From bf55f01688a77f9a1943d8302c1a930443448a69 Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Wed, 14 Oct 2009 16:53:58 +0000
Subject: [PATCH] fix up bugs in reporting feature coords, cut buffer may still
not be correct.
---
src/zmapWindow/zmapWindow.c | 304 +++++++++++++++++++-----------------
1 file changed, 162 insertions(+), 142 deletions(-)
diff --git a/src/zmapWindow/zmapWindow.c b/src/zmapWindow/zmapWindow.c
index e832826d1..e6db532c6 100755
--- a/src/zmapWindow/zmapWindow.c
+++ b/src/zmapWindow/zmapWindow.c
@@ -26,9 +26,9 @@
*
* Exported functions: See ZMap/zmapWindow.h
* HISTORY:
- * Last edited: Sep 25 10:11 2009 (edgrif)
+ * Last edited: Oct 14 17:53 2009 (edgrif)
* Created: Thu Jul 24 14:36:27 2003 (edgrif)
- * CVS info: $Id: zmapWindow.c,v 1.293 2009-09-25 13:27:15 edgrif Exp $
+ * CVS info: $Id: zmapWindow.c,v 1.294 2009-10-14 16:53:58 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -1246,7 +1246,7 @@ void zMapWindowUpdateInfoPanel(ZMapWindow window,
ZMapFeatureSubPartSpan sub_feature;
ZMapStrand query_strand = ZMAPSTRAND_NONE;
char *feature_term, *sub_feature_term;
- int feature_start, feature_end, feature_length, query_start, query_end ;
+ int feature_total_length, feature_start, feature_end, feature_length, query_start, query_end ;
int sub_feature_start, sub_feature_end, sub_feature_length;
int query_length ;
@@ -1289,22 +1289,36 @@ void zMapWindowUpdateInfoPanel(ZMapWindow window,
&(select.feature_desc.feature_source_description)) ;
/* zero all of this. */
- feature_start = feature_end = feature_length = query_start = query_end =
- sub_feature_start = sub_feature_end = sub_feature_length = query_length = 0;
+ feature_total_length = feature_start = feature_end = feature_length
+ = query_start = query_end
+ = sub_feature_start = sub_feature_end = sub_feature_length = query_length = 0 ;
feature_term = sub_feature_term = NULL;
+
if (zMapFeatureGetInfo((ZMapFeatureAny)feature, NULL,
- "start", &feature_start,
- "end", &feature_end,
+ "total-length", &feature_total_length,
+ "start", &feature_start,
+ "end", &feature_end,
"length", &feature_length,
- "term", &feature_term,
+ "term", &feature_term,
NULL))
{
+ if (feature_total_length)
+ select.feature_desc.feature_total_length = g_strdup_printf("%d", feature_total_length) ;
+
+ if (window->display_forward_coords)
+ {
+ feature_start = zmapWindowCoordToDisplay(window, feature_start) ;
+ feature_end = zmapWindowCoordToDisplay(window, feature_end) ;
+ }
+
select.feature_desc.feature_start = g_strdup_printf("%d", feature_start) ;
select.feature_desc.feature_end = g_strdup_printf("%d", feature_end) ;
- select.feature_desc.feature_length = g_strdup_printf("%d", feature_length) ;
- select.feature_desc.feature_strand = zMapFeatureStrand2Str(feature->strand) ;
+
+ if (feature_length)
+ select.feature_desc.feature_length = g_strdup_printf("%d", feature_length) ;
+
select.feature_desc.feature_term = feature_term;
}
@@ -1348,6 +1362,14 @@ void zMapWindowUpdateInfoPanel(ZMapWindow window,
"term", &sub_feature_term,
NULL))
{
+
+ if (window->display_forward_coords)
+ {
+ sub_feature_start = zmapWindowCoordToDisplay(window, sub_feature_start) ;
+ sub_feature_end = zmapWindowCoordToDisplay(window, sub_feature_end) ;
+ }
+
+
select.feature_desc.sub_feature_start = g_strdup_printf("%d", sub_feature_start) ;
select.feature_desc.sub_feature_end = g_strdup_printf("%d", sub_feature_end) ;
