From 3a0aed2a3493f91cb473aaed410ce81106efcc46 Mon Sep 17 00:00:00 2001
From: mh17 <mh17>
Date: Thu, 22 Apr 2010 14:31:52 +0000
Subject: [PATCH] fixed DNA not there bug where ACEDB is second server running
---
src/include/ZMap/zmapFeature.h | 3 +-
src/include/ZMap/zmapView.h | 13 +-
src/zmapConfig/zmapConfigLoader.c | 7 +-
src/zmapControl/zmapControl.c | 119 ++++++++----
src/zmapFeature/zmapFeature.c | 300 +++++------------------------
src/zmapFeature/zmapFeatureDNA.c | 94 +++++++--
src/zmapServer/pipe/pipeServer.c | 15 +-
src/zmapView/zmapView.c | 76 ++++++--
src/zmapWindow/zmapWindowFeature.c | 285 ++++++++++++++-------------
9 files changed, 440 insertions(+), 472 deletions(-)
diff --git a/src/include/ZMap/zmapFeature.h b/src/include/ZMap/zmapFeature.h
index 168609dc0..dbf2fef9e 100755
--- a/src/include/ZMap/zmapFeature.h
+++ b/src/include/ZMap/zmapFeature.h
@@ -27,7 +27,7 @@
* HISTORY:
* Last edited: Mar 3 13:40 2010 (edgrif)
* Created: Fri Jun 11 08:37:19 2004 (edgrif)
- * CVS info: $Id: zmapFeature.h,v 1.173 2010-03-19 08:56:41 mh17 Exp $
+ * CVS info: $Id: zmapFeature.h,v 1.174 2010-04-22 14:31:52 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_FEATURE_H
@@ -875,6 +875,7 @@ ZMapFeatureTypeStyle zMapFeatureContextFindStyle(ZMapFeatureContext context, cha
void zMapFeatureContextDestroy(ZMapFeatureContext context, gboolean free_data) ;
+gboolean zMapFeatureContextGetDNAStatus(ZMapFeatureContext context);
/* THOSE IN FEATURECONTEXT.C */
diff --git a/src/include/ZMap/zmapView.h b/src/include/ZMap/zmapView.h
index 55f53ea64..4fc9901a7 100755
--- a/src/include/ZMap/zmapView.h
+++ b/src/include/ZMap/zmapView.h
@@ -31,7 +31,7 @@
* HISTORY:
* Last edited: Jun 12 14:36 2009 (edgrif)
* Created: Thu May 13 14:59:14 2004 (edgrif)
- * CVS info: $Id: zmapView.h,v 1.57 2010-03-19 08:56:41 mh17 Exp $
+ * CVS info: $Id: zmapView.h,v 1.58 2010-04-22 14:31:52 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAPVIEW_H
@@ -84,6 +84,17 @@ typedef struct
+// tried to put these into ConnectionData but as ever there's scope issues
+typedef struct
+{
+ char *err_msg; // from the server mainly
+ GList *feature_sets ;
+ gboolean status; // load sucessful?
+ unsigned long xwid ; // X Window id for the xremote widg. */
+
+} LoadFeaturesDataStruct, *LoadFeaturesData ;
+
+
/* Holds a sequence to be fetched, in the end this will include aligns/blocks etc. */
typedef struct
{
diff --git a/src/zmapConfig/zmapConfigLoader.c b/src/zmapConfig/zmapConfigLoader.c
index 4578bccc6..ec8bdcc63 100644
--- a/src/zmapConfig/zmapConfigLoader.c
+++ b/src/zmapConfig/zmapConfigLoader.c
@@ -31,7 +31,7 @@
* HISTORY:
* Last edited: Mar 2 14:47 2010 (edgrif)
* Created: Thu Sep 25 14:12:05 2008 (rds)
- * CVS info: $Id: zmapConfigLoader.c,v 1.15 2010-04-20 12:00:37 mh17 Exp $
+ * CVS info: $Id: zmapConfigLoader.c,v 1.16 2010-04-22 14:31:52 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -654,7 +654,10 @@ gboolean zMapConfigIniGetStylesFromFile(char *styles_list, char *styles_file, GD
if(shape_param)
{
GQuark q = (GQuark) enum_value; // ie the name of the shape
- ZMapStyleGlyphShape shape = g_hash_table_lookup(shapes,GINT_TO_POINTER(q));
+ ZMapStyleGlyphShape shape = NULL;
+
+ if(shapes)
+ shape = g_hash_table_lookup(shapes,GINT_TO_POINTER(q));
if(shape)
{
diff --git a/src/zmapControl/zmapControl.c b/src/zmapControl/zmapControl.c
index 697f145a9..d38b0b646 100755
--- a/src/zmapControl/zmapControl.c
+++ b/src/zmapControl/zmapControl.c
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: Feb 1 15:12 2010 (edgrif)
* Created: Thu Jul 24 16:06:44 2003 (edgrif)
- * CVS info: $Id: zmapControl.c,v 1.98 2010-03-04 15:09:51 mh17 Exp $
+ * CVS info: $Id: zmapControl.c,v 1.99 2010-04-22 14:31:52 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -71,14 +71,14 @@ static ZMapCallbacks zmap_cbs_G = NULL ;
/* Holds callbacks we set in the level below us to be called back on. */
ZMapViewCallbacksStruct view_cbs_G = {
- enterCB,
+ enterCB,
leaveCB,
- dataLoadCB,
- controlFocusCB,
- controlSelectCB,
+ dataLoadCB,
+ controlFocusCB,
+ controlSelectCB,
controlSplitToPatternCB,
- controlVisibilityChangeCB,
- viewStateChangeCB,
+ controlVisibilityChangeCB,
+ viewStateChangeCB,
viewKilledCB
} ;
@@ -95,7 +95,7 @@ ZMapViewCallbacksStruct view_cbs_G = {
/* This routine must be called just once before any other zmaps routine, it is a fatal error
* if the caller calls this routine more than once. The caller must supply all of the callback
* routines.
- *
+ *
* Note that since this routine is called once per application we do not bother freeing it
* via some kind of zmaps terminate routine. */
void zMapInit(ZMapCallbacks callbacks)
@@ -145,7 +145,7 @@ gboolean zMapRaise(ZMap zmap)
/* Presents a window to the user. This may mean raising the window
* in the stacking order, deiconifying it, moving it to the current
* desktop, and/or giving it the keyboard focus, possibly dependent
- * on the user's platform, window manager, and preferences.
+ * on the user's platform, window manager, and preferences.
*/
gtk_window_present(GTK_WINDOW(zmap->toplevel));
@@ -183,7 +183,7 @@ gboolean zmapConnectViewConfig(ZMap zmap, ZMapView view, char *config)
result = zMapViewConnect(view, config) ;
zmapControlWindowSetGUIState(zmap) ;
-
+
return result ;
}
@@ -198,7 +198,7 @@ gboolean zMapConnectView(ZMap zmap, ZMapView view)
if ((result = zMapViewConnect(view, NULL)))
zmapControlWindowSetGUIState(zmap) ;
-
+
return result ;
}
@@ -236,15 +236,15 @@ gboolean zMapDeleteView(ZMap zmap, ZMapView view)
/* Reset an existing ZMap, this call will:
- *
+ *
* - Completely reset a ZMap window to blank with no sequences displayed and no
* threads attached or anything.
* - Frees all ZMap window data
* - Kills all existings server threads etc.
- *
+ *
* After this call the ZMap will be ready for the user to specify a new sequence to be
* loaded.
- *
+ *
* */
gboolean zMapReset(ZMap zmap)
{
@@ -319,7 +319,7 @@ gboolean zMapDestroy(ZMap zmap)
/*
* These functions are internal to zmapControl.
- *
+ *
*/
@@ -416,7 +416,7 @@ void zmapControlSetGUIVisChange(ZMap zmap, ZMapWindowVisibilityChange vis_change
/* Called when the user kills the toplevel window of the ZMap either by clicking the "quit"
* button or by using the window manager frame menu to kill the window.
