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Commit 24fa0508 authored by edgrif's avatar edgrif
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fix bug in setting up locus obj. for new feature which has a locus.

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src/zmapView/zmapViewRemoteReceive.c
+ 92
− 88
View file @ 24fa0508
......@@ -29,9 +29,9 @@
* Exported functions: See zmapView_P.h
*
* HISTORY:
* Last edited: Jan 22 12:25 2010 (edgrif)
* Last edited: Jan 27 15:46 2010 (edgrif)
* Created: Tue Jul 10 21:02:42 2007 (rds)
* CVS info: $Id: zmapViewRemoteReceive.c,v 1.39 2010-01-22 13:02:16 edgrif Exp $
* CVS info: $Id: zmapViewRemoteReceive.c,v 1.40 2010-02-05 11:48:11 edgrif Exp $
*-------------------------------------------------------------------
*/
......@@ -1466,18 +1466,6 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
if (result && !zMapXMLParserLastErrorMsg(parser))
{
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
ZMapFeatureTypeStyle style ;
style_name = (char *)g_quark_to_string(style_q);
style_id = zMapStyleCreateID(style_name);
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
feature_name = (char *)g_quark_to_string(feature_name_q);
if (result
......@@ -1509,102 +1497,118 @@ static gboolean xml_feature_start_cb(gpointer user_data, ZMapXMLElement feature_
GQuark new_locus_id = zMapXMLAttributeGetValue(attr);
GQuark locus_set_id = zMapStyleCreateID(ZMAP_FIXED_STYLE_LOCUS_NAME);
char *new_locus_name = (char *)g_quark_to_string(new_locus_id);
ZMapFeatureTypeStyle locus_style ;
/* Find locus feature set first ... */
if (!(locus_feature_set = zMapFeatureBlockGetSetByID(request_data->block, locus_set_id)))
if (!(locus_style
= zMapFindStyle(request_data->styles, zMapStyleCreateID(ZMAP_FIXED_STYLE_LOCUS_NAME))))
{
/* Can't find one, create one and add it. */
locus_feature_set = zMapFeatureSetCreate(ZMAP_FIXED_STYLE_LOCUS_NAME, NULL);
zMapFeatureBlockAddFeatureSet(request_data->block, locus_feature_set);
zMapLogWarning("Feature %s created but Locus %s could not be added"
" because Locus style could not be found.",
feature_name, new_locus_name) ;
}
else
{
/* Find locus feature set first ... */
if (!(locus_feature_set = zMapFeatureBlockGetSetByID(request_data->block, locus_set_id)))
{
/* Can't find one, create one and add it. */
locus_feature_set = zMapFeatureSetCreate(ZMAP_FIXED_STYLE_LOCUS_NAME, NULL);
zMapFeatureBlockAddFeatureSet(request_data->block, locus_feature_set);
}
/* For some reason lace passes over odd xml here...
<zmap action="delete_feature">
<featureset>
/* For some reason lace passes over odd xml here...
<zmap action="delete_feature">
<featureset>
<feature style="Known_CDS" name="RP23-383F20.1-004" locus="Oxsm" ... />
</featureset>
</zmap>
<zmap action="create_feature">
<featureset>
</featureset>
</zmap>
<zmap action="create_feature">
<featureset>
<feature style="Known_CDS" name="RP23-383F20.1-004" locus="Oxsm" ... />
...
i.e. deleting the locus name it's creating!
*/
...
i.e. deleting the locus name it's creating!
*/
old_feature =
(ZMapFeature)zMapFeatureContextFindFeatureFromFeature(request_data->orig_context,
(ZMapFeatureAny)request_data->feature);
old_feature =
(ZMapFeature)zMapFeatureContextFindFeatureFromFeature(request_data->orig_context,
(ZMapFeatureAny)request_data->feature);
if ((old_feature) && (old_feature->type == ZMAPSTYLE_MODE_TRANSCRIPT)
&& (old_feature->locus_id != 0) && (old_feature->locus_id != new_locus_id))
{
/* ^^^ check the old one was a transcript and had a locus that doesn't match this one */
ZMapFeature tmp_locus_feature;
ZMapFeatureAny old_locus_feature;
char *old_locus_name = (char *)g_quark_to_string(old_feature->locus_id);
if ((old_feature) && (old_feature->type == ZMAPSTYLE_MODE_TRANSCRIPT)
&& (old_feature->locus_id != 0) && (old_feature->locus_id != new_locus_id))
{
/* ^^^ check the old one was a transcript and had a locus that doesn't match this one */
ZMapFeature tmp_locus_feature;
ZMapFeatureAny old_locus_feature;
char *old_locus_name = (char *)g_quark_to_string(old_feature->locus_id);
/* I DON'T REALLY UNDERSTAND THIS BIT CURRENTLY...WHY DO WE ALWAYS LOG THIS... */
/* If we're here, assumptions have been made
* 1 - We are in an action=delete_feature request
* 2 - We are modifying an existing feature.
