Skip to content
Snippets Groups Projects
Commit 24df8a57 authored by rds's avatar rds
Browse files

added error handling to FeatureContextExecute

parent b2ed7035
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
src/zmapFeature/zmapFeatureContext.c
+ 157
− 67
View file @ 24df8a57
......@@ -27,9 +27,9 @@
*
* Exported functions: See ZMap/zmapFeature.h
* HISTORY:
* Last edited: Oct 13 16:51 2006 (edgrif)
* Last edited: Oct 18 14:41 2006 (rds)
* Created: Tue Jan 17 16:13:12 2006 (edgrif)
* CVS info: $Id: zmapFeatureContext.c,v 1.12 2006-10-16 10:27:25 edgrif Exp $
* CVS info: $Id: zmapFeatureContext.c,v 1.13 2006-10-18 15:13:29 rds Exp $
*-------------------------------------------------------------------
*/
......@@ -48,17 +48,22 @@ typedef struct
typedef struct
{
GDataForeachFunc callback;
ZMapGDataRecurseFunc start_callback;
ZMapGDataRecurseFunc end_callback;
gpointer callback_data;
char *error_string;
ZMapFeatureStructType stop;
ZMapFeatureStructType stopped_at;
ZMapFeatureContextExecuteStatus status;
}ContextExecuteStruct, *ContextExecute;
static char *getDNA(char *dna, int start, int end, gboolean revcomp) ;
static void revcompDNA(char *sequence, int seq_length) ;
static void revCompFeature(ZMapFeature feature, int end_coord);
static void revCompFeaturesCB(GQuark key,
gpointer data,
gpointer user_data);
static ZMapFeatureContextExecuteStatus revCompFeaturesCB(GQuark key,
gpointer data,
gpointer user_data,
char **error_out);
#ifdef RDS_DONT_INCLUDE_UNUSED
static void revcompFeatures(ZMapFeatureContext context) ;
static void doFeatureAnyCB(ZMapFeatureAny any_feature, gpointer user_data) ;
......@@ -72,6 +77,8 @@ static gboolean fetchBlockDNAPtr(ZMapFeature feature, char **dna);
static void executeDataForeachFunc(GQuark key, gpointer data, gpointer user_data);
static void executeListForeachFunc(gpointer data, gpointer user_data);
static void postExecuteProcess(ContextExecute execute_data);
/* Reverse complement a feature context.
*
* Efficiency does not allow us to simply throw everything away and reconstruct the context.
......@@ -225,7 +232,7 @@ char *zMapFeatureGetTranscriptDNA(ZMapFeatureContext context, ZMapFeature transc
void zMapFeatureContextExecute(ZMapFeatureAny feature_any,
ZMapFeatureStructType stop,
GDataForeachFunc callback,
ZMapGDataRecurseFunc callback,
gpointer data)
{
ContextExecuteStruct full_data = {0};
......@@ -234,11 +241,16 @@ void zMapFeatureContextExecute(ZMapFeatureAny feature_any,
if(stop != ZMAPFEATURE_STRUCT_INVALID)
{
context = (ZMapFeatureContext)zMapFeatureGetParentGroup(feature_any, ZMAPFEATURE_STRUCT_CONTEXT);
full_data.callback = callback;
full_data.callback_data = data;
full_data.stop = stop;
full_data.start_callback = callback;
full_data.end_callback = NULL;
full_data.callback_data = data;
full_data.stop = stop;
full_data.stopped_at = ZMAPFEATURE_STRUCT_INVALID;
full_data.status = ZMAP_CONTEXT_EXEC_STATUS_OK;
/* Start it all off with the alignments */
g_datalist_foreach(&(context->alignments), executeDataForeachFunc, &full_data);
postExecuteProcess(&full_data);
}
return ;
......@@ -246,20 +258,26 @@ void zMapFeatureContextExecute(ZMapFeatureAny feature_any,
void zMapFeatureContextExecuteSubset(ZMapFeatureAny feature_any,
ZMapFeatureStructType stop,
GDataForeachFunc callback,
ZMapGDataRecurseFunc callback,
gpointer data)
{
if(stop != ZMAPFEATURE_STRUCT_INVALID)
{
ContextExecuteStruct full_data = {0};
full_data.callback = callback;
full_data.callback_data = data;
full_data.stop = stop;
full_data.start_callback = callback;
full_data.end_callback = NULL;
full_data.callback_data = data;
full_data.stop = stop;
full_data.stopped_at = ZMAPFEATURE_STRUCT_INVALID;
full_data.status = ZMAP_CONTEXT_EXEC_STATUS_OK;
if(feature_any->struct_type <= stop)
executeDataForeachFunc(feature_any->unique_id, feature_any, &full_data);
else
zMapLogWarning("%s", "Too far down the hierarchy...");
full_data.error_string = g_strdup("Too far down the hierarchy...");
postExecuteProcess(&full_data);
}