- *
+ *
* Really this function just signals the zmap to be killed. */
void zmapControlSignalKill(ZMap zmap)
{
@@ -435,7 +435,7 @@ void zmapControlSignalKill(ZMap zmap)
void zmapControlDoKill(ZMap zmap)
{
g_return_if_fail((zmap->state != ZMAP_DYING)) ;
-
+
/* set our state to DYING....so we don't respond to anything anymore.... */
/* Must set this as this will prevent any further interaction with the ZMap as
@@ -468,7 +468,7 @@ void zmapControlLoadCB(ZMap zmap)
ZMapView curr_view ;
/* for now we are just doing the current view but this will need to change to allow a kind
- * of global load of all views if there is no current selected view, or perhaps be an error
+ * of global load of all views if there is no current selected view, or perhaps be an error
* if no view is selected....perhaps there should always be a selected view. */
zMapAssert(zmap->focus_viewwindow) ;
@@ -502,7 +502,7 @@ void zmapControlResetCB(ZMap zmap)
view_state = zMapViewGetStatus(curr_view) ;
/* for now we are just doing the current view but this will need to change to allow a kind
- * of global load of all views if there is no current selected view, or perhaps be an error
+ * of global load of all views if there is no current selected view, or perhaps be an error
* if no view is selected....perhaps there should always be a selected view. */
zMapViewReset(curr_view) ;
@@ -567,8 +567,8 @@ static ZMap createZMap(void *app_data)
/* Use default hashing functions, but THINK ABOUT THIS, MAY NEED TO ATTACH DESTROY FUNCTIONS. */
zmap->viewwindow_2_parent = g_hash_table_new(NULL, NULL) ;
-
-
+
+
zmap->view2infopanel = g_hash_table_new_full(NULL, NULL, NULL, infoPanelLabelsHashCB);
return zmap ;
@@ -595,15 +595,62 @@ static void destroyZMap(ZMap zmap)
+
/* Called when a view has loaded data. */
+/*
+ * mh17: this appear to be only for the GUI
+ * but we need to tell x-remote about this and also to give some data about what data got loaded
+ * as view_data is NULL in all existing calls I'll specify the following:
+ * - if view_data == NULL then update GUI stuff
+ * - else send a message to x-remote
+ */
static void dataLoadCB(ZMapView view, void *app_data, void *view_data)
{
ZMap zmap = (ZMap)app_data ;
- /* Update title etc. */
- updateControl(zmap, view) ;
+ if(!view_data)
+ {
+ /* Update title etc. */
+ updateControl(zmap, view) ;
- zmapControlWindowSetGUIState(zmap) ;
+ zmapControlWindowSetGUIState(zmap) ;
+ }
+ else if(zmap->xremote_client)
+ {
+ LoadFeaturesData lfd = (LoadFeaturesData ) view_data;
+ char *request ;
+ char *response = NULL;
+ GList *features;
+ char * featurelist = NULL;
+ char *f;
+
+ for(features = lfd->feature_sets;features;features = features->next)
+ {
+ f = (char *) g_quark_to_string(GPOINTER_TO_UINT(features->data));
+ if(!featurelist)
+ featurelist = g_strdup(f);
+ else
+ featurelist = g_strjoin(";",featurelist,f,NULL);
+ }
+
+ request = g_strdup_printf(
+ "<zmap> <request action=\"features_loaded\">"
+ " <client xwid=\"0x%lx\" />"
+ " <featureset names=\"%s\" />"
+ " <status value=\"%d\" message=\"%s\" />"
+ "</request></zmap>",
+ lfd->xwid, featurelist,(int) lfd->status,lfd->err_msg ? lfd->err_msg : "OK") ;
+
+ if (zMapXRemoteSendRemoteCommand(zmap->xremote_client, request, &response) != ZMAPXREMOTE_SENDCOMMAND_SUCCEED)
+ {
+ response = response ? response : zMapXRemoteGetResponse(zmap->xremote_client);
+ zMapLogWarning("Notify of view closing failed: \"%s\"", response) ;
+ }
+
+ g_free(request);
+ g_free(featurelist);
+
+ }
return ;
}
@@ -612,7 +659,7 @@ static void dataLoadCB(ZMapView view, void *app_data, void *view_data)
/* This routine gets called when someone clicks in one of the zmap windows....it
* handles general focus handling of windows etc.
- */
+ */
static void controlFocusCB(ZMapViewWindow view_window, void *app_data, void *view_data_unused)
{
ZMap zmap = (ZMap)app_data ;
@@ -628,7 +675,7 @@ static void controlFocusCB(ZMapViewWindow view_window, void *app_data, void *vie
/* Step through each of the navigators and get their size and
* maximise the current view_window->view navigator */
-
+
do
{
ZMapView view_item = (ZMapView)(list_item->data);
@@ -685,10 +732,10 @@ static void controlSelectCB(ZMapViewWindow view_window, void *app_data, void *vi
vselect->xml_handler.xml_events,
vselect->xml_handler.start_handlers,
vselect->xml_handler.end_handlers,
- vselect->xml_handler.handler_data);
+ vselect->xml_handler.handler_data);
}
#endif
-
+
return ;
}
@@ -721,7 +768,7 @@ static void controlSplitToPatternCB(ZMapViewWindow view_window, void *app_data,
{
GList *tmp_list = split->touched_window_list;
int i = 2; /* Go through loop twice */
-
+
/* First time sets to the last list member, second time if there is another, the one before that. */
for(tmp_list = g_list_last(tmp_list); i > 0 && tmp_list; i--)
{
@@ -757,7 +804,7 @@ static void controlSplitToPatternCB(ZMapViewWindow view_window, void *app_data,
split->touched_window_list = g_list_append(split->touched_window_list, new_view_window);
}
}
-
+
zmapControlWindowSetGUIState(zmap) ;
/* leave this to the last minute */
@@ -828,10 +875,10 @@ static void viewStateChangeCB(ZMapView view, void *app_data, void *view_data)
*
* 2) The View may have died because it has detected an error and is now signalling us
* to say it has died.
- *
+ *
* NOTE we have made a policy decision to kill the whole zmap when the last view
* goes away.
- *
+ *
* */
static void viewKilledCB(ZMapView view, void *app_data, void *view_data)
{
@@ -842,7 +889,7 @@ static void viewKilledCB(ZMapView view, void *app_data, void *view_data)
if (!zmap->view_list)
{
-
+
if (zmap->state != ZMAP_DYING)
{
zMapLogCritical("ZMap \"%s\": the last view has died but zmap is not in ZMAP_DYING state.,"
@@ -1029,7 +1076,7 @@ static void removeView(ZMap zmap, ZMapView view, unsigned long xwid)
else
{
g_hash_table_remove(zmap->view2infopanel, view);
-
+
zmap->view_list = g_list_remove(zmap->view_list, view) ;
if (zmap->xremote_client)
diff --git a/src/zmapFeature/zmapFeature.c b/src/zmapFeature/zmapFeature.c
index 1b43343f5..062aaff33 100755
--- a/src/zmapFeature/zmapFeature.c
+++ b/src/zmapFeature/zmapFeature.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Dec 14 11:20 2009 (edgrif)
* Created: Fri Jul 16 13:05:58 2004 (edgrif)
- * CVS info: $Id: zmapFeature.c,v 1.127 2010-04-15 11:19:03 mh17 Exp $
+ * CVS info: $Id: zmapFeature.c,v 1.128 2010-04-22 14:31:53 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -2295,13 +2295,41 @@ static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
if(new)
(*diff_path_ptr)->parent = *view_path_parent_ptr;
-
- if (feature_any->struct_type == ZMAPFEATURE_STRUCT_BLOCK &&
+#if MH17_OLD_CODE
+ if (feature_any->struct_type == ZMAPFEATURE_STRUCT_BLOCK &&
+ (*view_path_ptr)->unique_id == feature_any->unique_id)
+ {
+ ((ZMapFeatureBlock)(*view_path_ptr))->features_start =
+ ((ZMapFeatureBlock)(feature_any))->features_start;
+ ((ZMapFeatureBlock)(*view_path_ptr))->features_end =
+ ((ZMapFeatureBlock)(feature_any))->features_end;
+ }
+#else
+// debugging reveals that features start and end are 1.0 in the new data and semsible in the old
+// maybe 1,0 gets reprocessed into start,end?? so let's leave it as it used to run
+// BUT: this code should only run if not a new block 'cos if it's new then we've just
+// assinged the pointer
+// thsi is a block which may hold a sequence, the dna featureset is another struct
+ if (!new && feature_any->struct_type == ZMAPFEATURE_STRUCT_BLOCK &&
(*view_path_ptr)->unique_id == feature_any->unique_id)
{
- ((ZMapFeatureBlock)(*view_path_ptr))->features_start = ((ZMapFeatureBlock)(feature_any))->features_start;
- ((ZMapFeatureBlock)(*view_path_ptr))->features_end = ((ZMapFeatureBlock)(feature_any))->features_end;
- }
+ ZMapFeatureBlock vptr = (ZMapFeatureBlock)(*view_path_ptr);
+ ZMapFeatureBlock feat = (ZMapFeatureBlock) feature_any;
+
+ vptr->features_start = feat->features_start;
+ vptr->features_end = feat->features_end;
+
+ // mh17: DNA did not get merged from a non first source
+ // by analogy with the above we need to copy the sequence too, in fact any Block only data
+ // sequence contains a pointer to a (long) string - can we just copy it?
+ // seems to work without double frees...
