From 3d19c9e11f226a89451ad1e2f81dec29ea833af4 Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Wed, 18 Nov 2009 16:29:39 +0000
Subject: [PATCH] handle NULL return from dna routines.
---
src/zmapWindow/zmapWindowFeature.c | 47 ++++++++++--------
src/zmapWindow/zmapWindowMenus.c | 79 ++++++++++++++++--------------
2 files changed, 68 insertions(+), 58 deletions(-)
diff --git a/src/zmapWindow/zmapWindowFeature.c b/src/zmapWindow/zmapWindowFeature.c
index 947d674ab..41ad8b86c 100755
--- a/src/zmapWindow/zmapWindowFeature.c
+++ b/src/zmapWindow/zmapWindowFeature.c
@@ -28,9 +28,9 @@
*
* Exported functions: See zmapWindow_P.h
* HISTORY:
- * Last edited: Oct 16 14:17 2009 (edgrif)
+ * Last edited: Nov 18 16:17 2009 (edgrif)
* Created: Mon Jan 9 10:25:40 2006 (edgrif)
- * CVS info: $Id: zmapWindowFeature.c,v 1.165 2009-10-16 13:26:13 edgrif Exp $
+ * CVS info: $Id: zmapWindowFeature.c,v 1.166 2009-11-18 16:29:39 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -666,12 +666,13 @@ FooCanvasGroup *zmapWindowFeatureItemsMakeGroup(ZMapWindow window, GList *featur
* there's no falling over phase values and stop codons... */
char *zmapWindowFeatureTranscriptFASTA(ZMapFeature feature, gboolean spliced, gboolean cds_only)
{
- ZMapFeatureContext context;
- char *peptide_fasta = NULL;
+ char *peptide_fasta = NULL ;
+ ZMapFeatureContext context ;
+
- if((feature->type == ZMAPSTYLE_MODE_TRANSCRIPT) &&
- ((context = (ZMapFeatureContext)zMapFeatureGetParentGroup((ZMapFeatureAny)feature,
- ZMAPFEATURE_STRUCT_CONTEXT))))
+ if((feature->type == ZMAPSTYLE_MODE_TRANSCRIPT)
+ && ((context = (ZMapFeatureContext)zMapFeatureGetParentGroup((ZMapFeatureAny)feature,
+ ZMAPFEATURE_STRUCT_CONTEXT))))
{
ZMapPeptide peptide;
char *dna, *seq_name = NULL, *gene_name = NULL;
@@ -679,23 +680,27 @@ char *zmapWindowFeatureTranscriptFASTA(ZMapFeature feature, gboolean spliced, gb
seq_name = (char *)g_quark_to_string(context->original_id);
gene_name = (char *)g_quark_to_string(feature->original_id);
- dna = zMapFeatureGetTranscriptDNA(context, feature, spliced, cds_only) ;
-
- /* Adjust for when its known that the start exon is incomplete.... */
- if (feature->feature.transcript.flags.start_not_found)
- start_incr = feature->feature.transcript.start_phase - 1 ; /* Phase values are 1 <= phase <= 3 */
+
+ if ((dna = zMapFeatureGetTranscriptDNA(feature, spliced, cds_only)))
+ {
+ /* Adjust for when its known that the start exon is incomplete.... */
+ if (feature->feature.transcript.flags.start_not_found)
+ start_incr = feature->feature.transcript.start_phase - 1 ; /* Phase values are 1 <= phase <= 3 */
- peptide = zMapPeptideCreate(seq_name, gene_name, (dna + start_incr), NULL, TRUE) ;
+ peptide = zMapPeptideCreate(seq_name, gene_name, (dna + start_incr), NULL, TRUE) ;
- /* Note that we do not include the "Stop" in the peptide length, is this the norm ? */
- pep_length = zMapPeptideLength(peptide) ;
- if (zMapPeptideHasStopCodon(peptide))
- pep_length-- ;
+ /* Note that we do not include the "Stop" in the peptide length, is this the norm ? */
+ pep_length = zMapPeptideLength(peptide) ;
+ if (zMapPeptideHasStopCodon(peptide))
+ pep_length-- ;
- peptide_fasta = zMapFASTAString(ZMAPFASTA_SEQTYPE_AA,
- seq_name, "Protein",
- gene_name, pep_length,
- zMapPeptideSequence(peptide));
+ peptide_fasta = zMapFASTAString(ZMAPFASTA_SEQTYPE_AA,
+ seq_name, "Protein",
+ gene_name, pep_length,
+ zMapPeptideSequence(peptide));
+
+ g_free(dna) ;
+ }
}
return peptide_fasta;
diff --git a/src/zmapWindow/zmapWindowMenus.c b/src/zmapWindow/zmapWindowMenus.c
index ffe176176..d03b8d202 100755
--- a/src/zmapWindow/zmapWindowMenus.c
+++ b/src/zmapWindow/zmapWindowMenus.c
@@ -27,9 +27,9 @@
