From abfe25901c05d6fba7e7b17e0683e31ad8c03c33 Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Wed, 16 Dec 2009 11:05:07 +0000
Subject: [PATCH] Add new 'all matches with same name' option for blixem args +
fix bugs in error handling.
---
src/zmapView/zmapViewCallBlixem.c | 185 ++++++++++++++++++------------
1 file changed, 109 insertions(+), 76 deletions(-)
diff --git a/src/zmapView/zmapViewCallBlixem.c b/src/zmapView/zmapViewCallBlixem.c
index c61f3a856..805173cc0 100755
--- a/src/zmapView/zmapViewCallBlixem.c
+++ b/src/zmapView/zmapViewCallBlixem.c
@@ -29,9 +29,9 @@
* Exported functions: see zmapView_P.h
*
* HISTORY:
- * Last edited: Nov 18 16:15 2009 (edgrif)
+ * Last edited: Dec 15 16:04 2009 (edgrif)
* Created: Thu Jun 28 18:10:08 2007 (edgrif)
- * CVS info: $Id: zmapViewCallBlixem.c,v 1.22 2009-12-14 16:37:59 mh17 Exp $
+ * CVS info: $Id: zmapViewCallBlixem.c,v 1.23 2009-12-16 11:05:07 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -132,11 +132,13 @@ typedef struct BlixemDataStruct
/* User can specify sets of homologies that can be passed to blixem, if the set they selected
* is in one of these sets then all the features in all the sets are sent to blixem. */
ZMapHomolType align_type ; /* What type of alignment are we doing ? */
+
+ ZMapViewBlixemAlignSet align_set ; /* Which set of alignments ? */
+
GList *dna_sets ;
GList *protein_sets ;
GList *transcript_sets ;
- ZMapViewBlixemFlags flags;
int offset ;
int min, max ;
@@ -332,7 +334,7 @@ gboolean zmapViewBlixemLocalSequences(ZMapView view, ZMapFeature feature, GList
* process so that the blixems can be cleared up when the view exits.
* */
gboolean zmapViewCallBlixem(ZMapView view, ZMapFeature feature, GList *local_sequences,
- ZMapViewBlixemFlags flags, GPid *child_pid, gboolean *kill_on_exit)
+ ZMapViewBlixemAlignSet align_set, GPid *child_pid, gboolean *kill_on_exit)
{
gboolean status = TRUE ;
char *argv[BLX_ARGV_ARGC + 1] = {NULL} ;
@@ -346,7 +348,7 @@ gboolean zmapViewCallBlixem(ZMapView view, ZMapFeature feature, GList *local_seq
blixem_data.local_sequences = local_sequences ;
- blixem_data.flags = flags;
+ blixem_data.align_set = align_set;
if (status)
status = makeTmpfiles(&blixem_data) ;
@@ -875,7 +877,7 @@ static gboolean writeExblxSeqblFiles(blixemData blixem_data)
{
ZMapFeature feature = blixem_data->feature ;
ZMapFeatureSet feature_set ;
- GList *set_list = NULL;
+ GList *set_list = NULL ;
blixem_data->errorMsg = NULL ;
@@ -888,48 +890,64 @@ static gboolean writeExblxSeqblFiles(blixemData blixem_data)
blixem_data->required_feature_type = ZMAPSTYLE_MODE_ALIGNMENT ;
blixem_data->align_type = feature->feature.homol.type ;
- if (blixem_data->align_type == ZMAPHOMOL_N_HOMOL &&
- blixem_data->flags & BLIXEM_OBEY_DNA_SETS)
- set_list = blixem_data->dna_sets ;
- else if(blixem_data->flags & BLIXEM_OBEY_PROTEIN_SETS)
- set_list = blixem_data->protein_sets ;
- if(blixem_data->flags & BLIXEM_SINGLE_FEATURE)
- {
- writeExblxSeqblLine(feature, blixem_data);
- }
- /* Do a homol max list here.... */
- else if (blixem_data->homol_max)
+ /* Be better even for single feature to have it as a list and put it through some common
+ * code...and same for homol_max...just treat it all in one way.... */
+
+ if (blixem_data->homol_max || (blixem_data->align_set != BLIXEM_NO_MATCHES))
{
+ /* Do a homol max list here.... */
int num_homols = 0 ;
blixem_data->align_list = NULL ;
+ if (blixem_data->align_set == BLIXEM_FEATURE_SINGLE_MATCH)
+ {
+ blixem_data->align_list = g_list_append(blixem_data->align_list, feature) ;
+ }
