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Commit a7e1a091 authored by edgrif's avatar edgrif
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replace references to features style ptr with calls find names style.

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src/include/ZMap/zmapGFF.h
+ 5
− 3
View file @ a7e1a091
......@@ -28,9 +28,9 @@
* of ZMapFeatureStruct's, one for each GFF source.
*
* HISTORY:
* Last edited: Nov 4 09:49 2008 (rds)
* Last edited: Feb 3 13:36 2009 (edgrif)
* Created: Sat May 29 13:18:32 2004 (edgrif)
* CVS info: $Id: zmapGFF.h,v 1.14 2008-11-05 12:12:44 rds Exp $
* CVS info: $Id: zmapGFF.h,v 1.15 2009-02-03 13:48:12 edgrif Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_GFF_H
......@@ -88,6 +88,8 @@ gboolean zMapGFFTerminated(ZMapGFFParser parser) ;
void zMapGFFSetFreeOnDestroy(ZMapGFFParser parser, gboolean free_on_destroy) ;
void zMapGFFDestroyParser(ZMapGFFParser parser) ;
gboolean zMapGFFDump(ZMapFeatureAny dump_set, GIOChannel *file, GError **error_out);
gboolean zMapGFFDump(ZMapFeatureAny dump_set, GData *styles, GIOChannel *file, GError **error_out);
gboolean zMapGFFDumpRegion(ZMapFeatureAny dump_set, GData *styles,
ZMapSpan region_span, GIOChannel *file, GError **error_out) ;
#endif /* ZMAP_GFF_H */
src/zmapGFF/zmapGFF2Dumper.c
+ 30
− 21
View file @ a7e1a091
......@@ -26,15 +26,15 @@
*
* Exported functions: See ZMap/zmapGFF.h
* HISTORY:
* Last edited: Nov 24 15:17 2008 (rds)
* Last edited: Feb 3 13:39 2009 (edgrif)
* Created: Mon Nov 14 13:21:14 2005 (edgrif)
* CVS info: $Id: zmapGFF2Dumper.c,v 1.14 2008-11-24 15:41:07 rds Exp $
* CVS info: $Id: zmapGFF2Dumper.c,v 1.15 2009-02-03 13:47:53 edgrif Exp $
*-------------------------------------------------------------------
*/
#include <ZMap/zmapUtils.h>
#include <ZMap/zmapFeature.h>
#include <ZMap/zmapGFF.h>
#define GFF_SEPARATOR "\t"
#define GFF_SEQ "%s"
......@@ -85,6 +85,8 @@ typedef struct
/* Fields are: <sequence> <source> <feature> <start> <end> <score> <strand> <frame> <attributes> */
typedef struct _GFFDumpDataStruct
{
GData *styles ;
const char *gff_sequence; /* The sequence name. e.g. 16.12345-23456 */
char *gff_source; /* The source e.g. augustus, TrEMBL, trf, polya_site */
char *gff_feature; /* The feature type e.g. Sequence, intron, exon, CDS, coding_exon, misc_feature */
......@@ -100,16 +102,18 @@ typedef struct _GFFDumpDataStruct
}GFFDumpDataStruct;
/* Functions to dump the header section of gff files */
static gboolean dump_full_header(ZMapFeatureAny feature_any, GIOChannel *file, GError **error_out, const char **sequence_in_out);
static gboolean dump_full_header(ZMapFeatureAny feature_any, GIOChannel *file, GError **error_out,
const char **sequence_in_out) ;
static ZMapFeatureContextExecuteStatus get_type_seq_header_cb(GQuark key,
gpointer data,
gpointer user_data,
char **err_out);
char **err_out) ;
/* Functions to dump the body of the data */
/* ZMapFeatureDumpFeatureFunc to dump gff. writes lines into gstring buffer... */
static gboolean dump_gff_cb(ZMapFeatureAny feature_any,
static gboolean dump_gff_cb(ZMapFeatureAny feature_any,
GData *styles,
GString *gff_string,
GError **error,
gpointer user_data);
......@@ -207,16 +211,17 @@ static DumpGFFAttrFunc text_funcs_G[] = {
* sequences.
