diff --git a/src/zmapWindow/Makefile.am b/src/zmapWindow/Makefile.am
index 8612a1c23d3094f05ff50503f25d3d6cf9191dae..c831d58a17d83d17a85e2c34e19a28276c693840 100755
--- a/src/zmapWindow/Makefile.am
+++ b/src/zmapWindow/Makefile.am
@@ -111,8 +111,9 @@ items/zmapWindowContainerUtils.h \
items/zmapWindowGlyphItem.c \
items/zmapWindowGlyphItem.h \
items/zmapWindowGlyphItem_I.h \
-items/zmapWindowLong_Items.c \
-items/zmapWindowLong_Items_P.h \
+items/zmapWindowLongItem.c \
+items/zmapWindowLongItem_I.h \
+items/zmapWindowLongItem.h \
items/zmapWindowSequenceFeature.c \
items/zmapWindowSequenceFeature.h \
items/zmapWindowSequenceFeature_I.h \
diff --git a/src/zmapWindow/zmapWindow.c b/src/zmapWindow/zmapWindow.c
index 4883a93e16b7209779a5f333f62f34773cb3805b..0bed39632f4ec5537cee4ed18456fe127175fa37 100755
--- a/src/zmapWindow/zmapWindow.c
+++ b/src/zmapWindow/zmapWindow.c
@@ -26,9 +26,9 @@
*
* Exported functions: See ZMap/zmapWindow.h
* HISTORY:
- * Last edited: Jun 15 15:20 2009 (rds)
+ * Last edited: Jul 9 15:57 2009 (rds)
* Created: Thu Jul 24 14:36:27 2003 (edgrif)
- * CVS info: $Id: zmapWindow.c,v 1.287 2009-06-19 11:15:56 rds Exp $
+ * CVS info: $Id: zmapWindow.c,v 1.288 2009-07-27 03:15:09 rds Exp $
*-------------------------------------------------------------------
*/
@@ -1232,8 +1232,8 @@ void zmapWindowSetScrollRegion(ZMapWindow window,
* */
void zMapWindowUpdateInfoPanel(ZMapWindow window,
ZMapFeature feature_arg,
- FooCanvasItem *item,
- FooCanvasItem *highlight_item,
+ FooCanvasItem *sub_item,
+ FooCanvasItem *full_item,
gboolean replace_highlight_item,
gboolean highlight_same_names)
{
@@ -1243,9 +1243,12 @@ void zMapWindowUpdateInfoPanel(ZMapWindow window,
ZMapWindowSelectStruct select = {0} ;
ZMapFeatureSet set;
FooCanvasGroup *feature_group;
+ 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 sub_feature_start, sub_feature_end, sub_feature_length;
- int selected_start, selected_end, selected_length ;
+ int query_length ;
select.type = ZMAPWINDOW_SELECT_SINGLE;
@@ -1257,22 +1260,24 @@ void zMapWindowUpdateInfoPanel(ZMapWindow window,
return ;
}
- canvas_item = zMapWindowCanvasItemIntervalGetObject(item);
+ canvas_item = zMapWindowCanvasItemIntervalGetObject(sub_item);
zMapAssert(ZMAP_IS_CANVAS_ITEM(canvas_item));
+ sub_feature = zMapWindowCanvasItemIntervalGetData(sub_item);
+
feature = zMapWindowCanvasItemGetFeature(canvas_item);
zMapAssert(feature_arg == feature);
- top_canvas_item = zMapWindowCanvasItemIntervalGetTopLevelObject(item);
+ top_canvas_item = zMapWindowCanvasItemIntervalGetTopLevelObject(sub_item);
- feature_group = zmapWindowItemGetParentContainer(FOO_CANVAS_ITEM(top_canvas_item)) ;
+ feature_group = zmapWindowItemGetParentContainer(FOO_CANVAS_ITEM(top_canvas_item)) ;
- style = zmapWindowContainerFeatureSetStyleFromID((ZMapWindowContainerFeatureSet)feature_group, feature->style_id) ;
+ style = zmapWindowContainerFeatureSetStyleFromID((ZMapWindowContainerFeatureSet)feature_group,
+ feature->style_id) ;
select.feature_desc.struct_type = feature->struct_type ;
select.feature_desc.type = feature->type ;
-
select.feature_desc.feature_description = zmapWindowFeatureDescription(feature) ;
zmapWindowFeatureGetSetTxt(feature,
@@ -1283,39 +1288,83 @@ void zMapWindowUpdateInfoPanel(ZMapWindow window,
&(select.feature_desc.feature_source),
&(select.feature_desc.feature_source_description)) ;
- if (possiblyPopulateWithChildData(window, item, highlight_item,
- &sub_feature_start, &sub_feature_end,
- &sub_feature_length, &(select.feature_desc.subpart_type),
- &query_start, &query_end,
- &selected_start, &selected_end,
- &selected_length))
+ /* 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_term = sub_feature_term = NULL;
+
+ if(zMapFeatureGetInfo(feature, NULL,
+ "start", &feature_start,
+ "end", &feature_end,
+ "length", &feature_length,
+ "term", &feature_term,
+ NULL))
+ {
+ 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) ;
+ select.feature_desc.feature_term = feature_term;
+ }
+
+ if(zMapFeatureGetInfo(feature, NULL,
+ "query-start", &query_start,
+ "query-end", &query_end,
+ "query-length", &query_length,
+ "query-strand", &query_strand,
+ NULL))
{
- 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.feature_query_start = g_strdup_printf("%d", query_start) ;
+ select.feature_desc.feature_query_end = g_strdup_printf("%d", query_end) ;
+ select.feature_desc.feature_query_length = g_strdup_printf("%d", query_length) ;
+ select.feature_desc.feature_query_strand = zMapFeatureStrand2Str(query_strand) ;
+ }
- if (feature->type == ZMAPSTYLE_MODE_ALIGNMENT)
+ if(sub_feature) /* If sub_feature == NULL we'll only get the same as previous! */
+ {
+ feature_start = feature_end = feature_length = query_start = query_end =
+ sub_feature_start = sub_feature_end = sub_feature_length = query_length = 0;
+
+ if(zMapFeatureGetInfo(feature, sub_feature,
+ "start", &sub_feature_start,
+ "end", &sub_feature_end,
+ "length", &sub_feature_length,
+ "term", &sub_feature_term,
+ NULL))
+ {
+ 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) ;
+ select.feature_desc.sub_feature_term = sub_feature_term ;
+ }
+
+ if(zMapFeatureGetInfo(feature, sub_feature,
+ "query-start", &query_start,
+ "query-end", &query_end,
+ "query-length", &query_length,
+ NULL))
{
select.feature_desc.sub_feature_query_start = g_strdup_printf("%d", query_start) ;
select.feature_desc.sub_feature_query_end = g_strdup_printf("%d", query_end) ;
}
-
- select.feature_desc.sub_feature_length = g_strdup_printf("%d", sub_feature_length) ;
}
else
+ select.feature_desc.sub_feature_term = "-";
+
+ if (feature->type == ZMAPSTYLE_MODE_ALIGNMENT)
{
- if (feature->type == ZMAPSTYLE_MODE_ALIGNMENT)
- {
- if (feature_arg->feature.homol.align)
- select.feature_desc.sub_feature_none_txt = g_strdup("<GAPS NOT SHOWN>") ;
- else
- select.feature_desc.sub_feature_none_txt = g_strdup("<UNGAPPED ALIGNMENT>") ;
- }
- else if (feature->type == ZMAPSTYLE_MODE_TRANSCRIPT)
- select.feature_desc.sub_feature_none_txt = g_strdup("<NO INTRONS>") ;
+ if (feature_arg->feature.homol.align)
+ select.feature_desc.sub_feature_none_txt = g_strdup("<GAPS NOT SHOWN>") ;
+ else
+ select.feature_desc.sub_feature_none_txt = g_strdup("<UNGAPPED ALIGNMENT>") ;
}
-
- if (feature->locus_id)
- select.feature_desc.feature_locus = (char *)g_quark_to_string(feature->locus_id) ;
+ else if (feature->type == ZMAPSTYLE_MODE_TRANSCRIPT)
+ select.feature_desc.sub_feature_none_txt = g_strdup("<NO INTRONS>") ;
+
+ zMapFeatureGetInfo(feature, NULL,
+ "locus", &(select.feature_desc.feature_locus),
+ NULL);
/* Need to replicate this ... */
/* Sequence:"Em:BC043419.2" 166314 167858 (1545) vertebrate_mRNA 96.9 (1 - 1547) Em:BC043419.2 */
@@ -1327,25 +1376,6 @@ void zMapWindowUpdateInfoPanel(ZMapWindow window,
else if (feature->type == ZMAPSTYLE_MODE_TRANSCRIPT && feature->feature.transcript.known_name)
select.feature_desc.feature_known_name = (char *)g_quark_to_string(feature->feature.transcript.known_name) ;
- if (possiblyPopulateWithFullData(window, feature, item, highlight_item,
- &feature_start, &feature_end,
- &feature_length,
- &selected_start, &selected_end,
- &selected_length))
- {
- 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) ;
-
- if (feature->type == ZMAPSTYLE_MODE_ALIGNMENT)
- {
- select.feature_desc.feature_query_start = g_strdup_printf("%d", feature->feature.homol.y1) ;
- select.feature_desc.feature_query_end = g_strdup_printf("%d", feature->feature.homol.y2) ;
- select.feature_desc.feature_query_strand = zMapFeatureStrand2Str(feature->strand) ;
- if (feature->feature.homol.length)
- select.feature_desc.feature_query_length = g_strdup_printf("%d", feature->feature.homol.length) ;
- }
- }
select.feature_desc.feature_strand = zMapFeatureStrand2Str(feature->strand) ;
@@ -1360,12 +1390,10 @@ void zMapWindowUpdateInfoPanel(ZMapWindow window,
if ((set = (ZMapFeatureSet)zMapFeatureGetParentGroup((ZMapFeatureAny)feature, ZMAPFEATURE_STRUCT_FEATURESET)))
select.feature_desc.feature_set = (char *)g_quark_to_string(set->original_id) ;
- select.feature_desc.feature_style = zMapStyleGetName(style) ;
-
- if (highlight_item)
