data ;
+ GQuark style_quark = GPOINTER_TO_INT(user_data) ;
+
+ if (style_quark == style->unique_id)
+ result = 0 ;
+
+ return result ;
+}
+
+
--
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