+ if(!vptr->sequence.sequence) // let's keep the first one, should be the same
+ {
+ memcpy(&vptr->block_to_sequence,&feat->block_to_sequence,sizeof(ZMapAlignBlockStruct));
+ memcpy(&vptr->sequence,&feat->sequence,sizeof(ZMapSequenceStruct));
+ }
+ }
+#endif
}
/* general code stop */
@@ -2346,257 +2374,29 @@ static ZMapFeatureContextExecuteStatus mergePreCB(GQuark key,
break;
-#ifdef GENERALISING
- case ZMAPFEATURE_STRUCT_ALIGN:
- {
- ZMapFeatureAlignment feature_align = (ZMapFeatureAlignment)feature_any ;
- ZMapFeatureContext server_context = (ZMapFeatureContext)(feature_any->parent) ;
- gboolean is_master_align = FALSE;
-#ifdef MESSES_UP_HASH
- /* Always remove from the server context */
- result = zMapFeatureAnyRemoveFeature((ZMapFeatureAny)server_context, feature_any) ;
- zMapAssert(result) ;
-#endif /* MESSES_UP_HASH */
- if(server_context->master_align == feature_align)
- {
- is_master_align = TRUE;
- server_context->master_align = NULL;
- }
-
- feature_any->parent = NULL;
- status = ZMAP_CONTEXT_EXEC_STATUS_OK_DELETE;
- /* If there are no children then we don't add it, we don't keep empty aligns etc. */
- if (feature_any->children)
- {
- ZMapFeatureAny diff_align ;
- children = TRUE ;
-
- /* If its not in the current context then add it, otherwise copy it so we can add
- * features further down the tree. */
- if (!(merge_data->current_view_align
- = (ZMapFeatureAlignment)zMapFeatureAnyGetFeatureByID((ZMapFeatureAny)(merge_data->view_context),
- feature_any->unique_id)))
- {
-
- /* If its new we can simply copy a pointer over to the diff context
- * and stop recursing.... */
- zMapFeatureContextAddAlignment(merge_data->view_context, feature_align, FALSE);
- merge_data->current_view_align = feature_align ;
-
- merge_data->new_features = new = TRUE ;
-
- diff_align = (ZMapFeatureAny)feature_align ;
-
- /* but we need to reset parent pointer....*/
- diff_align->parent = (ZMapFeatureAny)(merge_data->view_context) ;
-
- status = ZMAP_CONTEXT_EXEC_STATUS_DONT_DESCEND ;
- }
- else
- {
- /* If the feature is there we need to copy it and then recurse down until
- * we get to the individual feature level. */
- diff_align = zmapFeatureAnyCopy((ZMapFeatureAny)feature_align, NULL) ;
- featureAnyAddToDestroyList(merge_data->diff_context, diff_align) ;
- }
-
- /* Add align to diff context, n.b. we do _not_ set a destroy function. */
- featureAnyAddFeature((ZMapFeatureAny)(merge_data->diff_context), (ZMapFeatureAny)diff_align) ;
- merge_data->current_diff_align = (ZMapFeatureAlignment)diff_align ;
-
- if (new)
- diff_align->parent = (ZMapFeatureAny)(merge_data->view_context) ;
-
- if (is_master_align)
- {
- merge_data->diff_context->master_align = (ZMapFeatureAlignment)diff_align ;
- }
- }
-
- break;
- }
-
- case ZMAPFEATURE_STRUCT_BLOCK:
- {
- ZMapFeatureBlock feature_block = (ZMapFeatureBlock)feature_any ;
- ZMapFeatureAlignment server_align = (ZMapFeatureAlignment)(feature_any->parent) ;
-#ifdef MESSES_UP_HASH
- /* remove from server align */
- result = zMapFeatureAnyRemoveFeature((ZMapFeatureAny)server_align, feature_any) ;
- zMapAssert(result) ;
-#endif
- feature_any->parent = NULL;
- status = ZMAP_CONTEXT_EXEC_STATUS_OK_DELETE;
-
- /* If there are no children then we don't add it, we don't keep empty aligns etc. */
- if (feature_any->children)
- {
- ZMapFeatureAny diff_block ;
-
- children = TRUE ;
-
- /* If its not in the current context then add it. */
- if (!(merge_data->current_view_block
- = (ZMapFeatureBlock)zMapFeatureAnyGetFeatureByID((ZMapFeatureAny)(merge_data->current_view_align),
- feature_any->unique_id)))
- {
- /* add to the full context align */
- zMapFeatureAlignmentAddBlock(merge_data->current_view_align, feature_block);
- merge_data->current_view_block = feature_block ;
-
- merge_data->new_features = new = TRUE ;
-
- /* If its new we can simply copy a pointer over to the diff context
- * and stop recursing.... */
- diff_block = (ZMapFeatureAny)feature_block ;
-
- /* but we need to reset parent pointer....*/
- diff_block->parent = (ZMapFeatureAny)(merge_data->current_view_align) ;
-
- status = ZMAP_CONTEXT_EXEC_STATUS_DONT_DESCEND ;
-
- }
- else
- {
- /* Add to diff align. */
- diff_block = zmapFeatureAnyCopy((ZMapFeatureAny)feature_block, NULL) ;
- featureAnyAddToDestroyList(merge_data->diff_context, (ZMapFeatureAny)diff_block) ;
- }
-
- featureAnyAddFeature((ZMapFeatureAny)(merge_data->current_diff_align), diff_block) ;
- merge_data->current_diff_block = (ZMapFeatureBlock)diff_block ;
-
- if (new)
- diff_block->parent = (ZMapFeatureAny)(merge_data->current_view_align) ;
-
- }
-
- break;
- }
-
- case ZMAPFEATURE_STRUCT_FEATURESET:
- {
- ZMapFeatureSet feature_set = (ZMapFeatureSet)feature_any ;
- ZMapFeatureBlock server_block = (ZMapFeatureBlock)(feature_any->parent);
-#ifdef MESSES_UP_HASH
- /* remove from server align */
- result = zMapFeatureAnyRemoveFeature((ZMapFeatureAny)server_block, feature_any) ;
- zMapAssert(result) ;
-#endif
- feature_any->parent = NULL;
- status = ZMAP_CONTEXT_EXEC_STATUS_OK_DELETE;
- /* If there are no children then we don't add it, we don't keep empty aligns etc. */
- if (feature_any->children)
- {
- ZMapFeatureAny diff_set ;
-
- children = TRUE ;
-
- if (!(merge_data->current_view_set
- = (ZMapFeatureSet)zMapFeatureAnyGetFeatureByID((ZMapFeatureAny)(merge_data->current_view_block),
- feature_any->unique_id)))
- {
- /* add to the full context block */
- zMapFeatureBlockAddFeatureSet(merge_data->current_view_block, (ZMapFeatureSet)feature_set);
- merge_data->current_view_set = feature_set;
-
- merge_data->new_features = new = TRUE ;
-
- /* If its new we can simply copy a pointer over to the diff context
- * and stop recursing.... */
- diff_set = (ZMapFeatureAny)feature_set ;
-
- /* but we need to reset parent pointer....*/
- diff_set->parent = (ZMapFeatureAny)(merge_data->current_view_block) ;
-
- status = ZMAP_CONTEXT_EXEC_STATUS_DONT_DESCEND ;
-
- }
- else
- {
- diff_set = zmapFeatureAnyCopy((ZMapFeatureAny)feature_set, NULL) ;
- ((ZMapFeatureSet)diff_set)->style = feature_set->style ;
-
- featureAnyAddToDestroyList(merge_data->diff_context, (ZMapFeatureAny)diff_set) ;
- }
-
- featureAnyAddFeature((ZMapFeatureAny)(merge_data->current_diff_block), diff_set) ;
- merge_data->current_diff_set = (ZMapFeatureSet)diff_set ;
-
- if (new)
- diff_set->parent = (ZMapFeatureAny)(merge_data->current_view_block) ;
-
- }
-
- break;
- }
-
- case ZMAPFEATURE_STRUCT_FEATURE:
- {
- ZMapFeature feature = (ZMapFeature)(feature_any) ;
- ZMapFeatureSet server_set = (ZMapFeatureSet)(feature_any->parent) ;
- ZMapFeatureAny diff_feature ;
-#ifdef MESSES_UP_HASH
- /* remove from the server set */
- result = zMapFeatureAnyRemoveFeature((ZMapFeatureAny)server_set, feature_any) ;
- zMapAssert(result) ;
-#endif
- feature_any->parent = NULL;
- status = ZMAP_CONTEXT_EXEC_STATUS_OK_DELETE;
-
- /* Note that features do not have children _ever_ so we are only concerned with copying
- * pointers if we find new features. */
-
- /* If its not in the current context then add it. */
- if (!(zMapFeatureAnyGetFeatureByID((ZMapFeatureAny)(merge_data->current_view_set),
- feature_any->unique_id)))
- {
- merge_data->new_features = new = TRUE ;
-
- /* If its new we can simply copy a pointer over to the diff context
- * and stop recursing.... */
- diff_feature = (ZMapFeatureAny)feature ;
-
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- /* I don't think we need to do this because features do not have children. */
-
- featureAnyAddToRemoveList(merge_data->diff_context, diff_feature) ;
- status = ZMAP_CONTEXT_EXEC_STATUS_DONT_DESCEND ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
- /* We need to reset parent pointer....and the style pointer....