- select.highlight_item = highlight_item ;
+ if (full_item)
+ select.highlight_item = full_item ;
else
- select.highlight_item = item ;
+ select.highlight_item = sub_item ;
select.replace_highlight_item = replace_highlight_item ;
@@ -1377,7 +1405,7 @@ void zMapWindowUpdateInfoPanel(ZMapWindow window,
/* 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. */
- select.secondary_text = makePrimarySelectionText(window, highlight_item);
+ select.secondary_text = makePrimarySelectionText(window, full_item);
zMapGUISetClipboard(window->toplevel, select.secondary_text);
@@ -1395,7 +1423,7 @@ void zMapWindowUpdateInfoPanel(ZMapWindow window,
g_free(select.feature_desc.feature_length) ;
g_free(select.feature_desc.feature_description) ;
- g_free(select.secondary_text) ;
+ //g_free(select.secondary_text) ;
return ;
}
@@ -4575,8 +4603,7 @@ static gboolean possiblyPopulateWithChildData(ZMapWindow window,
int *selected_start, int *selected_end,
int *selected_length)
{
- ZMapWindowItemFeature item_data;
- ZMapWindowItemFeatureType type ;
+ ZMapFeatureSubPartSpan item_data;
int fstart, fend, flength;
int sstart, send, slength;
gboolean populated = FALSE;
@@ -4587,55 +4614,50 @@ static gboolean possiblyPopulateWithChildData(ZMapWindow window,
selected_start && selected_end &&
selected_length && sub_feature_length && sub_type);
- type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(feature_item), ITEM_FEATURE_TYPE)) ;
- if (type == ITEM_FEATURE_CHILD)
+ if (window->display_forward_coords)
{
- 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) ;
-
- /* 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 ((populated = TRUE))
- {
- *sub_feature_start = fstart;
- *sub_feature_end = fend;
- *sub_feature_length = flength;
- *query_start = item_data->query_start;
- *query_end = item_data->query_end;
- *selected_start = sstart;
- *selected_end = send;
- *selected_length = slength;
- *sub_type = item_data->subpart;
- }
+ 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) ;
+
+ /* 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 ((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 */
+
+ *selected_start = sstart;
+ *selected_end = send;
+ *selected_length = slength;
+ *sub_type = item_data->subpart;
}
-
return populated;
}
@@ -4648,9 +4670,9 @@ static gboolean possiblyPopulateWithFullData(ZMapWindow window,
int *selected_start, int *selected_end,
int *selected_length)
{
- ZMapWindowItemFeatureType type;
gboolean populated = TRUE;
-
+ int type;
+
zMapAssert(feature_start && feature_end &&
selected_start && selected_end &&
feature_length && selected_length);
@@ -4686,7 +4708,7 @@ static gboolean possiblyPopulateWithFullData(ZMapWindow window,
break ;
}
- if (type != ITEM_FEATURE_CHILD || feature_item != highlight_item)
+ if (type != 1 || feature_item != highlight_item)
{
if(window->display_forward_coords)
{
@@ -4723,7 +4745,7 @@ static char *makePrimarySelectionText(ZMapWindow window,
item = FOO_CANVAS_ITEM(selected->data);
item_feature = zmapWindowItemGetFeature(item);
-
+#ifdef RDS_DONT_INCLUDE
/* Conditionally get the the full data if we don't get child data.
* i.e. if the item is not a ITEM_FEATURE_CHILD */
if(!(possiblyPopulateWithChildData(window, item, highlight_item,
@@ -4733,7 +4755,7 @@ static char *makePrimarySelectionText(ZMapWindow window,
possiblyPopulateWithFullData(window, item_feature, item, highlight_item,
&dummy, &dummy, &dummy, &selected_start,
&selected_end, &selected_length);
-
+#endif
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,
diff --git a/src/zmapWindow/zmapWindowColBump.c b/src/zmapWindow/zmapWindowColBump.c
index 094e371c2b8c9f753ba1e440bd58e2e667bfb4c5..70cf775aac3edb9979ae1c85d0996b88c0f46a26 100755
--- a/src/zmapWindow/zmapWindowColBump.c
+++ b/src/zmapWindow/zmapWindowColBump.c
@@ -27,9 +27,9 @@
*
* Exported functions: See zmapWindow_P.h
* HISTORY:
- * Last edited: Jun 12 23:09 2009 (rds)
+ * Last edited: Jun 24 16:27 2009 (rds)
* Created: Tue Sep 4 10:52:09 2007 (edgrif)
- * CVS info: $Id: zmapWindowColBump.c,v 1.46 2009-06-19 11:15:47 rds Exp $
+ * CVS info: $Id: zmapWindowColBump.c,v 1.47 2009-07-27 03:15:11 rds Exp $
*-------------------------------------------------------------------
*/
@@ -395,6 +395,8 @@ void zmapWindowColumnBumpRange(FooCanvasItem *bump_item, ZMapStyleBumpMode bump_
zmapWindowContainerShowAllHiddenFeatures(container);
+ zmapWindowContainerFeatureSetSortFeatures(container, 0);
+
bump_properties.container = container ;
bump_properties.window = window = container->window;
bump_properties.overlap_mode = bump_mode;
@@ -2064,7 +2066,8 @@ static void moveItemCB(gpointer data, gpointer user_data)
dx = (((width) * COMPLEX_BUMP_COMPRESS) - (x2 - x1)) / 2 ;
offset = col_data->offset + dx ;
-
+ if(offset < 0.0)
+ offset = 0.0;
my_foo_canvas_item_goto(item, &offset, NULL) ;
diff --git a/src/zmapWindow/zmapWindowDrawFeatures.c b/src/zmapWindow/zmapWindowDrawFeatures.c
index 5e63fef5d4e83aaa76380219a3dbfcf08d15c27f..8bd56f9a240f22716676460e60299e11d8866f96 100755
--- a/src/zmapWindow/zmapWindowDrawFeatures.c
+++ b/src/zmapWindow/zmapWindowDrawFeatures.c
@@ -26,9 +26,9 @@
*
* Exported functions:
* HISTORY:
- * Last edited: Jun 12 08:47 2009 (rds)
+ * Last edited: Jun 24 10:05 2009 (rds)
* Created: Thu Jul 29 10:45:00 2004 (rnc)
- * CVS info: $Id: zmapWindowDrawFeatures.c,v 1.248 2009-06-19 11:16:02 rds Exp $
+ * CVS info: $Id: zmapWindowDrawFeatures.c,v 1.249 2009-07-27 03:15:11 rds Exp $
*-------------------------------------------------------------------
*/
@@ -1783,10 +1783,6 @@ static FooCanvasGroup *createColumnFull(ZMapWindowContainerFeatures parent_group
/* This will create the stats if feature_set != NULL */
zmapWindowContainerAttachFeatureAny(container, (ZMapFeatureAny)feature_set);
- /* Add an overlay manager */
- if((overlay_manager = zmapWindowOverlayCreate(FOO_CANVAS_ITEM(container), NULL)))
- g_object_set_data(G_OBJECT(container), ITEM_FEATURE_OVERLAY_DATA, overlay_manager);
-
g_signal_connect(G_OBJECT(container), "destroy", G_CALLBACK(containerDestroyCB), (gpointer)window) ;
g_signal_connect(G_OBJECT(container), "event", G_CALLBACK(columnBoundingBoxEventCB), (gpointer)window) ;
@@ -2391,14 +2387,7 @@ static gboolean containerDestroyCB(FooCanvasItem *item, gpointer user_data)
/* If the focus column goes then so should the focus items as they should be in step. */
if (zmapWindowFocusGetHotColumn(window->focus) == group)
zmapWindowFocusReset(window->focus) ;
-
- /* get rid of the overlay manager */
- if((overlay_manager = g_object_get_data(G_OBJECT(group), ITEM_FEATURE_OVERLAY_DATA)))
- {
- /* making sure we clear any references to it as well. */
- zmapWindowFocusRemoveOverlayManager(window->focus, overlay_manager);
- overlay_manager = zmapWindowOverlayDestroy(overlay_manager);
- }
+
}
break ;
default:
@@ -2406,9 +2395,13 @@ static gboolean containerDestroyCB(FooCanvasItem *item, gpointer user_data)
zMapAssertNotReached() ;
}
}
-
+#ifdef RDS_REMOVED
+ /* It's not possible to check status as the parent containers
+ * get destroyed first, which call FToIRemove, leading to the
+ * removal of all the child hashes */
if(!status)
- zMapLogCritical("containerDestroyCB (%p): remove failed", group);
+ zMapLogCritical("containerDestroyCB (%p): %s remove failed", group, G_OBJECT_TYPE_NAME(item));
+#endif /* RDS_REMOVED */
}
else
{
diff --git a/src/zmapWindow/zmapWindowDump.c b/src/zmapWindow/zmapWindowDump.c
index 278f1b9ea112ea612132ff103e53f64b03d079bc..0aef595a51b6c7726ebe83bb7b412810d70ea196 100755
--- a/src/zmapWindow/zmapWindowDump.c
+++ b/src/zmapWindow/zmapWindowDump.c
@@ -27,9 +27,9 @@
*
* Exported functions: See ZMap/zmapWindow.h
* HISTORY:
- * Last edited: Jun 12 09:04 2009 (rds)
+ * Last edited: Jun 19 13:38 2009 (rds)
* Created: Thu Mar 30 16:48:34 2006 (edgrif)
- * CVS info: $Id: zmapWindowDump.c,v 1.8 2009-06-19 11:15:17 rds Exp $
+ * CVS info: $Id: zmapWindowDump.c,v 1.9 2009-07-27 03:15:12 rds Exp $
*-------------------------------------------------------------------
*/
@@ -783,12 +783,12 @@ static void itemCB(gpointer data, gpointer user_data)
static void dumpFeature(FooCanvasItem *item, gpointer user_data)