select.feature_desc.sub_feature_length = g_strdup_printf("%d", sub_feature_length) ;
@@ -1390,7 +1412,7 @@ void zMapWindowUpdateInfoPanel(ZMapWindow window,
select.feature_desc.feature_known_name = (char *)g_quark_to_string(feature->feature.transcript.known_name) ;
- select.feature_desc.feature_strand = zMapFeatureStrand2Str(feature->strand) ;
+ select.feature_desc.feature_strand = zMapFeatureStrand2Str(zmapWindowStrandToDisplay(window, feature->strand)) ;
if (zMapStyleIsFrameSpecific(style))
select.feature_desc.feature_frame = zMapFeatureFrame2Str(zmapWindowFeatureFrame(feature)) ;
@@ -1422,6 +1444,7 @@ void zMapWindowUpdateInfoPanel(ZMapWindow window,
zMapGUISetClipboard(window->toplevel, select.secondary_text);
+
/* Clear up.... */
g_free(select.feature_desc.sub_feature_start) ;
g_free(select.feature_desc.sub_feature_end) ;
@@ -1436,6 +1459,7 @@ void zMapWindowUpdateInfoPanel(ZMapWindow window,
g_free(select.feature_desc.feature_length) ;
g_free(select.feature_desc.feature_description) ;
+ /* UMMMM...WHY IS THIS NOT FREED....????? */
//g_free(select.secondary_text) ;
return ;
@@ -4609,6 +4633,58 @@ static void unhideItemsCB(gpointer data, gpointer user_data)
}
+/* I'm not too sure that this is all correct any more....should we putting exons in
+ * cut buffer or the whole transcript or what...??? */
+
+static char *makePrimarySelectionText(ZMapWindow window, FooCanvasItem *highlight_item)
+{
+ char *selection = NULL ;
+ GList *selected ;
+ GString *text ;
+ gint length, i = 0;
+ int selected_start, selected_end, selected_length;
+
+ selected = zmapWindowFocusGetFocusItems(window->focus) ;
+ length = g_list_length(selected) ;
+ text = g_string_sized_new(512) ;
+
+ while (selected)
+ {
+ FooCanvasItem *item;
+ ZMapFeature item_feature ;
+ ZMapFeatureSubPartSpan sub_feature ;
+ int dummy ;
+ ZMapFeatureSubpartType item_type_int ;
+
+ item = FOO_CANVAS_ITEM(selected->data) ;
+ item_feature = zmapWindowItemGetFeature(item) ;
+
+ if (!(possiblyPopulateWithChildData(window, item, highlight_item,
+ &dummy, &dummy, &dummy, &item_type_int,
+ &dummy, &dummy, &selected_start,
+ &selected_end, &selected_length)))
+ possiblyPopulateWithFullData(window, item_feature, item, highlight_item,
+ &dummy, &dummy, &dummy, &selected_start,
+ &selected_end, &selected_length) ;
+
+ g_string_append_printf(text, "\"%s\" %d %d (%d)%s",
+ (char *)g_quark_to_string(item_feature->original_id),
+ selected_start, selected_end, selected_length,
+ (i < (length - 1) ? "\n" : ""));
+
+ selected = selected->next;
+ i++;
+ }
+
+ selected = g_list_first(selected);
+ g_list_free(selected);
+
+ selection = text->str;
+ g_string_free(text, FALSE);
+
+ return selection;
+}
+
static gboolean possiblyPopulateWithChildData(ZMapWindow window,
FooCanvasItem *feature_item,
@@ -4620,6 +4696,12 @@ static gboolean possiblyPopulateWithChildData(ZMapWindow window,
int *selected_length)
{
ZMapFeatureSubPartSpan item_data;
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+ ZMapWindowItemFeatureType type ;
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+ ZMapFeatureSubPartSpan sub_feature;
+
int fstart, fend, flength;
int sstart, send, slength;
gboolean populated = FALSE;
@@ -4630,51 +4712,65 @@ static gboolean possiblyPopulateWithChildData(ZMapWindow window,
selected_start && selected_end &&
selected_length && sub_feature_length && sub_type);