- * order is critical here since featureany call resets parent... */
- featureAnyAddFeature((ZMapFeatureAny)merge_data->current_diff_set, diff_feature) ;
-
- /* add to the full context set */
- featureAnyAddFeature((ZMapFeatureAny)(merge_data->current_view_set), diff_feature);
-
-
- if (merge_debug_G)
- zMapLogWarning("feature(%p)->parent = %p. current_view_set = %p",
- feature, feature->parent, merge_data->current_view_set);
- }
-
- break;
- }
-#endif /* GENERALISING */
-
default:
{
- zMapAssertNotReached() ;
- break;
+ zMapAssertNotReached() ;
+ break;
}
}
-
if (merge_debug_G)
zMapLogWarning("%s (%p) '%s' is %s and has %s",
- zMapFeatureStructType2Str(feature_any->struct_type),
- feature_any,
- g_quark_to_string(feature_any->unique_id),
- (new == TRUE ? "new" : "old"),
- (children ? "children and was added" : "no children and was not added"));
+ zMapFeatureStructType2Str(feature_any->struct_type),
+ feature_any,
+ g_quark_to_string(feature_any->unique_id),
+ (new == TRUE ? "new" : "old"),
+ (children ? "children and was added" : "no children and was not added"));
+#if 0
+ printf("%s (%p) '%s' is %s and has %s\n",
+ zMapFeatureStructType2Str(feature_any->struct_type),
+ feature_any,
+ g_quark_to_string(feature_any->unique_id),
+ (new == TRUE ? "new" : "old"),
+ (children ? "children and was added" : "no children and was not added"));
+#endif
+
return status;
}
diff --git a/src/zmapFeature/zmapFeatureDNA.c b/src/zmapFeature/zmapFeatureDNA.c
index 34a8a3901..385d59d6d 100755
--- a/src/zmapFeature/zmapFeatureDNA.c
+++ b/src/zmapFeature/zmapFeatureDNA.c
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Jul 15 09:04 2009 (rds)
* Created: Tue Apr 7 10:32:21 2009 (rds)
- * CVS info: $Id: zmapFeatureDNA.c,v 1.5 2010-03-04 15:10:23 mh17 Exp $
+ * CVS info: $Id: zmapFeatureDNA.c,v 1.6 2010-04-22 14:31:53 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -48,7 +48,7 @@ gboolean zMapFeatureBlockDNA(ZMapFeatureBlock block,
zMapAssert( block ) ;
- if(block->sequence.sequence &&
+ if(block->sequence.sequence &&
block->sequence.type != ZMAPSEQUENCE_NONE &&
block->sequence.type == ZMAPSEQUENCE_DNA &&
(context = (ZMapFeatureContext)zMapFeatureGetParentGroup((ZMapFeatureAny)block,
@@ -89,7 +89,7 @@ GQuark zMapFeatureDNAFeatureID(ZMapFeatureBlock block)
dna_id = zMapFeatureCreateID(ZMAPSTYLE_MODE_RAW_SEQUENCE,
dna_name, ZMAPSTRAND_FORWARD,
block->block_to_sequence.q1,
- block->block_to_sequence.q2,
+ block->block_to_sequence.q2,
0, 0);
g_free(dna_name);
}
@@ -105,7 +105,7 @@ gboolean zMapFeatureDNACreateFeatureSet(ZMapFeatureBlock block, ZMapFeatureSet *
GQuark dna_set_id = 0;
dna_set_id = zMapFeatureSetCreateID(ZMAP_FIXED_STYLE_DNA_NAME);
-
+
if(!(dna_feature_set = zMapFeatureBlockGetSetByID(block, dna_set_id)))
{
GQuark original_id = 0;
@@ -140,9 +140,9 @@ void zMapFeatureDNAAddSequenceData(ZMapFeature dna_feature, char *dna_str, int s
return ;
}
-ZMapFeature zMapFeatureDNACreateFeature(ZMapFeatureBlock block,
+ZMapFeature zMapFeatureDNACreateFeature(ZMapFeatureBlock block,
ZMapFeatureTypeStyle style,
- char *dna_str,
+ char *dna_str,
int sequence_length)
{
ZMapFeatureSet dna_feature_set = NULL;
@@ -162,7 +162,7 @@ ZMapFeature zMapFeatureDNACreateFeature(ZMapFeatureBlock block,
char *feature_name, *sequence, *ontology;
GQuark dna_id;
int block_start, block_end;
-
+
block_start = block->block_to_sequence.q1 ;
block_end = block->block_to_sequence.q2 ;
@@ -205,13 +205,83 @@ ZMapFeature zMapFeatureDNACreateFeature(ZMapFeatureBlock block,
block->sequence.sequence = dna_feature->feature.sequence.sequence;
block->sequence.type = dna_feature->feature.sequence.type;
block->sequence.length = dna_feature->feature.sequence.length;
-
+
}
if(feature_name)
g_free(feature_name);
}
-
+
return dna_feature;
}
+
+
+
+typedef struct
+{
+ gboolean exists;
+}BlockHasDNAStruct, *BlockHasDNA;
+
+/* Function to check whether any of the blocks has dna */
+static ZMapFeatureContextExecuteStatus oneBlockHasDNA(GQuark key,
+ gpointer data,
+ gpointer user_data,
+ char **error_out)
+{
+ ZMapFeatureAny feature_any = (ZMapFeatureAny)data;
+ ZMapFeatureBlock feature_block = NULL;
+ ZMapFeatureStructType feature_type = ZMAPFEATURE_STRUCT_INVALID;
+
+ BlockHasDNA dna = (BlockHasDNA)user_data;
+
+ feature_type = feature_any->struct_type;
+
+ switch(feature_type)
+ {
+ case ZMAPFEATURE_STRUCT_BLOCK:
+ feature_block = (ZMapFeatureBlock)feature_any;
+ if(!dna->exists)
+ dna->exists = (gboolean)(feature_block->sequence.length ? TRUE : FALSE);
+ break;
+ case ZMAPFEATURE_STRUCT_CONTEXT:
+ case ZMAPFEATURE_STRUCT_FEATURESET:
+ case ZMAPFEATURE_STRUCT_FEATURE:
+ case ZMAPFEATURE_STRUCT_ALIGN:
+ break;
+ case ZMAPFEATURE_STRUCT_INVALID:
+ default:
+ zMapAssertNotReached();
+ break;
+
+ }
+
+ return ZMAP_CONTEXT_EXEC_STATUS_OK;
+}
+
+
+gboolean zMapFeatureContextGetDNAStatus(ZMapFeatureContext context)
+{
+ gboolean drawable = FALSE;
+ BlockHasDNAStruct dna = {0};
+
+ /* We just need one of the blocks to have DNA.
+ * This enables us to turn on this button as we
+ * can't have half sensitivity. Any block which
+ * doesn't have DNA creates a warning for the user
+ * to complain about.
+ */
+
+ if(context)
+ {
+ zMapFeatureContextExecute((ZMapFeatureAny)context,
+ ZMAPFEATURE_STRUCT_BLOCK,
+ oneBlockHasDNA,
+ &dna);
+
+ drawable = dna.exists;
+ }
+
+ return drawable;
+}
+
diff --git a/src/zmapServer/pipe/pipeServer.c b/src/zmapServer/pipe/pipeServer.c
index a9de40641..22b636629 100755
--- a/src/zmapServer/pipe/pipeServer.c
+++ b/src/zmapServer/pipe/pipeServer.c
@@ -34,7 +34,7 @@
* HISTORY:
* Last edited: Jan 14 10:10 2010 (edgrif)
* Created: 2009-11-26 12:02:40 (mh17)
- * CVS info: $Id: pipeServer.c,v 1.21 2010-03-19 14:20:54 mh17 Exp $
+ * CVS info: $Id: pipeServer.c,v 1.22 2010-04-22 14:31:53 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -385,7 +385,7 @@ static ZMapServerResponseType openConnection(void *server_in, gboolean sequence_
pipeGetSequence(server);
}
}
- else
+ if(!retval || result != ZMAP_SERVERRESPONSE_OK)
{
setLastErrorMsg(server, &gff_pipe_err) ;
result = ZMAP_SERVERRESPONSE_REQFAIL ;
@@ -958,14 +958,19 @@ static void addMapping(ZMapFeatureContext feature_context, ZMapGFFHeader header)
static void setLastErrorMsg(PipeServer server, GError **gff_pipe_err_inout)
{
GError *gff_pipe_err ;
+ char *msg = "failed";
- zMapAssert(server && gff_pipe_err_inout && *gff_pipe_err_inout) ;
+ zMapAssert(server && gff_pipe_err_inout);
gff_pipe_err = *gff_pipe_err_inout ;
+ if(gff_pipe_err)
+ {
+ msg = gff_pipe_err->message;
+ g_error_free(gff_pipe_err) ;
+ }
+ setErrMsg(server, g_strdup_printf("%s %s", server->script_path, msg)) ;
- setErrMsg(server, g_strdup_printf("%s %s", server->script_path, gff_pipe_err->message)) ;
- g_error_free(gff_pipe_err) ;
*gff_pipe_err_inout = NULL ;
diff --git a/src/zmapView/zmapView.c b/src/zmapView/zmapView.c
index 507d15d78..35accb874 100755
--- a/src/zmapView/zmapView.c
+++ b/src/zmapView/zmapView.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Apr 7 15:59 2010 (edgrif)
* Created: Thu May 13 15:28:26 2004 (edgrif)
- * CVS info: $Id: zmapView.c,v 1.194 2010-04-19 11:00:39 mh17 Exp $
+ * CVS info: $Id: zmapView.c,v 1.195 2010-04-22 14:31:53 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -50,7 +50,6 @@
#include <zmapView_P.h>
-
typedef struct
{
/* Processing options. */
@@ -65,18 +64,18 @@ typedef struct
char *database_title ;
char *database_path ;
-
-
+ char *err_msg; // from the server mainly
GList *feature_sets ;
GList *required_styles ;
gboolean server_styles_have_mode ;
+ gboolean status; // load sucessful?
- GHashTable *featureset_2_stylelist ; /* Mapping of each feature_set to all
- the styles it requires. */
+ GHashTable *featureset_2_stylelist ; /* Mapping of each feature_set to all
+ the styles it requires. */
- GData *curr_styles ; /* Styles for this context. */
+ GData *curr_styles ; /* Styles for this context. */
ZMapFeatureContext curr_context ;
ZMapServerReqType display_after ;
@@ -437,8 +436,6 @@ gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
free_this_list = settings_list ;
-// current_server = (ZMapConfigSource)settings_list->data ;
-
/* Current error handling policy is to connect to servers that we can and
@@ -470,7 +467,6 @@ gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
else if (!(current_server->featuresets))
{
/* featuresets are absolutely required, go on to next stanza if there aren't
-
* any. */
zMapWarning("Server \"%s\": no featuresets specified in configuration file so cannot connect.",
current_server->url) ;
@@ -487,7 +483,7 @@ gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
else if (!checkSequenceToServerMatch(zmap_view->sequence_2_server, &tmp_seq))
{
- /* If certain sequences must only be fetched from certain servers zmap_viewthen make sure
+ /* If certain sequences must only be fetched from certain servers then make sure
* we only make those connections. */
zMapLogMessage("server %s no sequence: ignored",current_server->url);
continue ;
@@ -1340,7 +1336,7 @@ static GHashTable *zmapViewGetFeatureSourceHash(GList *sources)
* retrieved the features are added via a gtk event. */
/* mh17:
* unlike zmapViewConnect() we request one feature set at a time from the relevant server
- * we scan the config file and create a hash table linking feature set
+ * we scan the config file and create a hash table linking feature set to source
*/
void zmapViewLoadFeatures(ZMapView view, ZMapFeatureBlock block_orig, GList *req_sources,
int features_start, int features_end)
@@ -1905,10 +1901,11 @@ static void stopStateConnectionChecking(ZMapView zmap_view)
* */
static gboolean checkStateConnections(ZMapView zmap_view)
{
- gboolean call_again = TRUE ; /* Normally we want to called continuously. */
+ gboolean call_again = TRUE ; /* Normally we want to be called continuously. */
gboolean state_change = TRUE ; /* Has view state changed ?. */
- gboolean reqs_finished = FALSE;
- int has_step_list = 0; // any requests still active?