{
DumpOptions cb_data = (DumpOptions)user_data ;
- ZMapWindowItemFeatureType type ;
+ int type ;
if (zmapWindowItemIsShown(item)
&& ((type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(item), ITEM_FEATURE_TYPE)))
- != ITEM_FEATURE_BOUNDING_BOX)
- && (!(type == ITEM_FEATURE_GROUP_BACKGROUND && !FOO_IS_CANVAS_LINE(item))))
+ != 7)
+ && (!(type == 2 && !FOO_IS_CANVAS_LINE(item))))
{
guint composite ;
int fill_colour = 0 ; /* default to white. */
diff --git a/src/zmapWindow/zmapWindowFeature.c b/src/zmapWindow/zmapWindowFeature.c
index 1aee2f274e1d5b6031061ab5c9a92011a7690ad3..352ac7cac2ff13c55736cc989ea28554981e7e3d 100755
--- a/src/zmapWindow/zmapWindowFeature.c
+++ b/src/zmapWindow/zmapWindowFeature.c
@@ -28,9 +28,9 @@
*
* Exported functions: See zmapWindow_P.h
* HISTORY:
- * Last edited: Jun 23 14:50 2009 (rds)
+ * Last edited: Jul 17 12:05 2009 (rds)
* Created: Mon Jan 9 10:25:40 2006 (edgrif)
- * CVS info: $Id: zmapWindowFeature.c,v 1.163 2009-06-23 15:42:00 rds Exp $
+ * CVS info: $Id: zmapWindowFeature.c,v 1.164 2009-07-27 03:15:12 rds Exp $
*-------------------------------------------------------------------
*/
@@ -163,7 +163,6 @@ static gboolean factoryFeatureSizeReq(ZMapFeature feature,
double *points_array_inout,
gpointer handler_data);
-static void cleanUpFeatureCB(gpointer data, gpointer user_data) ;
@@ -746,28 +745,12 @@ static gboolean canvasItemDestroyCB(FooCanvasItem *feature_item, gpointer data)
-static void cleanUpFeatureCB(gpointer data, gpointer user_data)
-{
- FooCanvasItem *feature_item = FOO_CANVAS_ITEM(data) ;
- ZMapWindow window = (ZMapWindow)user_data ;
- ZMapWindowItemFeature item_data ;
-
- if((item_data = g_object_get_data(G_OBJECT(feature_item), ITEM_SUBFEATURE_DATA)))
- g_free(item_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 ;
-}
static void featureCopySelectedItem(ZMapFeature feature_in,
ZMapFeature feature_out,
FooCanvasItem *selected)
{
- ZMapWindowItemFeature item_feature_data;
+ ZMapFeatureSubPartSpan item_feature_data;
ZMapSpanStruct span = {0};
ZMapAlignBlockStruct alignBlock = {0};
@@ -820,6 +803,7 @@ static gboolean canvasItemEventCB(FooCanvasItem *item, GdkEvent *event, gpointer
case GDK_2BUTTON_PRESS:
{
GdkEventButton *but_event = (GdkEventButton *)event ;
+ ZMapFeatureSubPartSpan sub_feature;
ZMapWindowCanvasItem canvas_item;
FooCanvasItem *sub_item = NULL ;
FooCanvasItem *highlight_item = NULL ;
@@ -835,7 +819,11 @@ static gboolean canvasItemEventCB(FooCanvasItem *item, GdkEvent *event, gpointer
/* Get the feature attached to the item, checking that its type is valid */
feature = zMapWindowCanvasItemGetFeature(canvas_item);
- sub_item = zMapWindowCanvasItemGetInterval(canvas_item, but_event->x, but_event->y);
+ sub_item = zMapWindowCanvasItemGetInterval(canvas_item, but_event->x, but_event->y, &sub_feature);
+
+ if(!g_type_class_peek(ZMAP_TYPE_FEATURE_DATA))
+ g_type_class_ref(ZMAP_TYPE_FEATURE_DATA);
+
if (but_event->type == GDK_BUTTON_PRESS)
{
@@ -1109,55 +1097,6 @@ void zmapMakeItemMenu(GdkEventButton *button_event, ZMapWindow window, FooCanvas
}
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-static void makeTextItemMenu(GdkEventButton *button_event, ZMapWindow window, FooCanvasItem *item)
-{
- static ZMapGUIMenuItemStruct separator[] =
- {
- {ZMAPGUI_MENU_SEPARATOR, NULL, 0, NULL, NULL},
- {ZMAPGUI_MENU_NONE, NULL, 0, NULL, NULL}
- } ;
- char *menu_title ;
- GList *menu_sets = NULL ;
- ItemMenuCBData menu_data ;
- ZMapFeature feature ;
- ZMapFeatureTypeStyle style ;
-
-
- /* Some parts of the menu are feature type specific so retrieve the feature item info
- * from the canvas item. */
- feature = zmapWindowItemGetFeature(item);
- zMapAssert(feature) ;
-
- style = zmapWindowItemGetStyle(item) ;
- zMapAssert(style) ;
-
- menu_title = zMapFeatureName((ZMapFeatureAny)feature) ;
-
- /* Call back stuff.... */
- menu_data = g_new0(ItemMenuCBDataStruct, 1) ;
- menu_data->item_cb = TRUE ;
- menu_data->window = window ;
- menu_data->item = item ;
-
- /* Make up the menu. */
-
- /* The select all, None, Copy... */
- menu_sets = g_list_append(menu_sets, makeMenuTextSelectOps(NULL, NULL, menu_data)) ;
-
- menu_sets = g_list_append(menu_sets, separator) ;
-
-
- /* General */
- menu_sets = g_list_append(menu_sets, makeMenuGeneralOps(NULL, NULL, menu_data)) ;
-
- /* DNA Search ????????????????? */
-
- zMapGUIMakeMenu(menu_title, menu_sets, button_event) ;
-
- return ;
-}
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
@@ -1987,7 +1926,7 @@ static gboolean factoryTopItemCreated(FooCanvasItem *top_item,
break;
}
- if(ZMAP_IS_WINDOW_SEQUENCE_FEATURE(top_item))
+ if(0 && ZMAP_IS_WINDOW_SEQUENCE_FEATURE(top_item))
g_signal_connect(G_OBJECT(top_item), "sequence-selected",
G_CALLBACK(sequence_selection_cb), handler_data);
diff --git a/src/zmapWindow/zmapWindowItem.c b/src/zmapWindow/zmapWindowItem.c
index df8886bef08fe76110401c37169e27f13c76ffec..0ab43ca8cc700b897700a3c6277038662371da75 100755
--- a/src/zmapWindow/zmapWindowItem.c
+++ b/src/zmapWindow/zmapWindowItem.c
@@ -26,9 +26,9 @@
*
* Exported functions: See zmapWindow_P.h
* HISTORY:
- * Last edited: Jun 15 11:27 2009 (rds)
+ * Last edited: Jul 16 08:41 2009 (rds)
* Created: Thu Sep 8 10:37:24 2005 (edgrif)
- * CVS info: $Id: zmapWindowItem.c,v 1.115 2009-06-19 11:14:59 rds Exp $
+ * CVS info: $Id: zmapWindowItem.c,v 1.116 2009-07-27 03:15:13 rds Exp $
*-------------------------------------------------------------------
*/
@@ -315,14 +315,12 @@ void zmapWindowHighlightObject(ZMapWindow window, FooCanvasItem *item,
gboolean replace_highlight_item, gboolean highlight_same_names)
{
ZMapFeature feature ;
- ZMapWindowItemFeatureType item_feature_type ;
GList *set_items ;
FooCanvasItem *dna_item, *framed_3ft;
/* Retrieve the feature item info from the canvas item. */
feature = zmapWindowItemGetFeature(item);
zMapAssert(feature) ;
- item_feature_type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(item), ITEM_FEATURE_TYPE)) ;
/* If any other feature(s) is currently in focus, revert it to its std colours */
@@ -368,19 +366,7 @@ void zmapWindowHighlightObject(ZMapWindow window, FooCanvasItem *item,
zmapWindowFocusClearOverlayManagers(window->focus);
- if((dna_item = zmapWindowItemGetDNAItem(window, item)))
- {
- ZMapWindowOverlay overlay_manager;
- FooCanvasGroup *container;
-
- container = (FooCanvasGroup *)zmapWindowContainerCanvasItemGetContainer(dna_item);
-
- if((overlay_manager = g_object_get_data(G_OBJECT(container), ITEM_FEATURE_OVERLAY_DATA)))
- {
- zmapWindowOverlaySetLimitItem(overlay_manager, NULL);
- zmapWindowFocusAddOverlayManager(window->focus, overlay_manager);
- }
- }
+ zmapWindowItemHighlightDNARegion(window, item, feature->x1, feature->x2);
{
int frame_itr;
@@ -388,20 +374,12 @@ void zmapWindowHighlightObject(ZMapWindow window, FooCanvasItem *item,
{
if((framed_3ft = zmapWindowItemGetTranslationItemFromItemFrame(window, item, frame_itr)))
{
- ZMapWindowOverlay overlay_manager;
FooCanvasGroup *container;
container = (FooCanvasGroup *)zmapWindowContainerCanvasItemGetContainer(framed_3ft);
- if((overlay_manager = g_object_get_data(G_OBJECT(container), ITEM_FEATURE_OVERLAY_DATA)))
- {
- zmapWindowOverlaySetLimitItem(overlay_manager, framed_3ft);
-
- zmapWindowOverlaySetSubTypeMask(overlay_manager, ZMAPFEATURE_SUBPART_EXON_CDS | ZMAPFEATURE_SUBPART_EXON | ZMAPFEATURE_SUBPART_MATCH);
-
- zmapWindowFocusAddOverlayManager(window->focus, overlay_manager);
- }
}
+
}
}
@@ -468,25 +446,6 @@ void zmapUnHighlightColumn(ZMapWindow window, FooCanvasGroup *column)
-gboolean zmapWindowItemIsCompound(FooCanvasItem *item)
-{
- gboolean result = FALSE ;
-
- if (FOO_IS_CANVAS_GROUP(item))
- {
- ZMapWindowItemFeatureType item_feature_type ;
-
- /* Retrieve the feature item info from the canvas item. */
- item_feature_type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(item), ITEM_FEATURE_TYPE)) ;
- zMapAssert(item_feature_type == ITEM_FEATURE_PARENT) ;
-
- result = TRUE ;
- }
-
- return result ;
-}
-
-
/* Get "parent" item of feature, for simple features, this is just the item itself but
* for compound features we need the parent group.