* Exported functions: ZMap/zmapWindows.h
*
* HISTORY:
- * Last edited: Jul 3 16:54 2009 (rds)
+ * Last edited: Nov 18 16:17 2009 (edgrif)
* Created: Thu Mar 10 07:56:27 2005 (edgrif)
- * CVS info: $Id: zmapWindowMenus.c,v 1.62 2009-07-27 03:15:13 rds Exp $
+ * CVS info: $Id: zmapWindowMenus.c,v 1.63 2009-11-18 16:30:02 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -410,14 +410,18 @@ static void dnaMenuCB(int menu_item_id, gpointer callback_data)
}
else if (feature->type == ZMAPSTYLE_MODE_TRANSCRIPT)
{
- dna = zMapFeatureGetTranscriptDNA(context, feature, spliced, cds) ;
+ dna = zMapFeatureGetTranscriptDNA(feature, spliced, cds) ;
}
else
{
- dna = zMapFeatureGetFeatureDNA(context, feature) ;
+ dna = zMapFeatureGetFeatureDNA(feature) ;
}
- if (dna)
+ if (!dna)
+ {
+ zMapWarning("%s", "No DNA available") ;
+ }
+ else
{
/* Would be better to have the dna functions calculate and return this.... */
seq_len = strlen(dna) ;
@@ -644,46 +648,47 @@ static void peptideMenuCB(int menu_item_id, gpointer callback_data)
molecule_type = "Protein" ;
gene_name = (char *)g_quark_to_string(feature->original_id) ;
- dna = zMapFeatureGetTranscriptDNA(menu_data->window->feature_context, feature, spliced, cds) ;
-
- /* Adjust for when its known that the start exon is incomplete.... */
- if (feature->feature.transcript.flags.start_not_found)
- start_incr = feature->feature.transcript.start_phase - 1 ; /* Phase values are 1 <= phase <= 3 */
+ if ((dna = zMapFeatureGetTranscriptDNA(feature, spliced, cds)))
+ {
+ /* Adjust for when its known that the start exon is incomplete.... */
+ if (feature->feature.transcript.flags.start_not_found)
+ start_incr = feature->feature.transcript.start_phase - 1 ; /* Phase values are 1 <= phase <= 3 */
- peptide = zMapPeptideCreate(seq_name, gene_name, (dna + start_incr), NULL, TRUE) ;
+ peptide = zMapPeptideCreate(seq_name, gene_name, (dna + start_incr), NULL, TRUE) ;
- /* Note that we do not include the "Stop" in the peptide length, is this the norm ? */
- pep_length = zMapPeptideLength(peptide) ;
- if (zMapPeptideHasStopCodon(peptide))
- pep_length-- ;
+ /* Note that we do not include the "Stop" in the peptide length, is this the norm ? */
+ pep_length = zMapPeptideLength(peptide) ;
+ if (zMapPeptideHasStopCodon(peptide))
+ pep_length-- ;
- if (menu_item_id == ZMAPCDS || menu_item_id == ZMAPTRANSCRIPT || menu_item_id == ZMAPUNSPLICED)
- {
- char *title ;
- char *peptide_fasta ;
+ if (menu_item_id == ZMAPCDS || menu_item_id == ZMAPTRANSCRIPT || menu_item_id == ZMAPUNSPLICED)
+ {
+ char *title ;
+ char *peptide_fasta ;
- peptide_fasta = zMapFASTAString(ZMAPFASTA_SEQTYPE_AA, seq_name, molecule_type, gene_name,
- pep_length, zMapPeptideSequence(peptide)) ;
+ peptide_fasta = zMapFASTAString(ZMAPFASTA_SEQTYPE_AA, seq_name, molecule_type, gene_name,
+ pep_length, zMapPeptideSequence(peptide)) ;
- title = g_strdup_printf("%s%s%s",
- seq_name,
- gene_name ? ":" : "",
- gene_name ? gene_name : "") ;
- zMapGUIShowText(title, peptide_fasta, FALSE) ;
- g_free(title) ;
+ title = g_strdup_printf("%s%s%s",
+ seq_name,
+ gene_name ? ":" : "",
+ gene_name ? gene_name : "") ;
+ zMapGUIShowText(title, peptide_fasta, FALSE) ;
+ g_free(title) ;
- g_free(peptide_fasta) ;
- }
- else
- {
- dumpFASTA(menu_data->window, ZMAPFASTA_SEQTYPE_AA,
- zMapPeptideSequence(peptide), seq_name,
- pep_length, molecule_type, gene_name) ;
- }
+ g_free(peptide_fasta) ;
+ }
+ else
+ {
+ dumpFASTA(menu_data->window, ZMAPFASTA_SEQTYPE_AA,
+ zMapPeptideSequence(peptide), seq_name,
+ pep_length, molecule_type, gene_name) ;
+ }
- zMapPeptideDestroy(peptide) ;
+ zMapPeptideDestroy(peptide) ;
- g_free(dna) ;
+ g_free(dna) ;
+ }
g_free(menu_data) ;
--
GitLab