+ else if (blixem_data->align_set == BLIXEM_FEATURE_ALL_MATCHES)
+ {
+ blixem_data->align_list = zMapFeatureSetGetNamedFeatures(feature_set, feature->original_id) ;
+ }
+ else if (blixem_data->align_set == BLIXEM_FEATURESET_MATCHES)
+ {
+ g_hash_table_foreach(feature_set->features, getFeatureCB, blixem_data) ;
+ }
+ else if (blixem_data->align_set == BLIXEM_MULTI_FEATURESET_MATCHES)
+ {
+ if (blixem_data->align_type == ZMAPHOMOL_N_HOMOL)
+ set_list = blixem_data->dna_sets ;
+ else
+ set_list = blixem_data->protein_sets ;
- if (set_list)
- g_list_foreach(set_list, getSetList, blixem_data) ;
- else
- g_hash_table_foreach(feature_set->features, getFeatureCB, blixem_data) ;
+ g_list_foreach(set_list, getSetList, blixem_data) ;
+ }
- if ((num_homols = g_list_length(blixem_data->align_list)) && blixem_data->homol_max < num_homols)
+ if (blixem_data->homol_max)
{
- GList *break_point ;
+ if ((num_homols = g_list_length(blixem_data->align_list)) && blixem_data->homol_max < num_homols)
+ {
+ GList *break_point ;
- blixem_data->align_list = g_list_sort(blixem_data->align_list, scoreOrderCB) ;
+ blixem_data->align_list = g_list_sort(blixem_data->align_list, scoreOrderCB) ;
- break_point = g_list_nth(blixem_data->align_list, blixem_data->homol_max + 1) ;
+ break_point = g_list_nth(blixem_data->align_list, blixem_data->homol_max + 1) ;
/* "+ 1" to go past last homol. */
- /* Now remove entries.... */
- if ((break_point = zMap_g_list_split(blixem_data->align_list, break_point)))
- g_list_free(break_point) ;
-
+ /* Now remove entries.... */
+ if ((break_point = zMap_g_list_split(blixem_data->align_list, break_point)))
+ g_list_free(break_point) ;
+ }
}
g_list_foreach(blixem_data->align_list, writeListEntry, blixem_data) ;
}
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
else
{
+ /* No homol_max...is this ever called ? */
+
if (set_list && (g_list_find(set_list, GUINT_TO_POINTER(feature_set->unique_id))))
{
g_list_foreach(set_list, processSetList, blixem_data) ;
@@ -939,6 +957,8 @@ static gboolean writeExblxSeqblFiles(blixemData blixem_data)
g_hash_table_foreach(feature_set->features, writeHashEntry, blixem_data) ;
}
}
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
/*
@@ -1453,50 +1473,68 @@ static gint scoreOrderCB(gconstpointer a, gconstpointer b)
* */
static gboolean writeFastAFile(blixemData blixem_data)
{
- enum { FASTA_CHARS = 50 };
- ZMapFeature feature = NULL;
- ZMapFeatureBlock block = NULL;
- gsize bytes_written;
- GError *channel_error = NULL;
- char *line;
- gboolean status = TRUE;
+ gboolean status = TRUE ;
+ ZMapFeature feature = NULL ;
+ ZMapFeatureBlock block = NULL ;
+ gsize bytes_written ;
+ GError *channel_error = NULL ;
+ char *line = NULL ;
+ enum { FASTA_CHARS = 50 } ;
char buffer[FASTA_CHARS + 2] ; /* FASTA CHARS + \n + \0 */
int lines = 0, chars_left = 0 ;
char *cp = NULL ;
int i ;
- feature = blixem_data->feature;
- if ((blixem_data->fasta_channel = g_io_channel_new_file(blixem_data->fastAFile, "w", &channel_error)))
+ feature = blixem_data->feature ;
+
+
+ if (!(block = (ZMapFeatureBlock)zMapFeatureGetParentGroup((ZMapFeatureAny)feature, ZMAPFEATURE_STRUCT_BLOCK))
+ || !zMapFeatureBlockDNA(block, NULL, NULL, &cp))
+ {
+ zMapShowMsg(ZMAP_MSG_WARNING, "Error: writing to file, failed to get feature's DNA");
+
+ status = FALSE ;
+ }
+ else
{
- line = g_strdup_printf(">%s\n",
- g_quark_to_string(blixem_data->view->features->parent_name));
- if (g_io_channel_write_chars(blixem_data->fasta_channel,
- line, -1, &bytes_written, &channel_error) != G_IO_STATUS_NORMAL)
