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Commit abfe2590 authored by edgrif's avatar edgrif
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Add new 'all matches with same name' option for blixem args + fix bugs in error handling.

parent 32f77833
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Tags RELEASE_0-1-77
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src/zmapView/zmapViewCallBlixem.c
+ 109
− 76
View file @ abfe2590
......@@ -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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