*
* */
gboolean zMapGFFDump(ZMapFeatureAny dump_set, GIOChannel *file, GError **error_out)
gboolean zMapGFFDump(ZMapFeatureAny dump_set, GData *styles, GIOChannel *file, GError **error_out)
{
gboolean result = TRUE;
result = zMapGFFDumpRegion(dump_set, NULL, file, error_out);
result = zMapGFFDumpRegion(dump_set, styles, NULL, file, error_out);
return result;
}
gboolean zMapGFFDumpRegion(ZMapFeatureAny dump_set, ZMapSpan region_span, GIOChannel *file, GError **error_out)
gboolean zMapGFFDumpRegion(ZMapFeatureAny dump_set, GData *styles,
ZMapSpan region_span, GIOChannel *file, GError **error_out)
{
const char *sequence = NULL;
gboolean result = TRUE ;
......@@ -238,16 +243,17 @@ gboolean zMapGFFDumpRegion(ZMapFeatureAny dump_set, ZMapSpan region_span, GIOCha
gff_data.transcript = transcript_funcs_G;
gff_data.homol = homol_funcs_G;
gff_data.text = text_funcs_G;
gff_data.styles = styles ;
/* This might get overwritten later, but as DumpToFile uses
* Subset, there's a chance it wouldn't get set at all */
gff_data.gff_sequence = sequence;
if(region_span)
result = zMapFeatureContextRangeDumpToFile((ZMapFeatureAny)dump_set, region_span,
result = zMapFeatureContextRangeDumpToFile((ZMapFeatureAny)dump_set, styles, region_span,
dump_gff_cb, &gff_data, file, error_out) ;
else
result = zMapFeatureContextDumpToFile((ZMapFeatureAny)dump_set, dump_gff_cb,
&gff_data, file, error_out) ;
result = zMapFeatureContextDumpToFile((ZMapFeatureAny)dump_set, styles, dump_gff_cb,
&gff_data, file, error_out) ;
}
return result ;
......@@ -256,7 +262,7 @@ gboolean zMapGFFDumpRegion(ZMapFeatureAny dump_set, ZMapSpan region_span, GIOCha
/*!
* \brief Dump a list of ZMapFeatureAny. sequence can be NULL
*/
gboolean zMapGFFDumpList(GList *dump_list, char *sequence, GIOChannel *file, GError **error_out)
gboolean zMapGFFDumpList(GList *dump_list, GData *styles, char *sequence, GIOChannel *file, GError **error_out)
{
const char *int_sequence = NULL;
gboolean result = FALSE ;
......@@ -284,14 +290,14 @@ gboolean zMapGFFDumpList(GList *dump_list, char *sequence, GIOChannel *file, GEr
* Subset, there's a chance it wouldn't get set at all */
gff_data.gff_sequence = int_sequence;
result = zMapFeatureListDumpToFile(dump_list, dump_gff_cb, &gff_data,
result = zMapFeatureListDumpToFile(dump_list, styles, dump_gff_cb, &gff_data,
file, error_out) ;
}
return result ;
}
gboolean zMapGFFDumpForeachList(ZMapFeatureAny first_feature, GIOChannel *file, GError **error_out,
gboolean zMapGFFDumpForeachList(ZMapFeatureAny first_feature, GData *styles, GIOChannel *file, GError **error_out,
char *sequence, GFunc *list_func_out, gpointer *list_data_out)
{
const char *int_sequence = NULL;
......@@ -321,7 +327,7 @@ gboolean zMapGFFDumpForeachList(ZMapFeatureAny first_feature, GIOChannel *file,
* Subset, there's a chance it wouldn't get set at all */
gff_data->gff_sequence = int_sequence;
result = zMapFeatureListForeachDumperCreate(dump_gff_cb, gff_data, g_free,
result = zMapFeatureListForeachDumperCreate(dump_gff_cb, styles, gff_data, g_free,
file, error_out,
list_func_out, list_data_out) ;
}
......@@ -446,6 +452,7 @@ static ZMapFeatureContextExecuteStatus get_type_seq_header_cb(GQuark key,
}
static gboolean dump_gff_cb(ZMapFeatureAny feature_any,
GData *styles,
GString *gff_string,
GError **error,
gpointer user_data)
......@@ -469,13 +476,15 @@ static gboolean dump_gff_cb(ZMapFeatureAny feature_any,
case ZMAPFEATURE_STRUCT_FEATURE:
{
ZMapFeature feature = (ZMapFeature)feature_any;
ZMapFeatureTypeStyle style ;
/* Fields are: <seqname> <source> <feature> <start> <end> <score> <strand> <frame> */
style = zMapFindStyle(gff_data->styles, feature->style_id) ;
/* Output a record for the whole feature. */
if(!(gff_data->gff_source = zMapStyleGetGFFSource(feature->style)))
gff_data->gff_source = zMapStyleGetName(feature->style);
if(!(gff_data->gff_feature = zMapStyleGetGFFFeature(feature->style)))
/* Output a record for the whole feature, fields are:
* <seqname> <source> <feature> <start> <end> <score> <strand> <frame> */
if(!(gff_data->gff_source = zMapStyleGetGFFSource(style)))
gff_data->gff_source = zMapStyleGetName(style);
if(!(gff_data->gff_feature = zMapStyleGetGFFFeature(style)))
gff_data->gff_feature = (char *)g_quark_to_string(feature->ontology);
/* Obligatory fields. */
......
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