+ gboolean reqs_finished = FALSE; // at least one thread just finished
+ int thread_status = 0; // current thread: -ve for fail 0 for pending +ve for ok
+ int has_step_list = 0; // any requests still active?
if (zmap_view->connection_list)
{
@@ -1924,9 +1921,12 @@ static gboolean checkStateConnections(ZMapView zmap_view)
void *data = NULL ;
char *err_msg = NULL ;
gboolean thread_has_died = FALSE ;
+ ConnectionData cd;
+ LoadFeaturesDataStruct lfd;
view_con = list_item->data ;
thread = view_con->thread ;
+ cd = (ConnectionData) view_con->request_data;
/* NOTE HOW THE FACT THAT WE KNOW NOTHING ABOUT WHERE THIS DATA CAME FROM
* MEANS THAT WE SHOULD BE PASSING A HEADER WITH THE DATA SO WE CAN SAY WHERE
@@ -1935,6 +1935,15 @@ static gboolean checkStateConnections(ZMapView zmap_view)
data = NULL ;
err_msg = NULL ;
+ thread_status = 0;
+
+ // need to copy this info in case of thread death which clears it up
+
+ if(cd)
+ {
+ lfd.feature_sets = cd->feature_sets;
+ lfd.xwid = zmap_view->xwid;
+ }
if (!(zMapThreadGetReplyWithData(thread, &reply, &data, &err_msg)))
{
@@ -2103,8 +2112,9 @@ static gboolean checkStateConnections(ZMapView zmap_view)
if(view_con->step_list)
reqs_finished = TRUE;
+ thread_status = -1;
- destroyConnection(zmap_view,view_con) ;
+ destroyConnection(zmap_view,view_con) ; //NB frees up what cd points to (view_com->request_data)
}
@@ -2123,11 +2133,26 @@ static gboolean checkStateConnections(ZMapView zmap_view)
{
zmapViewStepListDestroy(view_con) ;
reqs_finished = TRUE;
- //printf("step list %s finished\n",view_con->url);
- //zMapLogWarning("step list %s finished\n",view_con->url);
+ thread_status = 1;
+ //printf("step list %s finished\n",view_con->url);
+ //zMapLogWarning("step list %s finished\n",view_con->url);
}
}
+ if(thread_status) // tell otterlace
+ {
+ if(cd) // ie was valid at the start of the loop
+ {
+ if(thread_status < 0 && !err_msg)
+ err_msg = "Failed";
+
+ lfd.status = thread_status > 0 ? TRUE : FALSE;
+ lfd.err_msg = err_msg;
+
+ (*(view_cbs_G->load_data))(zmap_view, zmap_view->app_data,&lfd);
+ }
+ }
+
if (err_msg)
g_free(err_msg) ;
}
@@ -2474,8 +2499,9 @@ static gboolean processDataRequests(ZMapViewConnection view_con, ZMapServerReqAn
break ;
}
- case ZMAP_SERVERREQ_GETSEQUENCE:
- // never appears??
+// case ZMAP_SERVERREQ_GETSEQUENCE:
+ // never appears?? - see commandCB() and processGetSeqRequests() in this file
+
case ZMAP_SERVERREQ_TERMINATE:
{
break ;
@@ -2673,6 +2699,10 @@ static ZMapViewConnection createConnection(ZMapView zmap_view,
connect_data->featureset_2_stylelist = zMap_g_hashlist_create() ;
+ // we need to save this to tell otterlace when we've finished
+ // it also gets given to threads: when can we free it?
+ connect_data->feature_sets = req_featuresets;
+
view_con->request_data = connect_data ;
@@ -2960,6 +2990,8 @@ static gboolean justMergeContext(ZMapView view, ZMapFeatureContext *context_inou
new_features = *context_inout ;
+// printf("just Merge new = %s\n",zMapFeatureContextGetDNAStatus(new_features) ? "yes" : "non");
+
zMapPrintTimer(NULL, "Merge Context starting...") ;
if (view->revcomped_features)
@@ -2972,6 +3004,10 @@ static gboolean justMergeContext(ZMapView view, ZMapFeatureContext *context_inou
}
merge = zMapFeatureContextMerge(&(view->features), &new_features, &diff_context) ;
+
+// printf("just Merge view = %s\n",zMapFeatureContextGetDNAStatus(view->features) ? "yes" : "non");
+// printf("just Merge diff = %s\n",zMapFeatureContextGetDNAStatus(diff_context) ? "yes" : "non");
+
#ifdef MH17_NEVER
{
GError *err = NULL;
diff --git a/src/zmapWindow/zmapWindowFeature.c b/src/zmapWindow/zmapWindowFeature.c
index 2abcd02e9..911822386 100755
--- a/src/zmapWindow/zmapWindowFeature.c
+++ b/src/zmapWindow/zmapWindowFeature.c
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -30,7 +30,7 @@
* HISTORY:
* Last edited: Apr 15 09:29 2010 (edgrif)
* Created: Mon Jan 9 10:25:40 2006 (edgrif)
- * CVS info: $Id: zmapWindowFeature.c,v 1.179 2010-04-19 14:29:06 edgrif Exp $
+ * CVS info: $Id: zmapWindowFeature.c,v 1.180 2010-04-22 14:31:53 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -85,7 +85,7 @@ typedef struct
}PFetchDataStruct, *PFetchData;
-typedef struct
+typedef struct
{
ZMapWindow window;
FooCanvasGroup *column;
@@ -151,8 +151,8 @@ static void pfetchEntry(ZMapWindow window, char *sequence_name) ;
static void handle_dialog_close(GtkWidget *dialog, gpointer user_data);
-static ZMapFeatureContextExecuteStatus oneBlockHasDNA(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus oneBlockHasDNA(GQuark key,
+ gpointer data,
gpointer user_data,
char **error_out);
@@ -163,30 +163,30 @@ static gboolean factoryTopItemCreated(FooCanvasItem *top_item,
ZMapFeatureSet set,
ZMapFeature feature,
gpointer handler_data);
-static gboolean factoryFeatureSizeReq(ZMapFeature feature,
- double *limits_array,
- double *points_array_inout,
+static gboolean factoryFeatureSizeReq(ZMapFeature feature,
+ double *limits_array,
+ double *points_array_inout,
gpointer handler_data);
static gboolean sequenceSelectionCB(FooCanvasItem *item, int start, int end, gpointer user_data) ;
/* NOTE that we make some assumptions in this code including:
- *
+ *
* - the caller has found the correct context, alignment, block and set
* to put the feature in. Probably we will have to write some helper
* helper functions to do this if they have not already been written.
* There will need to map stuff like "block spec" -> ZMapFeatureBlock etc.
- *
- *
+ *
+ *
* */
-/*
+/*
* NOTE TO ROY: I've written the functions so that when you get the xml from James, you can
- * get the align/block/set information and then
+ * get the align/block/set information and then
* use the hash calls to get the foocanvasgroup that is the column you want to add/modify the feature
* in. The you can just call these routines with the group and the feature.
- *
+ *
* This way if there are errors in the xml and you can't find the right align/block/set then
* you can easily report back to lace what the error was....
* */
@@ -210,7 +210,7 @@ GData *zMapWindowFeatureAllStyles(ZMapWindow window)
/* Add a new feature to the feature_set given by the set canvas item.
- *
+ *
* Returns the new canvas feature item or NULL if there is some problem, e.g. the feature already
* exists in the feature_set.
* */
@@ -263,7 +263,7 @@ FooCanvasItem *zMapWindowFeatureSetAdd(ZMapWindow window,
feature_block = zmapWindowContainerGetFeatureBlock(ZMAP_CONTAINER_GROUP( block_group ));
zMapAssert(feature_block);
-
+
context = (ZMapFeatureContext)(zMapFeatureGetParentGroup((ZMapFeatureAny)feature_block, ZMAPFEATURE_STRUCT_CONTEXT));
zMapAssert(context);
@@ -297,16 +297,16 @@ FooCanvasItem *zMapWindowFeatureSetAdd(ZMapWindow window,
/* Create the columns */
zmapWindowCreateSetColumns(window,
- forward_features,
+ forward_features,
reverse_features,
- feature_block,
+ feature_block,
feature_set,
window->read_only_styles,
- ZMAPFRAME_NONE,
- &new_forward_set,
- &new_reverse_set,
+ ZMAPFRAME_NONE,
+ &new_forward_set,
+ &new_reverse_set,
NULL);
-
+
zmapWindowColOrderColumns(window);
}
@@ -319,12 +319,12 @@ FooCanvasItem *zMapWindowFeatureSetAdd(ZMapWindow window,
/* THERE IS A PROBLEM HERE IN THAT WE REMOVE THE EXISTING FOOCANVAS ITEM FOR THE FEATURE
* AND DRAW A NEW ONE, THIS WILL INVALIDATE ANY CODE THAT IS CACHING THE ITEM.
