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Commit bf55f016 authored by edgrif's avatar edgrif
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fix up bugs in reporting feature coords, cut buffer may still not be correct.

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src/zmapWindow/zmapWindow.c
+ 162
− 142
View file @ bf55f016
......@@ -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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