* */
@@ -589,28 +548,44 @@ FooCanvasItem *zmapWindowItemGetDNAParentItem(ZMapWindow window, FooCanvasItem *
FooCanvasItem *zmapWindowItemGetDNATextItem(ZMapWindow window, FooCanvasItem *item)
{
FooCanvasItem *dna_item = NULL;
+ ZMapFeature feature = NULL;
+ ZMapFeatureBlock block = NULL;
+ GQuark dna_set_id = 0;
+
+ feature = zmapWindowItemGetFeature(item);
- if ((dna_item = zmapWindowItemGetDNAParentItem(window, item))
- && FOO_IS_CANVAS_GROUP(dna_item)
- && FOO_CANVAS_GROUP(dna_item)->item_list)
+ if(feature != NULL)
+ block = zMapFeatureGetParentGroup((ZMapFeatureAny)feature, ZMAPFEATURE_STRUCT_BLOCK);
+
+ if(block != NULL)
{
- dna_item = FOO_CANVAS_ITEM(FOO_CANVAS_GROUP(dna_item)->item_list->data);
-
- if (!FOO_IS_CANVAS_ZMAP_TEXT(dna_item))
- dna_item = NULL;
- else if (!(FOO_CANVAS_ITEM(dna_item)->object.flags & FOO_CANVAS_ITEM_VISIBLE))
- dna_item = NULL;
+ GQuark dna_id = 0;
+ char *feature_name = NULL;
+
+ dna_set_id = zMapFeatureSetCreateID(ZMAP_FIXED_STYLE_DNA_NAME);
+
+ dna_id = zMapFeatureDNAFeatureID(block);
+
+ dna_item = zmapWindowFToIFindItemFull(window->context_to_item,
+ block->parent->unique_id,
+ block->unique_id,
+ dna_set_id,
+ ZMAPSTRAND_FORWARD, /* STILL ALWAYS FORWARD */
+ ZMAPFRAME_NONE,/* NO STRAND */
+ dna_id);
+ if(dna_item != NULL)
+ {
+ if(!(FOO_CANVAS_ITEM(dna_item)->object.flags & FOO_CANVAS_ITEM_VISIBLE))
+ dna_item = NULL;
+ }
+
+ if(feature_name)
+ g_free(feature_name);
}
return dna_item;
}
-FooCanvasItem *zmapWindowItemGetDNAItem(ZMapWindow window, FooCanvasItem *item)
-{
- /* lazy! */
- return zmapWindowItemGetDNATextItem(window, item);
-}
-
/* highlights the dna given any foocanvasitem (with a feature) and a start and end */
/* This _only_ highlights in the current window! */
void zmapWindowItemHighlightDNARegion(ZMapWindow window,
@@ -618,33 +593,20 @@ void zmapWindowItemHighlightDNARegion(ZMapWindow window,
int region_start,
int region_end)
{
+ ZMapWindowSequenceFeature sequence_feature;
FooCanvasItem *dna_item = NULL;
+ ZMapFeature feature;
- if((dna_item = zmapWindowItemGetDNAItem(window, item)))
+ if((dna_item = zmapWindowItemGetDNATextItem(window, item)))
{
- ZMapWindowOverlay overlay_manager;
- FooCanvasGroup *container;
-
- container = (FooCanvasGroup *)zmapWindowContainerCanvasItemGetContainer(dna_item);
-
- /* Check the column is visible, otherwise failure is imminent. */
- if((FOO_CANVAS_ITEM(container)->object.flags & FOO_CANVAS_ITEM_VISIBLE) &&
- (overlay_manager = g_object_get_data(G_OBJECT(container), ITEM_FEATURE_OVERLAY_DATA)))
- {
- StartEndTextHighlightStruct data = {0};
+ if(ZMAP_IS_WINDOW_SEQUENCE_FEATURE(dna_item) && item != dna_item)
+ {
+ feature = zmapWindowItemGetFeature(item);
- data.start = region_start;
- data.end = region_end;
- data.item = dna_item;
+ sequence_feature = (ZMapWindowSequenceFeature)dna_item;
- zmapWindowOverlayUnmaskAll(overlay_manager);
- if(window->highlights_set.item)
- zmapWindowOverlaySetGdkColorFromGdkColor(overlay_manager, &(window->colour_item_highlight));
- zmapWindowOverlaySetLimitItem(overlay_manager, NULL);
- zmapWindowOverlaySetSubject(overlay_manager, item);
- zmapWindowOverlayMaskFull(overlay_manager, simple_highlight_region, &data);
- }
-
+ zMapWindowSequenceFeatureSelectByRegion(sequence_feature, region_start, region_end, 0);
+ }
}
return ;
@@ -699,11 +661,12 @@ void zmapWindowItemHighlightTranslationRegion(ZMapWindow window, FooCanvasItem *
if((translation_item = zmapWindowItemGetTranslationItemFromItemFrame(window, item, required_frame)))
{
- ZMapWindowOverlay overlay_manager;
FooCanvasGroup *container;
container = (FooCanvasGroup *)zmapWindowContainerCanvasItemGetContainer(translation_item);
-
+
+ /* we just want to call sequenceSelect() */
+#ifdef RDS_REMOVED
if((overlay_manager = g_object_get_data(G_OBJECT(container), ITEM_FEATURE_OVERLAY_DATA)))
{
StartEndTextHighlightStruct data = {0};
@@ -719,7 +682,7 @@ void zmapWindowItemHighlightTranslationRegion(ZMapWindow window, FooCanvasItem *
zmapWindowOverlaySetSubject(overlay_manager, item);
zmapWindowOverlayMaskFull(overlay_manager, simple_highlight_region, &data);
}
-
+#endif /* RDS_REMOVED */
}
return ;
@@ -727,7 +690,7 @@ void zmapWindowItemHighlightTranslationRegion(ZMapWindow window, FooCanvasItem *
ZMapFrame zmapWindowItemFeatureFrame(FooCanvasItem *item)
{
- ZMapWindowItemFeature item_subfeature_data ;
+ ZMapFeatureSubPartSpan item_subfeature_data ;
ZMapFeature feature;
ZMapFrame frame = ZMAPFRAME_NONE;
@@ -914,27 +877,24 @@ FooCanvasItem *zmapWindowItemGetTranslationItemFromItem(ZMapWindow window, FooCa
return translation;
}
-
-
-/* Returns a features style. We need this function because we only attach the style
- * to the top item of the feature. It is a fatal error if a feature does not have a
- * style so this function will always return a valid style or it will abort.