- *
+ *
* THE FIX IS FOR ALL OUR CODE TO USE THE HASH TO GET TO FEATURE ITEMS AND NOT CACHE THEM....*/
/* Replace an existing feature in the feature context, this is the only way to modify
* a feature currently.
- *
+ *
* Returns FALSE if the feature does not exist. */
FooCanvasItem *zMapWindowFeatureReplace(ZMapWindow zmap_window,
FooCanvasItem *curr_feature_item,
@@ -363,7 +363,7 @@ FooCanvasItem *zMapWindowFeatureReplace(ZMapWindow zmap_window,
/* Remove an existing feature from the displayed feature context.
- *
+ *
* Returns FALSE if the feature does not exist. */
gboolean zMapWindowFeatureRemove(ZMapWindow zmap_window, FooCanvasItem *feature_item, gboolean destroy_feature)
{
@@ -382,13 +382,13 @@ gboolean zMapWindowFeatureRemove(ZMapWindow zmap_window, FooCanvasItem *feature_
/* Need to delete the feature from the feature set and from the hash and destroy the
* canvas item....NOTE this is very order dependent. */
- /* I'm still not sure this is all correct.
- * canvasItemDestroyCB has a FToIRemove!
+ /* I'm still not sure this is all correct.
+ * canvasItemDestroyCB has a FToIRemove!
*/
/* Firstly remove from the FToI hash... */
if (zmapWindowFToIRemoveFeature(zmap_window->context_to_item,
- container_set->strand,
+ container_set->strand,
container_set->frame, feature))
{
/* check the feature is in featureset. */
@@ -398,7 +398,7 @@ gboolean zMapWindowFeatureRemove(ZMapWindow zmap_window, FooCanvasItem *feature_
/* remove the item from the focus items list. */
zmapWindowFocusRemoveFocusItem(zmap_window->focus, feature_item);
- if(zmapWindowMarkIsSet(zmap_window->mark) &&
+ if(zmapWindowMarkIsSet(zmap_window->mark) &&
feature_item == zmapWindowMarkGetItem(zmap_window->mark) &&
zmapWindowMarkGetWorldRange(zmap_window->mark, &x1, &y1, &x2, &y2))
{
@@ -440,23 +440,23 @@ ZMapFrame zmapWindowFeatureFrame(ZMapFeature feature)
}
/* Encapulates the rules about which strand a feature will be drawn on.
- *
+ *
* For ZMap this amounts to:
* strand specific not strand specific
* features strand
- *
+ *
* ZMAPSTRAND_NONE + +
* ZMAPSTRAND_FORWARD + +
* ZMAPSTRAND_REVERSE - +
- *
+ *
* Some features (e.g. repeats) are derived from alignments that match to the
* forward or reverse strand and hence the feature can be said to have strand
* in the alignment sense but for the actual feature (the repeat) the strand
* is irrelevant.
- *
+ *
* Points to a data problem really, if features are not strand specific then
* their strand should be ZMAPSTRAND_NONE !
- *
+ *
* */
ZMapStrand zmapWindowFeatureStrand(ZMapWindow window, ZMapFeature feature)
{
@@ -468,7 +468,7 @@ ZMapStrand zmapWindowFeatureStrand(ZMapWindow window, ZMapFeature feature)
g_return_val_if_fail(style != NULL, strand);
if ((!(zMapStyleIsStrandSpecific(style))) ||
- ((feature->strand == ZMAPSTRAND_FORWARD) ||
+ ((feature->strand == ZMAPSTRAND_FORWARD) ||
(feature->strand == ZMAPSTRAND_NONE)))
strand = ZMAPSTRAND_FORWARD ;
else
@@ -495,7 +495,7 @@ void zmapWindowFeatureFactoryInit(ZMapWindow window)
/* Called to draw each individual feature. */
-FooCanvasItem *zmapWindowFeatureDraw(ZMapWindow window,
+FooCanvasItem *zmapWindowFeatureDraw(ZMapWindow window,
ZMapFeatureTypeStyle style,
FooCanvasGroup *set_group,
ZMapFeature feature)
@@ -519,22 +519,22 @@ FooCanvasItem *zmapWindowFeatureDraw(ZMapWindow window,
/* These should be parameters, rather than continually fetch them, caller will almost certainly know these! */
- set = (ZMapFeatureSet)zMapFeatureGetParentGroup((ZMapFeatureAny)feature,
+ set = (ZMapFeatureSet)zMapFeatureGetParentGroup((ZMapFeatureAny)feature,
ZMAPFEATURE_STRUCT_FEATURESET) ;
- block = (ZMapFeatureBlock)zMapFeatureGetParentGroup((ZMapFeatureAny)set,
+ block = (ZMapFeatureBlock)zMapFeatureGetParentGroup((ZMapFeatureAny)set,
ZMAPFEATURE_STRUCT_BLOCK) ;
- alignment = (ZMapFeatureAlignment)zMapFeatureGetParentGroup((ZMapFeatureAny)block,
+ alignment = (ZMapFeatureAlignment)zMapFeatureGetParentGroup((ZMapFeatureAny)block,
ZMAPFEATURE_STRUCT_ALIGN) ;
- context = (ZMapFeatureContext)zMapFeatureGetParentGroup((ZMapFeatureAny)alignment,
+ context = (ZMapFeatureContext)zMapFeatureGetParentGroup((ZMapFeatureAny)alignment,
ZMAPFEATURE_STRUCT_CONTEXT) ;
-
+
new_feature = zmapWindowFToIFactoryRunSingle(window->item_factory,
NULL,
- set_group,
- context,
- alignment,
- block,
- set,
+ set_group,
+ context,
+ alignment,
+ block,
+ set,
feature);
return new_feature;
}
@@ -626,12 +626,7 @@ gboolean zMapWindowGetDNAStatus(ZMapWindow window)
if(window->feature_context &&
zMapFindStyle(window->read_only_styles, zMapStyleCreateID(ZMAP_FIXED_STYLE_DNA_NAME)))
{
- zMapFeatureContextExecute((ZMapFeatureAny)(window->feature_context),
- ZMAPFEATURE_STRUCT_BLOCK,
- oneBlockHasDNA,
- &dna);
-
- drawable = dna.exists;
+ drawable = zMapFeatureContextGetDNAStatus(window->feature_context);
}
return drawable;
@@ -678,13 +673,13 @@ char *zmapWindowFeatureTranscriptFASTA(ZMapFeature feature, gboolean spliced, gb
if((feature->type == ZMAPSTYLE_MODE_TRANSCRIPT)
- && ((context = (ZMapFeatureContext)zMapFeatureGetParentGroup((ZMapFeatureAny)feature,
+ && ((context = (ZMapFeatureContext)zMapFeatureGetParentGroup((ZMapFeatureAny)feature,
ZMAPFEATURE_STRUCT_CONTEXT))))
{
ZMapPeptide peptide;
char *dna, *seq_name = NULL, *gene_name = NULL;
int pep_length, start_incr = 0;
-
+
seq_name = (char *)g_quark_to_string(context->original_id);
gene_name = (char *)g_quark_to_string(feature->original_id);
@@ -693,15 +688,15 @@ char *zmapWindowFeatureTranscriptFASTA(ZMapFeature feature, gboolean spliced, gb
/* 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) ;
-
+
/* 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,
+
+ peptide_fasta = zMapFASTAString(ZMAPFASTA_SEQTYPE_AA,
seq_name, "Protein",
gene_name, pep_length,
zMapPeptideSequence(peptide));
@@ -716,7 +711,7 @@ char *zmapWindowFeatureTranscriptFASTA(ZMapFeature feature, gboolean spliced, gb
-/*
+/*
* Internal functions.