* 3 - Lace has passed a locus="name" which does not = existing feature locus name.
* 4 - Locus start and end are based on feature start end.
* If they are the extent of the locus as they should be...
* The unique_id will be different and therefore the next
* zMapFeatureContextFindFeatureFromFeature will fail.
* This means the locus won't be deleted as it should be.
*/
zMapLogMessage("loci '%s' & '%s' don't match will delete '%s'",
old_locus_name, new_locus_name, old_locus_name);
/* If we're here, assumptions have been made
* 1 - We are in an action=delete_feature request
* 2 - We are modifying an existing feature.
* 3 - Lace has passed a locus="name" which does not = existing feature locus name.
* 4 - Locus start and end are based on feature start end.
* If they are the extent of the locus as they should be...
* The unique_id will be different and therefore the next
* zMapFeatureContextFindFeatureFromFeature will fail.
* This means the locus won't be deleted as it should be.
*/
zMapLogMessage("loci '%s' & '%s' don't match will delete '%s'",
old_locus_name, new_locus_name, old_locus_name);
tmp_locus_feature = zMapFeatureCreateFromStandardData(old_locus_name,
NULL, "",
ZMAPSTYLE_MODE_BASIC, locus_style,
start, end, FALSE, 0.0,
ZMAPSTRAND_NONE,
ZMAPPHASE_NONE);
zMapFeatureSetAddFeature(locus_feature_set, tmp_locus_feature);
tmp_locus_feature = zMapFeatureCreateFromStandardData(old_locus_name,
NULL, "", ZMAPSTYLE_MODE_BASIC, NULL,
start, end, FALSE, 0.0,
ZMAPSTRAND_NONE,
ZMAPPHASE_NONE);
zMapFeatureSetAddFeature(locus_feature_set, tmp_locus_feature);
if ((old_locus_feature
= zMapFeatureContextFindFeatureFromFeature(request_data->orig_context,
(ZMapFeatureAny)tmp_locus_feature)))
{
zMapLogMessage("Found old locus '%s', deleting.", old_locus_name);
locus_feature = (ZMapFeature)zMapFeatureAnyCopy(old_locus_feature);
}
else
{
zMapLogMessage("Failed to find old locus '%s' during delete.", old_locus_name);
/* make the locus feature itself. */
locus_feature = zMapFeatureCreateFromStandardData(old_locus_name,
NULL, "",
ZMAPSTYLE_MODE_BASIC, locus_style,
start, end, FALSE, 0.0,
ZMAPSTRAND_NONE,
ZMAPPHASE_NONE);
}
if((old_locus_feature = zMapFeatureContextFindFeatureFromFeature(request_data->orig_context,
(ZMapFeatureAny)tmp_locus_feature)))
{
zMapLogMessage("Found old locus '%s', deleting.", old_locus_name);
locus_feature = (ZMapFeature)zMapFeatureAnyCopy(old_locus_feature);
zMapFeatureDestroy(tmp_locus_feature);
}
else
{
zMapLogMessage("Failed to find old locus '%s' during delete.", old_locus_name);
/* make the locus feature itself. */
locus_feature = zMapFeatureCreateFromStandardData(old_locus_name,
NULL, "", ZMAPSTYLE_MODE_BASIC, NULL,
locus_feature = zMapFeatureCreateFromStandardData(new_locus_name,
NULL, "",
ZMAPSTYLE_MODE_BASIC, locus_style,
start, end, FALSE, 0.0,
ZMAPSTRAND_NONE,
ZMAPPHASE_NONE);
}
zMapFeatureDestroy(tmp_locus_feature);
}
else
{
/* make the locus feature itself. */
locus_feature = zMapFeatureCreateFromStandardData(new_locus_name,
NULL, "", ZMAPSTYLE_MODE_BASIC, NULL,
start, end, FALSE, 0.0,
ZMAPSTRAND_NONE,
ZMAPPHASE_NONE);
}
}
/* The feature set and feature need to have their styles set... */
/* The feature set and feature need to have their styles set... */
/* managed to get the styles set up. Add the feature to
* feature set and finish up the locus. */
zMapFeatureSetAddFeature(locus_feature_set,
locus_feature);
zMapFeatureAddLocus(locus_feature, new_locus_id);
/* managed to get the styles set up. Add the feature to
* feature set and finish up the locus. */
zMapFeatureSetAddFeature(locus_feature_set,
locus_feature);
zMapFeatureAddLocus(locus_feature, new_locus_id);
/* We'll still add the locus to the transcript
* feature so at least this information is
* preserved whatever went on with the styles */
zMapFeatureAddLocus(request_data->feature, new_locus_id);
/* We'll still add the locus to the transcript
* feature so at least this information is
* preserved whatever went on with the styles */
zMapFeatureAddLocus(request_data->feature, new_locus_id);
}
}
......
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