+ /* AGGGGHHHHH, WE NEED TO KNOW THE TYPE OF THE THING WE ARE LOOKING AT... */
- if (window->display_forward_coords)
- {
- fstart = zmapWindowCoordToDisplay(window, item_data->start) ;
- fend = zmapWindowCoordToDisplay(window, item_data->end) ;
- }
- else
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+ type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(feature_item), ITEM_FEATURE_TYPE)) ;
+
+ if (type == ITEM_FEATURE_CHILD)
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
+ if ((sub_feature = zMapWindowCanvasItemIntervalGetData(feature_item)))
{
- fstart = item_data->start ;
- fend = item_data->end ;
- }
+ item_data = g_object_get_data(G_OBJECT(feature_item), ITEM_SUBFEATURE_DATA) ;
+ zMapAssert(item_data) ;
+
+ if (window->display_forward_coords)
+ {
+ fstart = zmapWindowCoordToDisplay(window, item_data->start) ;
+ fend = zmapWindowCoordToDisplay(window, item_data->end) ;
+ }
+ else
+ {
+ fstart = item_data->start ;
+ fend = item_data->end ;
+ }
- flength = (item_data->end - item_data->start + 1) ;
+ flength = (item_data->end - item_data->start + 1) ;
- /* ignore_this_restriction added as the makePrimarySelectionText was
- * getting uninitialised values for selected_* when selecting multiple
- * exons. I'm not sure the reason for the equality check so I've left
- * it incase we want to parameterise ignore_this_restriction ;) */
+ /* ignore_this_restriction added as the makePrimarySelectionText was
+ * getting uninitialised values for selected_* when selecting multiple
+ * exons. I'm not sure the reason for the equality check so I've left
+ * it incase we want to parameterise ignore_this_restriction ;) */
- /* If the canvas item's match... */
- if (feature_item == highlight_item || ignore_this_restriction)
- {
- sstart = fstart ;
- send = fend ;
- slength = flength ;
- }
+ /* If the canvas item's match... */
+ if (feature_item == highlight_item || ignore_this_restriction)
+ {
+ sstart = fstart ;
+ send = fend ;
+ slength = flength ;
+ }
- if ((populated = TRUE))
- {
*sub_feature_start = fstart;
*sub_feature_end = fend;
*sub_feature_length = flength;
-
-#ifdef FEATURE_FUNCTION_NEEDED_HERE
- *query_start = item_data->query_start;
- *query_end = item_data->query_end;
-#endif /* FEATURE_FUNCTION_NEEDED_HERE */
-
+
+ if (item_data->subpart == ZMAPFEATURE_SUBPART_MATCH)
+ {
+ *query_start = item_data->start ;
+ *query_end = item_data->end ;
+ }
+
*selected_start = sstart;
*selected_end = send;
*selected_length = slength;
*sub_type = item_data->subpart;
+
+ populated = TRUE ;
}
- return populated;
+ return populated ;
}
static gboolean possiblyPopulateWithFullData(ZMapWindow window,
@@ -4693,18 +4789,19 @@ static gboolean possiblyPopulateWithFullData(ZMapWindow window,
selected_start && selected_end &&
feature_length && selected_length);
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+ /* We could be using this here..... */
+
+ zMapFeatureGetInfo((ZMapFeatureAny)item_feature, NULL,
+ "start", &selected_start,
+ "end", &selected_end,
+ "length", &selected_length,
+ NULL);
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
+
type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(feature_item), ITEM_FEATURE_TYPE)) ;
- if (window->display_forward_coords)
- {
- *feature_start = zmapWindowCoordToDisplay(window, feature->x1) ;
- *feature_end = zmapWindowCoordToDisplay(window, feature->x2) ;
- }
- else
- {
- *feature_start = feature->x1 ;
- *feature_end = feature->x2 ;