- *
- * */
-ZMapFeatureTypeStyle zmapWindowItemGetStyle(FooCanvasItem *feature_item)
+#ifdef RDS_NEVER
+ZMapFeatureTypeStyle zmapWindowItemGetStyle(ZMapWindow window, FooCanvasItem *item)
{
- ZMapFeatureTypeStyle style = NULL ;
- FooCanvasItem *parent_item = NULL ;
+ ZMapWindowCanvasItem canvas_item = NULL;
+ ZMapFeatureTypeStyle style = NULL;
+ ZMapFeature feature = NULL;
- parent_item = feature_item;
-
- style = g_object_get_data(G_OBJECT(parent_item), ITEM_FEATURE_ITEM_STYLE);
+ canvas_item = zMapWindowCanvasItemIntervalGetTopLevelObject(item);
+
+ if((canvas_item != NULL) &&
+ (feature = zMapWindowCanvasItemGetFeature(canvas_item)))
+ {
+ style = zMapFindStyle(window->display_styles, feature->style_id);
+ }
return style;
}
-
-
-
+#endif
@@ -966,10 +926,10 @@ FooCanvasItem *zMapWindowFindFeatureItemByItem(ZMapWindow window, FooCanvasItem
feature) ;
if(FALSE)
{
- ZMapWindowItemFeature item_subfeature_data ;
+ ZMapFeatureSubPartSpan item_subfeature_data ;
- item_subfeature_data = (ZMapWindowItemFeature)g_object_get_data(G_OBJECT(item),
- ITEM_SUBFEATURE_DATA) ;
+ item_subfeature_data = (ZMapFeatureSubPartSpan)g_object_get_data(G_OBJECT(item),
+ ITEM_SUBFEATURE_DATA) ;
matching_item = zmapWindowFToIFindItemChild(window->context_to_item,
container->strand, container->frame,
@@ -1325,43 +1285,6 @@ gboolean zMapWindowScrollToItem(ZMapWindow window, FooCanvasItem *item)
}
-void zmapWindowShowItem(FooCanvasItem *item)
-{
- /* Looks like old code and we're changing the style stuff. Yes I'm being lazy... */
- g_return_if_fail(item == NULL);
-
-#ifdef OLD_CODE__
- ZMapFeature feature ;
- ZMapWindowItemFeatureType item_feature_type ;
- ZMapWindowItemFeature item_subfeature_data ;
-
- /* Retrieve the feature item info from the canvas item. */
- feature = zmapWindowItemGetFeature(item);
- zMapAssert(feature) ;
-
- item_feature_type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(item),
- ITEM_FEATURE_TYPE)) ;
-
- item_subfeature_data = g_object_get_data(G_OBJECT(item), ITEM_SUBFEATURE_DATA) ;
-
-
- printf("\nItem:\n"
- "Name: %s, type: %s, style: %s, x1: %d, x2: %d, "
- "item_x1: %d, item_x1: %d\n",
- (char *)g_quark_to_string(feature->original_id),
-
- zMapStyleMode2ExactStr(zMapStyleGetMode(feature->style)),
-
- zMapStyleGetName(zMapFeatureGetStyle((ZMapFeatureAny)feature)),
- feature->x1,
- feature->x2,
- item_subfeature_data->start, item_subfeature_data->end) ;
-
-#endif /* OLD_CODE__ */
-
- return ;
-}
-
/* Prints out an items coords in local coords, good for debugging.... */
void zmapWindowPrintLocalCoords(char *msg_prefix, FooCanvasItem *item)
@@ -1463,106 +1386,6 @@ void zMapWindowMoveItem(ZMapWindow window, ZMapFeature origFeature,
}
-void zMapWindowMoveSubFeatures(ZMapWindow window,
- ZMapFeature originalFeature,
- ZMapFeature modifiedFeature,
- GArray *origArray, GArray *modArray,
- gboolean isExon)
-{
- FooCanvasItem *item = NULL, *intron, *intron_box;
- FooCanvasPoints *points ;
- ZMapSpanStruct origSpan, modSpan;
- ZMapWindowItemFeatureType itemFeatureType;
- int i, offset;
- double top, bottom, left, right, middle;
- double x1, y1, x2, y2, transcriptOrigin, transcriptBottom;
- ZMapWindowItemFeature box_data, intron_data ;
-
-
- offset = ((ZMapFeatureBlock)(modifiedFeature->parent->parent))->block_to_sequence.q1;
- transcriptOrigin = modifiedFeature->x1;
- transcriptBottom = modifiedFeature->x2;
- zmapWindowSeq2CanOffset(&transcriptOrigin, &transcriptBottom, offset);
-
- for (i = 0; i < modArray->len; i++)
- {
- /* get the FooCanvasItem using original feature */
- origSpan = g_array_index(origArray, ZMapSpanStruct, i);
-
-
- /* needs changing....to accept frame/strand.... */
-
-#warning "code needs changing for strand/frame"
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-
- item = zmapWindowFToIFindItemChild(window->context_to_item,
- originalFeature, origSpan.x1, origSpan.x2);
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
-
-
- /* coords are relative to start of transcript. */
- modSpan = g_array_index(modArray, ZMapSpanStruct, i);
- top = (double)modSpan.x1 - transcriptOrigin;
- bottom = (double)modSpan.x2 - transcriptOrigin;
-
- if (isExon)
- {
- foo_canvas_item_set(item, "y1", top, "y2", bottom, NULL);
-
- box_data = g_object_get_data(G_OBJECT(item), ITEM_SUBFEATURE_DATA);
- box_data->start = top + transcriptOrigin;
- box_data->end = bottom + transcriptOrigin;
- }
- else
- {
- itemFeatureType = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(item), ITEM_FEATURE_TYPE));
-
- if (itemFeatureType == ITEM_FEATURE_BOUNDING_BOX)
- {
- intron_box = item;
- foo_canvas_item_get_bounds(item, &x1, &y1, &x2, &y2);
- box_data = g_object_get_data(G_OBJECT(intron_box), ITEM_SUBFEATURE_DATA);
- intron = box_data->twin_item;
-
- box_data->start = top + transcriptOrigin;
- box_data->end = bottom + transcriptOrigin;
- }
- else
- {
- intron = item;
- intron_data = g_object_get_data(G_OBJECT(item), ITEM_SUBFEATURE_DATA);
- intron_box = intron_data->twin_item;
- foo_canvas_item_get_bounds(intron_box, &x1, &y1, &x2, &y2);
-
- intron_data->start = top + transcriptOrigin;
- intron_data->end = bottom + transcriptOrigin;
- }
-
- points = foo_canvas_points_new(ZMAP_WINDOW_INTRON_POINTS) ;
-
- left = (x2 - x1)/2;
- right = x2;
- middle = top + (bottom - top + 1)/2;
-
- points->coords[0] = left;
- points->coords[1] = top;
- points->coords[2] = right;
- points->coords[3] = middle;
- points->coords[4] = left;
- points->coords[5] = bottom;
-
- foo_canvas_item_set(intron_box, "y1", top, "y2", bottom, NULL);
- foo_canvas_item_set(intron, "points", points, NULL);
-
- foo_canvas_points_free(points);
- }
- }
- return;
-}
-
/* Returns the sequence coords that correspond to the given _world_ foocanvas coords.
*
* NOTE that although we only return y coords, we need the world x coords as input
diff --git a/src/zmapWindow/zmapWindowItemFactory.c b/src/zmapWindow/zmapWindowItemFactory.c
index 4e954b001a05347059fc1d8c9b2e1c111a066095..aa669f3c7e428d4b5a10e1d91ea2fb4c77f40b57 100755
--- a/src/zmapWindow/zmapWindowItemFactory.c
+++ b/src/zmapWindow/zmapWindowItemFactory.c
@@ -28,9 +28,9 @@
*
* Exported functions: See zmapWindowItemFactory.h
* HISTORY:
- * Last edited: Jun 19 12:13 2009 (rds)
+ * Last edited: Jul 17 12:07 2009 (rds)
* Created: Mon Sep 25 09:09:52 2006 (rds)
- * CVS info: $Id: zmapWindowItemFactory.c,v 1.62 2009-06-19 11:14:12 rds Exp $
+ * CVS info: $Id: zmapWindowItemFactory.c,v 1.63 2009-07-27 03:15:13 rds Exp $
*-------------------------------------------------------------------
*/
@@ -64,9 +64,6 @@ typedef struct _ZMapWindowFToIFactoryStruct
{
guint line_width; /* window->config.feature_line_width */
ZMapWindowFToIFactoryMethodsStruct *methods;
- ZMapWindowFToIFactoryMethodsStruct *basic_methods;
- ZMapWindowFToIFactoryMethodsStruct *text_methods;
- ZMapWindowFToIFactoryMethodsStruct *graph_methods;
GHashTable *ftoi_hash;
ZMapWindowLongItems long_items;
ZMapWindowFToIFactoryProductionTeam user_funcs;
@@ -95,14 +92,6 @@ static void copyCheckMethodTable(const ZMapWindowFToIFactoryMethodsStruct *tabl
ZMapWindowFToIFactoryMethodsStruct **table_out) ;
static void datalistRun(gpointer key, gpointer list_data, gpointer user_data);
-inline
-static void callItemHandler(ZMapWindowFToIFactory factory,
- FooCanvasItem *new_item,
- ZMapWindowItemFeatureType new_item_type,
- ZMapFeature full_feature,
- ZMapWindowItemFeature sub_feature,
- double new_item_y1,
- double new_item_y2);
/* ZMapWindowFToIFactoryInternalMethod prototypes */
static FooCanvasItem *invalidFeature(RunSet run_data, ZMapFeature feature,
@@ -113,6 +102,10 @@ static FooCanvasItem *drawSimpleFeature(RunSet run_data, ZMapFeature feature,
double feature_offset,
double x1, double y1, double x2, double y2,
ZMapFeatureTypeStyle style);
+static FooCanvasItem *drawAssemblyFeature(RunSet run_data, ZMapFeature feature,
+ double feature_offset,
+ double x1, double y1, double x2, double y2,
+ ZMapFeatureTypeStyle style);
static FooCanvasItem *drawGlyphFeature(RunSet run_data, ZMapFeature feature,
double feature_offset,