else
zMapAssertNotReached();
......@@ -269,8 +287,17 @@ void zMapFeatureContextExecuteSubset(ZMapFeatureAny feature_any,
void zMapFeatureContextExecuteFull(ZMapFeatureAny feature_any,
ZMapFeatureStructType stop,
GDataForeachFunc callback,
ZMapGDataRecurseFunc callback,
gpointer data)
{
return zMapFeatureContextExecuteComplete(feature_any, stop, callback, NULL, data);
}
void zMapFeatureContextExecuteComplete(ZMapFeatureAny feature_any,
ZMapFeatureStructType stop,
ZMapGDataRecurseFunc start_callback,
ZMapGDataRecurseFunc end_callback,
gpointer data)
{
ContextExecuteStruct full_data = {0};
ZMapFeatureContext context = NULL;
......@@ -278,10 +305,16 @@ void zMapFeatureContextExecuteFull(ZMapFeatureAny feature_any,
if(stop != ZMAPFEATURE_STRUCT_INVALID)
{
context = (ZMapFeatureContext)zMapFeatureGetParentGroup(feature_any, ZMAPFEATURE_STRUCT_CONTEXT);
full_data.callback = callback;
full_data.callback_data = data;
full_data.stop = stop;
full_data.start_callback = start_callback;
full_data.end_callback = end_callback;
full_data.callback_data = data;
full_data.stop = stop;
full_data.stopped_at = ZMAPFEATURE_STRUCT_INVALID;
full_data.status = ZMAP_CONTEXT_EXEC_STATUS_OK;
executeDataForeachFunc(context->unique_id, context, &full_data);
postExecuteProcess(&full_data);
}
return ;
......@@ -289,7 +322,6 @@ void zMapFeatureContextExecuteFull(ZMapFeatureAny feature_any,
/*
* Internal functions.
*/
......@@ -429,11 +461,13 @@ static void revCompFeature(ZMapFeature feature, int end_coord)
return ;
}
static void revCompFeaturesCB(GQuark key,
gpointer data,
gpointer user_data)
static ZMapFeatureContextExecuteStatus revCompFeaturesCB(GQuark key,
gpointer data,
gpointer user_data,
char **error_out)
{
ZMapFeatureAny feature_any = (ZMapFeatureAny)data;
ZMapFeatureContextExecuteStatus status = ZMAP_CONTEXT_EXEC_STATUS_OK;
RevCompData cb_data = (RevCompData)user_data;
......@@ -481,7 +515,7 @@ static void revCompFeaturesCB(GQuark key,
}
return ;
return status;
}
static void revcompSpan(GArray *spans, int seq_end)
......@@ -503,9 +537,10 @@ static void revcompSpan(GArray *spans, int seq_end)
#ifdef RDS_TEMPLATE_USER_DATALIST_FOREACH
/* Use this function while descending through a feature context */
static void templateDataListForeach(GQuark key,
gpointer data,
gpointer user_data)
static ZMapFeatureContextExecuteStatus templateDataListForeach(GQuark key,
gpointer data,
gpointer user_data,
char **error_out)
{
ZMapFeatureAny feature_any = (ZMapFeatureAny)data;
ZMapFeatureContext feature_context = NULL;
......@@ -514,6 +549,7 @@ static void templateDataListForeach(GQuark key,
ZMapFeatureSet feature_set = NULL;
ZMapFeature feature_ft = NULL;
ZMapFeatureStructType feature_type = ZMAPFEATURE_STRUCT_INVALID;
ZMapFeatureContextExecuteStatus status = ZMAP_CONTEXT_EXEC_STATUS_ERROR;
YourDataType all_data = (YourDataType)user_data;
......@@ -543,7 +579,7 @@ static void templateDataListForeach(GQuark key,
}
return ;
return status;
}
#endif /* RDS_TEMPLATE_USER_DATALIST_FOREACH */
......@@ -558,49 +594,91 @@ static void executeDataForeachFunc(GQuark key, gpointer data, gpointer user_data
ZMapFeature feature_ft = NULL;
ZMapFeatureStructType feature_type = ZMAPFEATURE_STRUCT_INVALID;
feature_type = feature_any->struct_type;
if(full_data->callback) /* want some error handling here... */
(full_data->callback)(key, data, full_data->callback_data);
else
zMapLogWarning("%s", "Context Execute Callback Not Set.");
if(feature_type == full_data->stop)
if(full_data->status == ZMAP_CONTEXT_EXEC_STATUS_OK)
{
/* zMapLogWarning("%s", "zMapFeatureContextExecute Finished."); */
}
else
{
switch(feature_type)
feature_type = feature_any->struct_type;
if(full_data->start_callback)
full_data->status = (full_data->start_callback)(key, data,
full_data->callback_data,
&(full_data->error_string));
if(!(full_data->stop == feature_type ||
full_data->status != ZMAP_CONTEXT_EXEC_STATUS_OK))
{
case ZMAPFEATURE_STRUCT_CONTEXT:
feature_context = (ZMapFeatureContext)feature_any;