+ if (!(blixem_data->fasta_channel = g_io_channel_new_file(blixem_data->fastAFile, "w", &channel_error)))
{
- zMapShowMsg(ZMAP_MSG_WARNING, "Error writing header record to fastA file: %50s... : %s",
- line, channel_error->message) ;
+ zMapShowMsg(ZMAP_MSG_WARNING, "Error: could not open fastA file: %s",
+ channel_error->message) ;
g_error_free(channel_error) ;
channel_error = NULL;
- g_free(line);
- status = FALSE ;
+ status = FALSE;
}
- else if((block = (ZMapFeatureBlock)zMapFeatureGetParentGroup((ZMapFeatureAny)feature,
- ZMAPFEATURE_STRUCT_BLOCK)) &&
- zMapFeatureBlockDNA(block, NULL, NULL, &cp))
+ else
{
- int total_chars ;
+ line = g_strdup_printf(">%s\n",
+ g_quark_to_string(blixem_data->view->features->parent_name));
- g_free(line); /* ugh...just horrible coding.... */
+ if (g_io_channel_write_chars(blixem_data->fasta_channel,
+ line, -1, &bytes_written, &channel_error) != G_IO_STATUS_NORMAL)
+ {
+ zMapShowMsg(ZMAP_MSG_WARNING, "Error writing header record to fastA file: %50s... : %s",
+ line, channel_error->message) ;
+ g_error_free(channel_error) ;
+ channel_error = NULL;
+
+ status = FALSE ;
+ }
+
+ g_free(line) ;
+ }
+
+
+ if (status)
+ {
+ int total_chars ;
total_chars = (blixem_data->max - blixem_data->min + 1) ;
lines = total_chars / FASTA_CHARS ;
chars_left = total_chars % FASTA_CHARS ;
-#ifdef RDS_DONT_INCLUDE
- cp = blixem_data->view->feature_context->sequence->sequence + blixem_data->min - 1 ;
-#endif
cp += (blixem_data->min - 1);
/* Do the full length lines. */
@@ -1504,10 +1542,12 @@ static gboolean writeFastAFile(blixemData blixem_data)
{
buffer[FASTA_CHARS] = '\n' ;
buffer[FASTA_CHARS + 1] = '\0' ;
- for (i = 0 ; i < lines && status; i++)
+
+ for (i = 0 ; i < lines && status ; i++)
{
memcpy(&buffer[0], cp, FASTA_CHARS) ;
cp += FASTA_CHARS ;
+
if (g_io_channel_write_chars(blixem_data->fasta_channel,
&buffer[0], -1,
&bytes_written, &channel_error) != G_IO_STATUS_NORMAL)
@@ -1516,44 +1556,37 @@ static gboolean writeFastAFile(blixemData blixem_data)
}
/* Do the last line. */
- if (chars_left > 0 && status)
+ if (status && chars_left > 0)
{
memcpy(&buffer[0], cp, chars_left) ;
buffer[chars_left] = '\n' ;
- buffer[chars_left + 1] = '\0' ;
+ buffer[chars_left + 1] = '\0' ;
+
if (g_io_channel_write_chars(blixem_data->fasta_channel,
&buffer[0], -1,
&bytes_written, &channel_error) != G_IO_STATUS_NORMAL)
status = FALSE ;
}
- if (status == FALSE)
+
+ if (!status)
{
- zMapShowMsg(ZMAP_MSG_WARNING, "Error: writing to fastA file: %s",
+ zMapShowMsg(ZMAP_MSG_WARNING, "Error writing to fastA file: %s",
channel_error->message) ;
g_error_free(channel_error) ;
- channel_error = NULL;
+ channel_error = NULL ;
}
- } /* if g_io_channel_write_chars(.... */
- else
- zMapShowMsg(ZMAP_MSG_WARNING, "Error: writing to file, failed to get feature's DNA");
+ }
- g_io_channel_shutdown(blixem_data->fasta_channel, TRUE, &channel_error);
- if (channel_error)
+ if (g_io_channel_shutdown(blixem_data->fasta_channel, TRUE, &channel_error) != G_IO_STATUS_NORMAL)
{
- g_error_free(channel_error);
- channel_error = NULL;
+ zMapShowMsg(ZMAP_MSG_WARNING, "Error closing fastA file: %s",
+ channel_error->message) ;
+ g_error_free(channel_error) ;
+ channel_error = NULL ;
}
}
- else /* if (blixem_data->fasta_channel = ... */
- {
- zMapShowMsg(ZMAP_MSG_WARNING, "Error: could not open fastA file: %s",
- channel_error->message) ;
- g_error_free(channel_error) ;
- channel_error = NULL;
- status = FALSE;
- }
- return status;
+ return status ;
}
--
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