double x1, double y1, double x2, double y2,
@@ -156,13 +149,6 @@ static void GapAlignBlockFromAdjacentBlocks2(ZMapAlignBlock block_a, ZMapAlignBl
gboolean *t_indel_gt_1,
gboolean *q_indel_gt_1);
-static void null_item_created(FooCanvasItem *new_item,
- ZMapWindowItemFeatureType new_item_type,
- ZMapFeature full_feature,
- ZMapWindowItemFeature sub_feature,
- double new_item_y1,
- double new_item_y2,
- gpointer handler_data);
static gboolean null_top_item_created(FooCanvasItem *top_item,
ZMapFeatureContext context,
ZMapFeatureAlignment align,
@@ -193,56 +179,13 @@ const static ZMapWindowFToIFactoryMethodsStruct factory_methods_G[] = {
{ZMAPSTYLE_MODE_TRANSCRIPT, drawTranscriptFeature},
{ZMAPSTYLE_MODE_RAW_SEQUENCE, drawSeqFeature},
{ZMAPSTYLE_MODE_PEP_SEQUENCE, drawPepFeature},
- {ZMAPSTYLE_MODE_ASSEMBLY_PATH, drawSimpleFeature},
- {ZMAPSTYLE_MODE_TEXT, drawSimpleAsTextFeature},
- {ZMAPSTYLE_MODE_GRAPH, drawSimpleGraphFeature},
- {ZMAPSTYLE_MODE_GLYPH, drawGlyphFeature},
- {-1, NULL}
-};
-
-const static ZMapWindowFToIFactoryMethodsStruct factory_text_methods_G[] = {
- {ZMAPSTYLE_MODE_INVALID, invalidFeature},
- {ZMAPSTYLE_MODE_BASIC, drawSimpleAsTextFeature},
- {ZMAPSTYLE_MODE_ALIGNMENT, drawAlignFeature},
- {ZMAPSTYLE_MODE_TRANSCRIPT, drawTranscriptFeature},
- {ZMAPSTYLE_MODE_RAW_SEQUENCE, drawSeqFeature},
- {ZMAPSTYLE_MODE_PEP_SEQUENCE, drawPepFeature},
- {ZMAPSTYLE_MODE_ASSEMBLY_PATH, drawSimpleFeature},
- {ZMAPSTYLE_MODE_TEXT, drawSimpleAsTextFeature},
- {ZMAPSTYLE_MODE_GRAPH, drawSimpleGraphFeature},
- {ZMAPSTYLE_MODE_GLYPH, drawGlyphFeature},
- {-1, NULL}
-};
-
-const static ZMapWindowFToIFactoryMethodsStruct factory_graph_methods_G[] = {
- {ZMAPSTYLE_MODE_INVALID, invalidFeature},
- {ZMAPSTYLE_MODE_BASIC, drawSimpleGraphFeature},
- {ZMAPSTYLE_MODE_ALIGNMENT, drawSimpleGraphFeature},
- {ZMAPSTYLE_MODE_TRANSCRIPT, drawSimpleGraphFeature},
- {ZMAPSTYLE_MODE_RAW_SEQUENCE, drawSimpleGraphFeature},
- {ZMAPSTYLE_MODE_PEP_SEQUENCE, drawSimpleGraphFeature},
- {ZMAPSTYLE_MODE_ASSEMBLY_PATH, drawSimpleFeature},
- {ZMAPSTYLE_MODE_TEXT, drawSimpleAsTextFeature},
- {ZMAPSTYLE_MODE_GRAPH, drawSimpleGraphFeature},
- {ZMAPSTYLE_MODE_GLYPH, drawGlyphFeature},
- {-1, NULL}
-};
-
-const static ZMapWindowFToIFactoryMethodsStruct factory_basic_methods_G[] = {
- {ZMAPSTYLE_MODE_INVALID, invalidFeature},
- {ZMAPSTYLE_MODE_BASIC, drawSimpleFeature},
- {ZMAPSTYLE_MODE_ALIGNMENT, drawSimpleFeature},
- {ZMAPSTYLE_MODE_TRANSCRIPT, drawSimpleFeature},
- {ZMAPSTYLE_MODE_RAW_SEQUENCE, drawSimpleFeature},
- {ZMAPSTYLE_MODE_PEP_SEQUENCE, drawSimpleFeature},
- {ZMAPSTYLE_MODE_ASSEMBLY_PATH, drawSimpleFeature},
+ {ZMAPSTYLE_MODE_ASSEMBLY_PATH, drawAssemblyFeature},
{ZMAPSTYLE_MODE_TEXT, drawSimpleAsTextFeature},
{ZMAPSTYLE_MODE_GRAPH, drawSimpleGraphFeature},
{ZMAPSTYLE_MODE_GLYPH, drawGlyphFeature},
{-1, NULL}
};
-
ZMapWindowFToIFactory zmapWindowFToIFactoryOpen(GHashTable *feature_to_item_hash,
ZMapWindowLongItems long_items)
{
@@ -257,14 +200,7 @@ ZMapWindowFToIFactory zmapWindowFToIFactoryOpen(GHashTable *feature_to_item_hash
copyCheckMethodTable(&(factory_methods_G[0]),
&(factory->methods));
- copyCheckMethodTable(&(factory_basic_methods_G[0]),
- &(factory->basic_methods));
- copyCheckMethodTable(&(factory_text_methods_G[0]),
- &(factory->text_methods));
- copyCheckMethodTable(&(factory_graph_methods_G[0]),
- &(factory->graph_methods));
-
- user_funcs->item_created = null_item_created;
+
user_funcs->top_item_created = null_top_item_created;
user_funcs->feature_size_request = null_feature_size_request;
factory->user_funcs = user_funcs;
@@ -280,9 +216,6 @@ void zmapWindowFToIFactorySetup(ZMapWindowFToIFactory factory,
{
zMapAssert(signal_handlers);
- if(signal_handlers->item_created)
- factory->user_funcs->item_created = signal_handlers->item_created;
-
if(signal_handlers->top_item_created)
factory->user_funcs->top_item_created = signal_handlers->top_item_created;
@@ -342,7 +275,6 @@ FooCanvasItem *zmapWindowFToIFactoryRunSingle(ZMapWindowFToIFactory factory,
zMapAssert(factory->user_funcs &&
- factory->user_funcs->item_created &&
factory->user_funcs->top_item_created);
#ifdef RDS_REMOVED
ZMapWindowItemFeatureSetData set_data = NULL;
@@ -417,7 +349,7 @@ FooCanvasItem *zmapWindowFToIFactoryRunSingle(ZMapWindowFToIFactory factory,
stats->features++ ;
stats->items++ ;
#endif
- method_table = factory->basic_methods;
+ method_table = factory->methods;
if(feature->flags.has_score)
zmapWindowGetPosFromScore(style, feature->score, &(points[0]), &(points[2])) ;
@@ -485,7 +417,7 @@ FooCanvasItem *zmapWindowFToIFactoryRunSingle(ZMapWindowFToIFactory factory,
stats->features++ ;
stats->items++ ;
#endif
- method_table = factory->text_methods;
+ method_table = factory->methods;
method = &(method_table[style_mode]);
@@ -500,7 +432,7 @@ FooCanvasItem *zmapWindowFToIFactoryRunSingle(ZMapWindowFToIFactory factory,
stats->features++ ;
stats->items++ ;
#endif
- method_table = factory->graph_methods;
+ method_table = factory->methods;
method = &(method_table[style_mode]);
@@ -700,38 +632,6 @@ static void datalistRun(gpointer key, gpointer list_data, gpointer user_data)
return ;
}
-inline
-static void callItemHandler(ZMapWindowFToIFactory factory,
- FooCanvasItem *new_item,
- ZMapWindowItemFeatureType new_item_type,
- ZMapFeature full_feature,
- ZMapWindowItemFeature sub_feature,
- double new_item_y1,
- double new_item_y2)
-{
- /* what was the non signal part of attachDataToItem. _ALL_ our canvas feature MUST have these */
-#ifdef RDS_DONT_INCLUDE
- g_object_set_data(G_OBJECT(new_item), ITEM_FEATURE_TYPE, GINT_TO_POINTER(new_item_type)) ;
-
- g_object_set_data(G_OBJECT(new_item), ITEM_FEATURE_DATA, full_feature) ;
-#endif
-
- if(sub_feature != NULL)
- g_object_set_data(G_OBJECT(new_item), ITEM_SUBFEATURE_DATA, sub_feature);
- else
- zMapAssert(new_item_type != ITEM_FEATURE_CHILD &&
- new_item_type != ITEM_FEATURE_BOUNDING_BOX);
-
- if(factory->long_items && 0)
- zmapWindowLongItemCheck(factory->long_items, new_item, new_item_y1, new_item_y2);
-
- (factory->user_funcs->item_created)(new_item, new_item_type, full_feature, sub_feature,
- new_item_y1, new_item_y2, factory->user_data);
-
- return ;
-}
-
-
static double getWidthFromScore(ZMapFeatureTypeStyle style, double score)
{
@@ -793,8 +693,6 @@ static FooCanvasItem *drawSimpleFeature(RunSet run_data, ZMapFeature feature,
if((new_canvas_item = zMapWindowCanvasItemCreate(parent, y1, feature, style)))
{
- zMapWindowCanvasItemSetIntervalType(new_canvas_item, ZMAP_WINDOW_BASIC_BOX);
-
zMapWindowCanvasItemAddInterval(new_canvas_item, NULL, 0.0, y2 - y1, x1, x2);
feature_item = FOO_CANVAS_ITEM(new_canvas_item);
@@ -803,6 +701,133 @@ static FooCanvasItem *drawSimpleFeature(RunSet run_data, ZMapFeature feature,
return feature_item ;
}
+static FooCanvasItem *drawAssemblyFeature(RunSet run_data, ZMapFeature feature,
+ double feature_offset,/* item offset from block */
+ double x1, double y1, double x2, double y2,
+ ZMapFeatureTypeStyle style)
+{
+ FooCanvasGroup *parent = run_data->container;
+ FooCanvasItem *feature_item = NULL;
+ ZMapWindowCanvasItem new_canvas_item;
+ double canvas_item_position;
+ gboolean debug_assembly_drawing = FALSE;
+
+ canvas_item_position = y1 - feature_offset;
+
+ if(debug_assembly_drawing)
+ {
+ printf("->drawAssemblyFeature(feature=%p, feature_offset=%f, x1=%f, y1=%f, x2=%f, y2=%f)\n",
+ feature, feature_offset, x1, y1, x2, y2);
+ printf("y1=%f, drawing@%f\n", y1, canvas_item_position);
+ }
+
+ if((new_canvas_item = zMapWindowCanvasItemCreate(parent, canvas_item_position, feature, style)))
+ {
+ ZMapFeatureSubPartSpanStruct sub_feature = {};
+ ZMapAssemblyPath assembly_path;
+ ZMapSpan golden_span;
+ double item_start, item_end;
+
+ assembly_path = &(feature->feature.assembly_path);
+
+ /* or should this be feature_offset += item_start [feature->x1 - feature_offset in seq2can()] */
+ feature_offset += canvas_item_position; /* the "new" offset of the items */
+
+ if(debug_assembly_drawing)
+ g_object_set(G_OBJECT(new_canvas_item), "debug", debug_assembly_drawing, NULL);