g_datalist_foreach(&(feature_context->alignments), executeDataForeachFunc, full_data);
break;
case ZMAPFEATURE_STRUCT_ALIGN:
feature_align = (ZMapFeatureAlignment)feature_any;
g_list_foreach(feature_align->blocks, executeListForeachFunc, full_data);
switch(feature_type)
{
case ZMAPFEATURE_STRUCT_CONTEXT:
feature_context = (ZMapFeatureContext)feature_any;
g_datalist_foreach(&(feature_context->alignments), executeDataForeachFunc, full_data);
if(full_data->end_callback)
{
if((full_data->status = (full_data->end_callback)(key, data,
full_data->callback_data,
&(full_data->error_string))) == ZMAP_CONTEXT_EXEC_STATUS_ERROR)
full_data->stopped_at = feature_type;
else if(full_data->status == ZMAP_CONTEXT_EXEC_STATUS_DONT_DESCEND)
full_data->status = ZMAP_CONTEXT_EXEC_STATUS_OK;
}
break;
case ZMAPFEATURE_STRUCT_ALIGN:
feature_align = (ZMapFeatureAlignment)feature_any;
g_list_foreach(feature_align->blocks, executeListForeachFunc, full_data);
#ifdef RDS_WHEN_BLOCKS_ARE_GDATA
/* If blocks is a GData use this instead */
g_datalist_foreach(&(feature_align->blocks), executeDataForeachFunc, full_data);
/* If blocks is a GData use this instead */
g_datalist_foreach(&(feature_align->blocks), executeDataForeachFunc, full_data);
#endif /* RDS_WHEN_BLOCKS_ARE_GDATA */
break;
case ZMAPFEATURE_STRUCT_BLOCK:
feature_block = (ZMapFeatureBlock)feature_any;
g_datalist_foreach(&(feature_block->feature_sets), executeDataForeachFunc, full_data);
break;
case ZMAPFEATURE_STRUCT_FEATURESET:
feature_set = (ZMapFeatureSet)feature_any;
g_datalist_foreach(&(feature_set->features), executeDataForeachFunc, full_data);
break;
case ZMAPFEATURE_STRUCT_FEATURE:
feature_ft = (ZMapFeature)feature_any;
/* No children here. */
break;
case ZMAPFEATURE_STRUCT_INVALID:
default:
zMapAssertNotReached();
break;
if(full_data->end_callback)
{
if((full_data->status = (full_data->end_callback)(key, data,
full_data->callback_data,
&(full_data->error_string))) == ZMAP_CONTEXT_EXEC_STATUS_ERROR)
full_data->stopped_at = feature_type;
else if(full_data->status == ZMAP_CONTEXT_EXEC_STATUS_DONT_DESCEND)
full_data->status = ZMAP_CONTEXT_EXEC_STATUS_OK;
}
break;
case ZMAPFEATURE_STRUCT_BLOCK:
feature_block = (ZMapFeatureBlock)feature_any;
g_datalist_foreach(&(feature_block->feature_sets), executeDataForeachFunc, full_data);
if(full_data->end_callback)
{
if((full_data->status = (full_data->end_callback)(key, data,
full_data->callback_data,
&(full_data->error_string))) == ZMAP_CONTEXT_EXEC_STATUS_ERROR)
full_data->stopped_at = feature_type;
else if(full_data->status == ZMAP_CONTEXT_EXEC_STATUS_DONT_DESCEND)
full_data->status = ZMAP_CONTEXT_EXEC_STATUS_OK;
}
break;
case ZMAPFEATURE_STRUCT_FEATURESET:
feature_set = (ZMapFeatureSet)feature_any;
g_datalist_foreach(&(feature_set->features), executeDataForeachFunc, full_data);
if(full_data->end_callback)
{
if((full_data->status = (full_data->end_callback)(key, data,
full_data->callback_data,
&(full_data->error_string))) == ZMAP_CONTEXT_EXEC_STATUS_ERROR)
full_data->stopped_at = feature_type;
else if(full_data->status == ZMAP_CONTEXT_EXEC_STATUS_DONT_DESCEND)
full_data->status = ZMAP_CONTEXT_EXEC_STATUS_OK;
}
break;
case ZMAPFEATURE_STRUCT_FEATURE:
feature_ft = (ZMapFeature)feature_any;
/* No children here. can't possibly go further down, so no end-callback either. */
break;
case ZMAPFEATURE_STRUCT_INVALID:
default:
zMapAssertNotReached();
break;
}
}
else if(full_data->status == ZMAP_CONTEXT_EXEC_STATUS_DONT_DESCEND)
full_data->status = ZMAP_CONTEXT_EXEC_STATUS_OK;
else
{
full_data->stopped_at = feature_type;
}
}
......@@ -624,6 +702,18 @@ static void executeListForeachFunc(gpointer data, gpointer user_data)
return ;
}
static void postExecuteProcess(ContextExecute execute_data)
{
if(execute_data->status == ZMAP_CONTEXT_EXEC_STATUS_ERROR)
{
printf("ContextExecute: Error, function stopped @ level %d, message = %s\n",
execute_data->stopped_at,
execute_data->error_string);
}
return ;
}
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment