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Commit 3d19c9e1 authored by edgrif's avatar edgrif
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handle NULL return from dna routines.

parent 357293aa
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src/zmapWindow/zmapWindowFeature.c
+ 26
− 21
View file @ 3d19c9e1
......@@ -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;
......
src/zmapWindow/zmapWindowMenus.c
+ 42
− 37
View file @ 3d19c9e1
......@@ -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) ;
......
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