- }
switch (feature->type)
{
@@ -4724,110 +4821,33 @@ static gboolean possiblyPopulateWithFullData(ZMapWindow window,
break ;
}
- if (type != 1 || feature_item != highlight_item)
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+ if (feature_item == highlight_item)
{
- if(window->display_forward_coords)
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
+ if (window->display_forward_coords)
{
- *selected_start = zmapWindowCoordToDisplay(window, feature->x1);
- *selected_end = zmapWindowCoordToDisplay(window, feature->x2);
+ *selected_start = zmapWindowCoordToDisplay(window, feature->x1) ;
+ *selected_end = zmapWindowCoordToDisplay(window, feature->x2) ;
}
else
{
- *selected_start = feature->x1;
- *selected_end = feature->x2;
+ *selected_start = feature->x1 ;
+ *selected_end = feature->x2 ;
}
- *selected_length = *feature_length;
- }
-
- return populated;
-}
-
-
-static char *makePrimarySelectionText(ZMapWindow window, FooCanvasItem *highlight_item)
-{
- GList *selected = zmapWindowFocusGetFocusItems(window->focus);
- GString *text = g_string_sized_new(512);
- gint length = g_list_length(selected), i = 0;
- char *selection;
- int selected_start, selected_end, selected_length;
-
- while (selected)
- {
- FooCanvasItem *item;
- ZMapFeature item_feature ;
- ZMapFeatureSubPartSpan sub_feature ;
-
-
- item = FOO_CANVAS_ITEM(selected->data) ;
- item_feature = zmapWindowItemGetFeature(item) ;
-
-
+ *selected_length = *feature_length ;
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- /* IT SEEMS THAT ROY WAS HALF WAY THROUGH DOING THIS....IT SHOULD EITHER BE THESE
- * TWO CALLS OR THE ONES BELOW.... */
-
- /* Conditionally get the the full data if we don't get child data.
- * i.e. if the item is not a ITEM_FEATURE_CHILD */
- {
- int dummy, item_type_int ;
-
- if (!(possiblyPopulateWithChildData(window, item, highlight_item,
- &dummy, &dummy, &dummy, &item_type_int,
- &dummy, &dummy, &selected_start,
- &selected_end, &selected_length)))
- possiblyPopulateWithFullData(window, item_feature, item, highlight_item,
- &dummy, &dummy, &dummy, &selected_start,
- &selected_end, &selected_length);
- }
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
- /* OH GOSH....WHAT HAS BEEN GOING ON HERE...SO MUCH HAS CHANGED AND NOW DOESN'T WORK.... */
-
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- if (sub_feature)
- {
- zMapFeatureGetInfo((ZMapFeatureAny)feature, sub_feature,
- "query-start", &selected_start,
- "query-end", &selected_end,
- "query-length", &selected_length,
- NULL);
- }
- else
- {
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
- zMapFeatureGetInfo((ZMapFeatureAny)item_feature, NULL,
- "start", &selected_start,
- "end", &selected_end,
- "length", &selected_length,
- NULL);
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- }
+ }
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+ return populated ;
+}
- g_string_append_printf(text, "\"%s\" %d %d (%d)%s",
- (char *)g_quark_to_string(item_feature->original_id),
- selected_start, selected_end, selected_length,
- (i < (length - 1) ? "\n" : ""));
-
- selected = selected->next;
- i++;
- }
-
- selected = g_list_first(selected);
- g_list_free(selected);
-
- selection = text->str;
- g_string_free(text, FALSE);
- return selection;
-}
static void rehighlightCB(gpointer list_data, gpointer user_data)
--
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