+
+ if(assembly_path->path)
+ {
+ int i = 0;
+
+ golden_span = &(g_array_index(assembly_path->path, ZMapSpanStruct, i));
+
+ sub_feature.subpart = ZMAPFEATURE_SUBPART_MATCH;
+ sub_feature.start = item_start = golden_span->x1;
+ sub_feature.end = item_end = golden_span->x2;
+
+ if(clip_feature_coords(run_data->factory, feature, feature_offset,
+ &item_start, &item_end))
+ {
+ zMapWindowCanvasItemAddInterval(new_canvas_item, &sub_feature,
+ item_start, item_end,
+ x1, x2);
+ }
+
+ if(feature->x1 != golden_span->x1)
+ {
+ sub_feature.subpart = ZMAPFEATURE_SUBPART_GAP;
+ sub_feature.start = item_start = feature->x1;
+ sub_feature.end = item_end = golden_span->x1 - 1;
+
+ if(clip_feature_coords(run_data->factory, feature, feature_offset,
+ &item_start, &item_end))
+ {
+ zMapWindowCanvasItemAddInterval(new_canvas_item, &sub_feature,
+ item_start, item_end,
+ x1, x2);
+ }
+
+ }
+
+ for(i = 1; i < assembly_path->path->len; i++)
+ {
+ int prev_start, prev_end;
+
+ /* record the previous match to draw the gap later */
+ prev_start = golden_span->x1;
+ prev_end = golden_span->x2;
+ /* get the current match */
+ golden_span = &(g_array_index(assembly_path->path, ZMapSpanStruct, i));
+
+ sub_feature.subpart = ZMAPFEATURE_SUBPART_MATCH;
+ sub_feature.start = item_start = golden_span->x1;
+ sub_feature.end = item_end = golden_span->x2;
+ /* possibly draw the current match */
+ if(clip_feature_coords(run_data->factory, feature, feature_offset,
+ &item_start, &item_end))
+ {
+ zMapWindowCanvasItemAddInterval(new_canvas_item, &sub_feature,
+ item_start, item_end,
+ x1, x2);
+ }
+
+ /* now for the gap */
+ sub_feature.subpart = ZMAPFEATURE_SUBPART_GAP;
+ sub_feature.start = item_start = prev_end + 1;
+ sub_feature.end = item_end = golden_span->x1 - 1;
+ /* possibly draw.... */
+ if(clip_feature_coords(run_data->factory, feature, feature_offset,
+ &item_start, &item_end))
+ {
+ zMapWindowCanvasItemAddInterval(new_canvas_item, &sub_feature,
+ item_start, item_end,
+ x1, x2);
+ }
+ }
+
+ if(feature->x2 != golden_span->x2)
+ {
+ sub_feature.subpart = ZMAPFEATURE_SUBPART_GAP;
+ sub_feature.start = item_start = golden_span->x2 + 1;
+ sub_feature.end = item_end = feature->x2;
+
+ if(clip_feature_coords(run_data->factory, feature, feature_offset,
+ &item_start, &item_end))
+ {
+ zMapWindowCanvasItemAddInterval(new_canvas_item, &sub_feature,
+ item_start, item_end,
+ x1, x2);
+ }
+ }
+ }
+
+ feature_item = FOO_CANVAS_ITEM(new_canvas_item);
+ }
+
+ return feature_item ;
+}
+
static FooCanvasItem *drawGlyphFeature(RunSet run_data, ZMapFeature feature,
double feature_offset,
@@ -903,12 +928,7 @@ static FooCanvasItem *drawGlyphFeature(RunSet run_data, ZMapFeature feature,
#endif
if((new_canvas_item = zMapWindowCanvasItemCreate(parent, y1, feature, style)))
{
- int interval_type;
- /* interval_type = style->interval_type; ... */
- interval_type = ZMAP_WINDOW_BASIC_BOX;
- zMapWindowCanvasItemSetIntervalType(new_canvas_item, interval_type);
-
zMapWindowCanvasItemAddInterval(new_canvas_item, NULL, 0.0, y2 - y1, x1, x2);
feature_item = FOO_CANVAS_ITEM(new_canvas_item);
@@ -960,20 +980,11 @@ static FooCanvasItem *drawAlignFeature(RunSet run_data, ZMapFeature feature,
ZMapWindowCanvasItem new_canvas_item;
ZMapWindowFToIFactory factory = run_data->factory;
ZMapFeatureBlock block = run_data->block;
- GdkColor *outline = NULL, *foreground = NULL, *background = NULL ;
guint match_threshold = 0, line_width = 0;
- gboolean status ;
-
- /* Get the colours, it's an error at this stage if none set we don't draw. */
- /* We could speed performance by caching these colours and only changing them when the style
- * quark changes. */
- status = zMapStyleGetColours(style, ZMAPSTYLE_COLOURTARGET_NORMAL, ZMAPSTYLE_COLOURTYPE_NORMAL,
- &background, &foreground, &outline) ;
- zMapAssert(status) ;
/* If we are here, style should be ok for display. */
-
- if (!zMapStyleIsAlignGaps(style) || !(feature->feature.homol.align))
+ //zMapStyleSetGappedAligns(style, 1.0, 1.0);
+ if ((!zMapStyleIsAlignGaps(style) || !(feature->feature.homol.align)))
{
double feature_start, feature_end;
feature_start = feature->x1;
@@ -991,8 +1002,6 @@ static FooCanvasItem *drawAlignFeature(RunSet run_data, ZMapFeature feature,
zMapWindowCanvasItemClear(new_canvas_item);
}
- zMapWindowCanvasItemSetIntervalType(new_canvas_item, ZMAP_WINDOW_ALIGNMENT_NO_GAPS);
-
zmapWindowExt2Zero(&feature_start, &feature_end);
zMapWindowCanvasItemAddInterval(new_canvas_item, NULL, feature_start, feature_end, x1, x2);
@@ -1077,7 +1086,7 @@ static FooCanvasItem *drawAlignFeature(RunSet run_data, ZMapFeature feature,
/* Do any more we have... */
for (i = 1; prev_match_block && i < feature->feature.homol.align->len ; i++)
{
- ZMapWindowItemFeature gap_data, align_data ;
+ ZMapFeatureSubPartSpanStruct gap_data, align_data ;
ZMapAlignBlockStruct gap_block, *match_block;
FooCanvasItem *match;
double item_top, item_bottom;
@@ -1164,32 +1173,30 @@ static FooCanvasItem *drawAlignFeature(RunSet run_data, ZMapFeature feature,
FooCanvasItem *gap;
double gap_top, gap_bottom;
- gap_data = g_new0(ZMapWindowItemFeatureStruct, 1) ;
- gap_data->subpart = ZMAPFEATURE_SUBPART_GAP ;
- gap_data->start = gap_block.t1;
- gap_data->end = gap_block.t2;
+ gap_data.subpart = ZMAPFEATURE_SUBPART_GAP ;
+ gap_data.start = gap_block.t1;
+ gap_data.end = gap_block.t2;
+#ifdef NO_NEED
gap_data->query_start = 0;
gap_data->query_end = 0;
-
if(q_indel_set)
{
gap_data->query_start = gap_block.q1;
gap_data->query_end = gap_block.q2;
}
+#endif
gap_top = gap_block.t1;
gap_bottom = gap_block.t2;
/* we don't need to clip check here, but item that do have feature_offset seq2can so add here. */
zmapWindowSeq2CanOffset(&gap_top, &gap_bottom, feature_start + feature_offset);
- zMapWindowCanvasItemSetIntervalType(new_canvas_item, ZMAP_WINDOW_ALIGNMENT_GAP);
#ifdef DEBUG_COORDS
printf("\tgap %f, %f\n", gap_top, gap_bottom);
#endif /* DEBUG_COORDS */
- gap = zMapWindowCanvasItemAddInterval(new_canvas_item, gap_data,
+ gap = zMapWindowCanvasItemAddInterval(new_canvas_item, &gap_data,
gap_top, gap_bottom, x1, x2);
- g_object_set_data(G_OBJECT(gap), ITEM_SUBFEATURE_DATA, gap_data);
#ifdef RDS_BREAKING_STUFF
if(q_indel - 1 > match_threshold)
@@ -1198,20 +1205,18 @@ static FooCanvasItem *drawAlignFeature(RunSet run_data, ZMapFeature feature,
}
- align_data = g_new0(ZMapWindowItemFeatureStruct, 1) ;
- align_data->subpart = ZMAPFEATURE_SUBPART_MATCH ;
- align_data->start = match_block->t1 ;
- align_data->end = match_block->t2 ;
+ align_data.subpart = ZMAPFEATURE_SUBPART_MATCH ;
+ align_data.start = match_block->t1 ;
+ align_data.end = match_block->t2 ;
+#ifdef NO_NEED
align_data->query_start = match_block->q1 ;
align_data->query_end = match_block->q2 ;
+#endif
- zMapWindowCanvasItemSetIntervalType(new_canvas_item, ZMAP_WINDOW_ALIGNMENT_MATCH);
#ifdef DEBUG_COORDS
printf("\tmatch %f, %f\n", item_top, item_bottom);
#endif /* DEBUG_COORDS */
- match = zMapWindowCanvasItemAddInterval(new_canvas_item, align_data, item_top, item_bottom, x1, x2);
-
- g_object_set_data(G_OBJECT(match), ITEM_SUBFEATURE_DATA, align_data);
+ match = zMapWindowCanvasItemAddInterval(new_canvas_item, &align_data, item_top, item_bottom, x1, x2);
/* Save this block for next iteration... Incl. the
* Seq2CanOffset of the Bottom of this drawn align box */
@@ -1223,18 +1228,17 @@ static FooCanvasItem *drawAlignFeature(RunSet run_data, ZMapFeature feature,
if(first_match_block)
{
FooCanvasItem *match;
- ZMapWindowItemFeature align_data;
+ ZMapFeatureSubPartSpanStruct align_data;
- align_data = g_new0(ZMapWindowItemFeatureStruct, 1) ;
- align_data->subpart = ZMAPFEATURE_SUBPART_MATCH ;
- align_data->start = first_match_block->t1 ;
- align_data->end = first_match_block->t2 ;
+ align_data.subpart = ZMAPFEATURE_SUBPART_MATCH ;
+ align_data.start = first_match_block->t1 ;
+ align_data.end = first_match_block->t2 ;
+#ifdef NO_NEED
align_data->query_start = first_match_block->q1 ;
align_data->query_end = first_match_block->q2 ;
-