*/
@@ -728,7 +723,7 @@ static gboolean canvasItemDestroyCB(FooCanvasItem *feature_item, gpointer data)
/* Check to see if there is an entry in long items for this feature.... */
zmapWindowLongItemRemove(window->long_items, feature_item) ; /* Ignore boolean result. */
-
+
zmapWindowFocusRemoveFocusItem(window->focus, feature_item);
return event_handled ;
@@ -737,8 +732,8 @@ static gboolean canvasItemDestroyCB(FooCanvasItem *feature_item, gpointer data)
-static void featureCopySelectedItem(ZMapFeature feature_in,
- ZMapFeature feature_out,
+static void featureCopySelectedItem(ZMapFeature feature_in,
+ ZMapFeature feature_out,
FooCanvasItem *selected)
{
ZMapFeatureSubPartSpan item_feature_data;
@@ -759,13 +754,13 @@ static void featureCopySelectedItem(ZMapFeature feature_in,
/* copy the selected intron/exon */
span.x1 = item_feature_data->start;
span.x2 = item_feature_data->end;
- if(item_feature_data->subpart == ZMAPFEATURE_SUBPART_EXON ||
+ if(item_feature_data->subpart == ZMAPFEATURE_SUBPART_EXON ||
item_feature_data->subpart == ZMAPFEATURE_SUBPART_EXON_CDS)
zMapFeatureAddTranscriptExonIntron(feature_out, &span, NULL);
else
zMapFeatureAddTranscriptExonIntron(feature_out, NULL, &span);
}
- else if (feature_out->type == ZMAPSTYLE_MODE_ALIGNMENT &&
+ else if (feature_out->type == ZMAPSTYLE_MODE_ALIGNMENT &&
item_feature_data->subpart == ZMAPFEATURE_SUBPART_MATCH)
{
feature_out->feature.homol.align = NULL;
@@ -827,8 +822,8 @@ static gboolean canvasItemEventCB(FooCanvasItem *item, GdkEvent *event, gpointer
* press generated by clicks but catch the button2 press (see below). */
if (but_event->time - last_but_press > 250)
{
- GdkModifierType shift_mask = GDK_SHIFT_MASK,
- control_mask = GDK_CONTROL_MASK,
+ GdkModifierType shift_mask = GDK_SHIFT_MASK,
+ control_mask = GDK_CONTROL_MASK,
shift_control_mask = GDK_SHIFT_MASK | GDK_CONTROL_MASK,
unwanted_masks = GDK_LOCK_MASK | GDK_MOD2_MASK | GDK_MOD3_MASK | GDK_MOD4_MASK | GDK_MOD5_MASK,
locks_mask;
@@ -939,7 +934,7 @@ static gboolean canvasItemEventCB(FooCanvasItem *item, GdkEvent *event, gpointer
/* Pass information about the object clicked on back to the application. */
zMapWindowUpdateInfoPanel(window, feature, sub_item, highlight_item, NULL,
replace_highlight, highlight_same_names) ;
-
+
if (but_event->button == 3)
{
/* Pop up an item menu. */
@@ -1008,8 +1003,8 @@ void zmapMakeItemMenu(GdkEventButton *button_event, ZMapWindow window, FooCanvas
zMapAssert(feature);
column_group = zmapWindowContainerCanvasItemGetContainer(item) ;
-
- style = zmapWindowContainerFeatureSetStyleFromID((ZMapWindowContainerFeatureSet)column_group,
+
+ style = zmapWindowContainerFeatureSetStyleFromID((ZMapWindowContainerFeatureSet)column_group,
feature->style_id);
@@ -1037,7 +1032,7 @@ void zmapMakeItemMenu(GdkEventButton *button_event, ZMapWindow window, FooCanvas
if (feature->type == ZMAPSTYLE_MODE_TRANSCRIPT && feature->strand == ZMAPSTRAND_FORWARD)
menu_sets = g_list_append(menu_sets, makeMenuShowTranslation(NULL, NULL, menu_data));
-
+
if (feature->url)
menu_sets = g_list_append(menu_sets, makeMenuURL(NULL, NULL, menu_data)) ;
@@ -1125,7 +1120,7 @@ static void itemMenuCB(int menu_item_id, gpointer callback_data)
ZMapStrand set_strand ;
ZMapFrame set_frame ;
gboolean result ;
-
+
result = zmapWindowItemGetStrandFrame(menu_data->item, &set_strand, &set_frame) ;
zMapAssert(result) ;
@@ -1137,9 +1132,9 @@ static void itemMenuCB(int menu_item_id, gpointer callback_data)
zMapFeatureStrand2Str(set_strand),
zMapFeatureFrame2Str(set_frame));
- zmapWindowListWindow(menu_data->window,
+ zmapWindowListWindow(menu_data->window,
menu_data->item,
- (char *)g_quark_to_string(feature->parent->original_id),
+ (char *)g_quark_to_string(feature->parent->original_id),
NULL, NULL,
(ZMapWindowListSearchHashFunc)zmapWindowFToISetSearchPerform, search_data,
(GDestroyNotify)zmapWindowFToISetSearchDestroy, zoom_to_item) ;
@@ -1158,9 +1153,9 @@ static void itemMenuCB(int menu_item_id, gpointer callback_data)
search_data = zmapWindowFToISetSearchCreate(zmapWindowFToIFindSameNameItems, feature,
0, 0, 0, 0, zMapFeatureStrand2Str(set_strand),
zMapFeatureFrame2Str(set_frame));
- zmapWindowListWindow(menu_data->window,
+ zmapWindowListWindow(menu_data->window,
menu_data->item,
- (char *)g_quark_to_string(feature->parent->original_id),
+ (char *)g_quark_to_string(feature->parent->original_id),
NULL, NULL,
(ZMapWindowListSearchHashFunc)zmapWindowFToISetSearchPerform, search_data,
(GDestroyNotify)zmapWindowFToISetSearchDestroy, zoom_to_item) ;
@@ -1177,7 +1172,7 @@ static void itemMenuCB(int menu_item_id, gpointer callback_data)
break ;
case ITEM_MENU_SEARCH:
- zmapWindowCreateSearchWindow(menu_data->window,
+ zmapWindowCreateSearchWindow(menu_data->window,
NULL, NULL,
menu_data->item) ;
@@ -1211,7 +1206,7 @@ static void itemMenuCB(int menu_item_id, gpointer callback_data)
}
case ITEM_MENU_SHOW_TRANSLATION:
{
- zmapWindowItemShowTranslation(menu_data->window,
+ zmapWindowItemShowTranslation(menu_data->window,
menu_data->item);
}
break;
@@ -1332,7 +1327,7 @@ static ZMapGUIMenuItem makeMenuURL(int *start_index_inout,
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-static void textSelectCB(int menu_item_id, gpointer callback_data)
+static void textSelectCB(int menu_item_id, gpointer callback_data)
{
#ifdef RDS_BREAKING_STUFF
ItemMenuCBData menu_data = (ItemMenuCBData)callback_data ;
@@ -1419,7 +1414,7 @@ static void pfetchEntry(ZMapWindow window, char *sequence_name)
PFetchHandle pfetch = NULL;
PFetchUserPrefsStruct prefs = {NULL};
gboolean debug_pfetch = FALSE;
-
+
if((zmapWindowGetPFetchUserPrefs(&prefs)) &&
(prefs.location != NULL))
{
@@ -1427,20 +1422,20 @@ static void pfetchEntry(ZMapWindow window, char *sequence_name)
if(prefs.mode && strncmp(prefs.mode, "pipe", 4) == 0)
pfetch_type = PFETCH_TYPE_PIPE_HANDLE;
-
+
pfetch_data->pfetch = pfetch = PFetchHandleNew(pfetch_type);
-
+
if((pfetch_data->title = g_strdup_printf(PFETCH_TITLE_FORMAT, sequence_name)))
{
pfetch_data->dialog = zMapGUIShowTextFull(pfetch_data->title, "pfetching...\n",
FALSE, &(pfetch_data->text_buffer));
-
- pfetch_data->widget_destroy_handler_id =
- g_signal_connect(G_OBJECT(pfetch_data->dialog), "destroy",
- G_CALLBACK(handle_dialog_close), pfetch_data);
+
+ pfetch_data->widget_destroy_handler_id =
+ g_signal_connect(G_OBJECT(pfetch_data->dialog), "destroy",
+ G_CALLBACK(handle_dialog_close), pfetch_data);
}
- PFetchHandleSettings(pfetch,
+ PFetchHandleSettings(pfetch,
"debug", debug_pfetch,
"full", prefs.full_record,
"pfetch", prefs.location,
@@ -1448,20 +1443,20 @@ static void pfetchEntry(ZMapWindow window, char *sequence_name)
NULL);
if(PFETCH_IS_HTTP_HANDLE(pfetch))
- PFetchHandleSettings(pfetch,
+ PFetchHandleSettings(pfetch,
"port", prefs.port,
"cookie-jar", prefs.cookie_jar,
NULL);
-
+
g_free(prefs.location);
g_free(prefs.cookie_jar);
-
+
g_signal_connect(G_OBJECT(pfetch), "reader", G_CALLBACK(pfetch_reader_func), pfetch_data);
g_signal_connect(G_OBJECT(pfetch), "error", G_CALLBACK(pfetch_reader_func), pfetch_data);
-
+
g_signal_connect(G_OBJECT(pfetch), "closed", G_CALLBACK(pfetch_closed_func), pfetch_data);
-
+
if(PFetchHandleFetch(pfetch, sequence_name) == PFETCH_STATUS_FAILED)
zMapWarning("Error fetching sequence '%s'", sequence_name);
}
@@ -1490,9 +1485,9 @@ static void handle_dialog_close(GtkWidget *dialog, gpointer user_data)
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
/* We may wish to make this public some time but as the rest of the long item calls for features
* are in this file then there is no need for it to be exposed.
- *
+ *
* Deals with removing all the items contained in a compound object from the longitem list.
- *
+ *
* */
static void removeFeatureLongItems(ZMapWindowLongItems long_items, FooCanvasItem *feature_item)
{
@@ -1539,8 +1534,8 @@ static void removeLongItemCB(gpointer data, gpointer user_data)
/* Function to check whether any of the blocks has dna */
-static ZMapFeatureContextExecuteStatus oneBlockHasDNA(GQuark key,
- gpointer data,
+static ZMapFeatureContextExecuteStatus oneBlockHasDNA(GQuark key,
+ gpointer data,
gpointer user_data,
char **error_out)
{
@@ -1549,7 +1544,7 @@ static ZMapFeatureContextExecuteStatus oneBlockHasDNA(GQuark key,
ZMapFeatureStructType feature_type = ZMAPFEATURE_STRUCT_INVALID;
BlockHasDNA dna = (BlockHasDNA)user_data;
-
+
feature_type = feature_any->struct_type;
switch(feature_type)
@@ -1611,24 +1606,24 @@ static double getWidthFromScore(ZMapFeatureTypeStyle style, double score)
if (score <= style->min_score)
tmp = 0 ;
- else if (score >= style->max_score)
+ else if (score >= style->max_score)
tmp = style->width ;
- else
+ else
tmp = fac * (score - style->min_score) ;
width = tmp ;
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- if (seg->data.f <= bc->meth->minScore)
+ if (seg->data.f <= bc->meth->minScore)
x = 0 ;
- else if (seg->data.f >= bc->meth->maxScore)
+ else if (seg->data.f >= bc->meth->maxScore)
x = bc->width ;
- else
+ else
x = fac * (seg->data.f - bc->meth->minScore) ;
box = graphBoxStart() ;
- if (x > origin + 0.5 || x < origin - 0.5)
+ if (x > origin + 0.5 || x < origin - 0.5)
graphLine (bc->offset+origin, y, bc->offset+x, y) ;
else if (x > origin)
graphLine (bc->offset+origin-0.5, y, bc->offset+x, y) ;
@@ -1696,7 +1691,7 @@ static void showSplices (FeatureMap look, SegType type, BoxCol *bc, float origin
float fac;
fac = bc->width / (bc->meth->maxScore - bc->meth->minScore);
-
+
for (i = 0 ; i < arrayMax(look->segs) ; ++i)
{ seg = arrp(look->segs, i, SEG) ;
if (seg->x1 > look->max
@@ -1705,14 +1700,14 @@ static void showSplices (FeatureMap look, SegType type, BoxCol *bc, float origin
|| seg->type != type)
continue ;
y = MAP2GRAPH(look->map, seg->x2) ;
- if (seg->data.f <= bc->meth->minScore)
+ if (seg->data.f <= bc->meth->minScore)
x = 0 ;
- else if (seg->data.f >= bc->meth->maxScore)
+ else if (seg->data.f >= bc->meth->maxScore)
x = bc->width ;
- else
+ else
x = fac * (seg->data.f - bc->meth->minScore) ;
box = graphBoxStart() ;
- if (x > origin + 0.5 || x < origin - 0.5)
+ if (x > origin + 0.5 || x < origin - 0.5)
graphLine (bc->offset+origin, y, bc->offset+x, y) ;
else if (x > origin)
graphLine (bc->offset+origin-0.5, y, bc->offset+x, y) ;
@@ -1783,21 +1778,21 @@ static gboolean sequenceSelectionCB(FooCanvasItem *item, int start, int end, gpo
{
ZMapFrame frame;
int window_origin;
-
+
frame = zMapFeatureFrame(feature) ;
-
+
start = origin_index ;
end = current_index ;
-
+
/* Do some monkeying to get the dna coords */
origin_index-- ;
origin_index *= 3 ;
origin_index += frame ;
current_index = origin_index + ((end - start + 1) * 3) - 1;
-
+
dna_start = origin_index ;
dna_end = current_index ;
-
+
/* zmapWindowCoordToDisplay() doesn't work for protein coord space,
* whether this is useful though.... */
if (window->origin == window->min_coord)
@@ -1810,32 +1805,32 @@ static gboolean sequenceSelectionCB(FooCanvasItem *item, int start, int end, gpo
/* CHECK THIS OUT! TEST THE + 4 is required */
window_origin = (window->origin + 4 ) / 3;
}
-
+
start = start - (window_origin - 1);
end = end - (window_origin - 1);
-
+
coords_text = "Protein Coords: ";
-
+
select.feature_desc.sub_feature_start = g_strdup_printf("%s%d", coords_text, start);
select.feature_desc.sub_feature_end = g_strdup_printf("%d", end);
select.feature_desc.sub_feature_length = g_strdup_printf("%d", end - start + 1);
-
+
coords_text = "DNA Coords: "; /* reset */
}
-
+
display_start = zmapWindowCoordToDisplay(window, origin_index);
display_end = zmapWindowCoordToDisplay(window, current_index);
-
+
select.feature_desc.feature_start = g_strdup_printf("%s%d", coords_text, display_start);
select.feature_desc.feature_end = g_strdup_printf("%d", display_end);
select.feature_desc.feature_length = g_strdup_printf("%d", current_index - origin_index + 1);
select.feature_desc.feature_name = (char *)g_quark_to_string(feature->original_id);
-
-
+
+
/* update the info panel */
(*(window->caller_cbs->select))(window, window->app_data, (void *)&select) ;
-
+
/* Update the highlighting, note that for peptides we highlight the
* corresponding dna sequence as well as the peptide. */
@@ -1844,32 +1839,32 @@ static gboolean sequenceSelectionCB(FooCanvasItem *item, int start, int end, gpo
g_free(select.feature_desc.sub_feature_start);
g_free(select.feature_desc.sub_feature_end);
g_free(select.feature_desc.sub_feature_length);
-
+
zmapWindowItemHighlightDNARegion(window, item, origin_index, current_index);
}
else
{
zmapWindowItemHighlightRegionTranslations(window, item, origin_index, current_index);
}
-
+
g_free(select.feature_desc.feature_start);
g_free(select.feature_desc.feature_end);
g_free(select.feature_desc.feature_length);
-
-
+
+
/* We wait until here to do this so we are only setting the
* clipboard text once. i.e. for this window. And so that we have
* updated the focus object correctly. */
if (feature->type == ZMAPSTYLE_MODE_RAW_SEQUENCE)
{
char *dna_string, *seq_name;
-
+
dna_string = zMapFeatureGetDNA((ZMapFeatureAny)feature, start, end, FALSE);
-
+
seq_name = g_strdup_printf("%d-%d", display_start, display_end);
-
- select.secondary_text = zMapFASTAString(ZMAPFASTA_SEQTYPE_DNA,
- seq_name, "DNA", NULL,
+
+ select.secondary_text = zMapFASTAString(ZMAPFASTA_SEQTYPE_DNA,
+ seq_name, "DNA", NULL,
end - start + 1,
dna_string);
g_free(seq_name);
@@ -1886,8 +1881,8 @@ static gboolean sequenceSelectionCB(FooCanvasItem *item, int start, int end, gpo
dna_string = zMapFeatureGetDNA((ZMapFeatureAny)feature, dna_start, dna_end, FALSE) ;
seq_name = g_strdup_printf("%d-%d (%d-%d)", start, end, dna_start, dna_end) ;
translation = zMapPeptideCreate(seq_name, NULL, dna_string, NULL, TRUE) ;
- select.secondary_text = zMapFASTAString(ZMAPFASTA_SEQTYPE_AA,
- seq_name, "Protein", NULL,
+ select.secondary_text = zMapFASTAString(ZMAPFASTA_SEQTYPE_AA,
+ seq_name, "Protein", NULL,
zMapPeptideLength(translation),
zMapPeptideSequence(translation)) ;
g_free(seq_name);
@@ -1927,18 +1922,18 @@ static gboolean factoryTopItemCreated(FooCanvasItem *top_item,
break;
}
- /* ummmmm....I don't like this....suggests that all is not fully implemented in the new
+ /* ummmmm....I don't like this....suggests that all is not fully implemented in the new
* feature item stuff..... */
if (ZMAP_IS_WINDOW_SEQUENCE_FEATURE(top_item))
- g_signal_connect(G_OBJECT(top_item), "sequence-selected",
+ g_signal_connect(G_OBJECT(top_item), "sequence-selected",
G_CALLBACK(sequenceSelectionCB), handler_data) ;
return TRUE ;
}
-static gboolean factoryFeatureSizeReq(ZMapFeature feature,
- double *limits_array,
- double *points_array_inout,
+static gboolean factoryFeatureSizeReq(ZMapFeature feature,
+ double *limits_array,
+ double *points_array_inout,
gpointer handler_data)
{
gboolean outside = FALSE;
@@ -1959,11 +1954,11 @@ static gboolean factoryFeatureSizeReq(ZMapFeature feature,
{
ZMapWindow window = (ZMapWindow)handler_data;
double x1, x2;
-
+
points_array_inout[1] = points_array_inout[3] = x1 = x2 = 0.0;
/* Get scrolled region (clamped to sequence coords) */
zmapWindowGetScrollRegion(window,
- &x1, &(points_array_inout[1]),
+ &x1, &(points_array_inout[1]),
&x2, &(points_array_inout[3]));
}
else
@@ -1978,12 +1973,12 @@ static gboolean factoryFeatureSizeReq(ZMapFeature feature,
start_end_crossing |= ((x2_in > block_end) << 2);
start_end_crossing |= ((x1_in > block_end) << 3);
start_end_crossing |= ((x2_in < block_start) << 4);
-
+
/* Now check whether we cross! */
- if(start_end_crossing & 8 ||
+ if(start_end_crossing & 8 ||
start_end_crossing & 16) /* everything is out of range don't display! */
- outside = TRUE;
-
+ outside = TRUE;
+
if(start_end_crossing & 2)
points_array_inout[1] = block_start;
if(start_end_crossing & 4)
@@ -2011,7 +2006,7 @@ FooCanvasItem *addNewCanvasItem(ZMapWindow window, FooCanvasGroup *feature_group
container_features = FOO_CANVAS_GROUP(zmapWindowContainerGetFeatures((ZMapWindowContainerGroup)feature_group));
column_is_empty = !(container_features->item_list);
-
+
/* This function will add the new feature to the hash. */
new_feature = zmapWindowFeatureDraw(window, style, FOO_CANVAS_GROUP(feature_group), feature) ;
--
GitLab