- match = zMapWindowCanvasItemAddInterval(new_canvas_item, align_data,
+#endif
+ match = zMapWindowCanvasItemAddInterval(new_canvas_item, &align_data,
first_item_top, first_item_bottom, x1, x2);
- g_object_set_data(G_OBJECT(match), ITEM_SUBFEATURE_DATA, align_data);
#ifdef DEBUG_COORDS
printf("\t1st %f, %f\n", first_item_top, first_item_bottom);
#endif /* DEBUG_COORDS */
@@ -1327,12 +1331,11 @@ static void new_draw_feature_exon(FooCanvasItem *feature_item,
for(j = last; j >= first; --j)
{
FooCanvasItem *exon_item = NULL;
- ZMapWindowItemFeature exon_data;
+ ZMapFeatureSubPartSpanStruct exon_data;
- exon_data = g_new0(ZMapWindowItemFeatureStruct, 1);
/* actual start will be canvas coord + feature_offset */
- exon_data->start = regions[j].x1 + feature_offset;
- exon_data->end = regions[j].x2;
+ exon_data.start = regions[j].x1 + feature_offset;
+ exon_data.end = regions[j].x2;
/* we have to translate these to the feature_item coord space */
regions[j].x2 -= top;
regions[j].x1 -= top;
@@ -1340,17 +1343,15 @@ static void new_draw_feature_exon(FooCanvasItem *feature_item,
/* Do something about data here... */
if(j == cds_idx)
{
- exon_data->subpart = ZMAPFEATURE_SUBPART_EXON_CDS;
- zMapWindowCanvasItemSetIntervalType(canvas_item, ZMAP_WINDOW_TRANSCRIPT_EXON_CDS);
+ exon_data.subpart = ZMAPFEATURE_SUBPART_EXON_CDS;
}
else
{
- exon_data->subpart = ZMAPFEATURE_SUBPART_EXON;
- zMapWindowCanvasItemSetIntervalType(canvas_item, ZMAP_WINDOW_TRANSCRIPT_EXON);
+ exon_data.subpart = ZMAPFEATURE_SUBPART_EXON;
}
exon_item = zMapWindowCanvasItemAddInterval(canvas_item,
- exon_data,
+ &exon_data,
(double)(regions[j].x1),
(double)(regions[j].x2),
(double)0.0,
@@ -1470,11 +1471,9 @@ static FooCanvasItem *drawTranscriptFeature(RunSet run_data, ZMapFeature featur
parent_ypos = FOO_CANVAS_GROUP(feature_item)->ypos;
- zMapWindowCanvasItemSetIntervalType(canvas_item, ZMAP_WINDOW_TRANSCRIPT_INTRON);
-
for (i = 0 ; i < feature->feature.transcript.introns->len ; i++)
{
- ZMapWindowItemFeature intron;
+ ZMapFeatureSubPartSpanStruct intron;
FooCanvasItem *intron_line ;
double item_top, item_bottom ;
ZMapSpan intron_span ;
@@ -1489,10 +1488,18 @@ static FooCanvasItem *drawTranscriptFeature(RunSet run_data, ZMapFeature featur
continue;
/* set up the item sub feature data */
- intron = g_new0(ZMapWindowItemFeatureStruct, 1);
- intron->start = intron_span->x1;
- intron->end = intron_span->x2;
- intron->subpart = ZMAPFEATURE_SUBPART_INTRON;
+ intron.start = intron_span->x1;
+ intron.end = intron_span->x2;
+
+ if(has_cds)
+ {
+ if(!((item_bottom < cds_start) || (item_top > cds_end)))
+ intron.subpart = ZMAPFEATURE_SUBPART_INTRON_CDS;
+ else
+ intron.subpart = ZMAPFEATURE_SUBPART_INTRON;
+ }
+ else
+ intron.subpart = ZMAPFEATURE_SUBPART_INTRON;
/* this is a sub item we're drawing _within_ the feature_item,
* so we need to zero in its space. new_draw_feature_exon does
@@ -1501,7 +1508,7 @@ static FooCanvasItem *drawTranscriptFeature(RunSet run_data, ZMapFeature featur
item_bottom -= parent_ypos;
/* And draw the item. */
- intron_line = zMapWindowCanvasItemAddInterval(canvas_item, intron,
+ intron_line = zMapWindowCanvasItemAddInterval(canvas_item, &intron,
item_top, item_bottom,
item_left, item_right);
}
@@ -1717,7 +1724,7 @@ static gint canvas_allocate_dna_cb(FooCanvasItem *item,
buffer_size = zMapWindowTextItemCalculateZoomBufferSize(item, draw_data, buffer_size);
- return buffer_size;
+ return buffer_size + 1;
}
static gint canvas_fetch_feature_text_cb(FooCanvasItem *text_item,
@@ -1823,194 +1830,6 @@ static gint canvas_fetch_feature_text_cb(FooCanvasItem *text_item,
}
-static gboolean item_to_char_cell_coords2(FooCanvasPoints **points_out,
- FooCanvasItem *subject,
- gpointer user_data)
-{
- FooCanvasItem *overlay_item;
- FooCanvasGroup *overlay_group, *container;
- ZMapFeature subject_feature, overlay_feature;
- FooCanvasPoints *points;
- double first[ITEMTEXT_CHAR_BOUND_COUNT], last[ITEMTEXT_CHAR_BOUND_COUNT];
- int index1, index2;
- gboolean first_found, last_found;
- gboolean do_overlay = FALSE;
- gboolean redraw = FALSE;
-
- if(FOO_IS_CANVAS_ITEM(user_data) &&
- FOO_IS_CANVAS_GROUP(user_data))
- {
- overlay_group = FOO_CANVAS_GROUP(user_data);
- overlay_item = FOO_CANVAS_ITEM(overlay_group->item_list->data);
-
- container = (FooCanvasGroup *)zmapWindowContainerCanvasItemGetContainer(overlay_item);
-
- do_overlay = (gboolean)(FOO_CANVAS_ITEM(container)->object.flags & FOO_CANVAS_ITEM_VISIBLE);
- }
-
- if(do_overlay)
- {
- ZMapWindowItemFeatureType feature_type;
- ZMapFrame subject_frame, overlay_frame;
-#ifdef RDS_DONT_INCLUDE
- subject_feature = g_object_get_data(G_OBJECT(subject),
- ITEM_FEATURE_DATA);
- overlay_feature = g_object_get_data(G_OBJECT(overlay_group),
- ITEM_FEATURE_DATA);
- feature_type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(subject),
- ITEM_FEATURE_TYPE));
-#endif
- index1 = subject_feature->x1;
- index2 = subject_feature->x2;
- do_overlay = FALSE;
-
- if(feature_type == ITEM_FEATURE_CHILD)
- {
- ZMapWindowItemFeature sub_feature_data;
-
- sub_feature_data = g_object_get_data(G_OBJECT(subject),
- ITEM_SUBFEATURE_DATA);
- switch(sub_feature_data->subpart)
- {
- case ZMAPFEATURE_SUBPART_EXON:
- case ZMAPFEATURE_SUBPART_EXON_CDS:
- {
- gboolean select_only_matching_frame = FALSE;
- index1 = sub_feature_data->start;
- index2 = sub_feature_data->end;
- do_overlay = TRUE;
-
- if(overlay_feature->type == ZMAPSTYLE_MODE_PEP_SEQUENCE)
- {
- if(sub_feature_data->subpart == ZMAPFEATURE_SUBPART_EXON_CDS)
- {
- subject_frame = zMapFeatureTranscriptFrame(subject_feature);
- subject_frame = zMapFeatureSubPartFrame(subject_feature, index1);
- }
- else
- subject_frame = zMapFeatureFrame(subject_feature);
-
- overlay_frame = zMapFeatureFrame(overlay_feature);
-
- if(select_only_matching_frame &&
- subject_frame != overlay_frame)
- do_overlay = FALSE;
- else
- {
- int cds_index1, cds_index2;
- int end_phase = 0, start_phase = 0;
-
- /* We can't highlight the phase codons accurately... */
-
- /* I'm fairly sure what we need is zMapFeatureTranslationStartCoord(feature) */
-
- /* These come back 1 based. */
- zMapFeatureWorld2CDS(subject_feature, index1, index2,
- &cds_index1, &cds_index2);
- /* Coord space: 1 2 3 | 4 5 6 | 7 8 9 | . . . */
- /* Exon coords: ^ ^ ^ ^ */
- /* Start phase: 1-1%3=0 - - 6-1%3=2 (dashes=missing bases) */
-
- /* missing start bases, need to skip forward to get codon start */
- start_phase = (cds_index1 - 1) % 3;
- /* missing end bases, need to skip backward to get full codon */
- end_phase = (cds_index2 % 3);
-#ifdef RDS_DONT_INCLUDE
- printf("indices are %d %d\n", index1, index2);
- printf("phases are %d %d\n", start_phase, end_phase);
-#endif
- if(start_phase != 0)
- index1 += 3 - start_phase;
- if(end_phase != 0)
- index2 -= end_phase;
-#ifdef RDS_DONT_INCLUDE
- printf("indices are %d %d\n", index1, index2);
-#endif
- }
- }
- }
- break;
- case ZMAPFEATURE_SUBPART_MATCH:
- {
- index1 = sub_feature_data->start;
- index2 = sub_feature_data->end;
- do_overlay = TRUE;
-
- if(overlay_feature->type == ZMAPSTYLE_MODE_PEP_SEQUENCE)
- {
- subject_frame = zMapFeatureFrame(subject_feature);
- overlay_frame = zMapFeatureFrame(overlay_feature);
- if(subject_frame != overlay_frame)
- do_overlay = FALSE;
- }
- }
- break;
- default:
- break;
- }
- }
- else if(feature_type == ITEM_FEATURE_SIMPLE)
- {
- switch(subject_feature->type)
- {
- case ZMAPSTYLE_MODE_ALIGNMENT:
- do_overlay = TRUE;
- if(overlay_feature->type == ZMAPSTYLE_MODE_PEP_SEQUENCE)
- {
- subject_frame = zMapFeatureFrame(subject_feature);
- overlay_frame = zMapFeatureFrame(overlay_feature);
- if(subject_frame != overlay_frame)
- do_overlay = FALSE;
- }
- break;
- case ZMAPSTYLE_MODE_GRAPH:
- case ZMAPSTYLE_MODE_TEXT:
- case ZMAPSTYLE_MODE_BASIC:
- do_overlay = TRUE;
- break;
- default:
- break;
- }
- }
- }
-
- if(do_overlay)
- {
- if(index1 > index2)
- ZMAP_SWAP_TYPE(int, index1, index2);
-
- /* From the text indices, get the bounds of that char */
- first_found = zmapWindowItemTextIndex2Item(overlay_item, index1, &first[0]);
- last_found = zmapWindowItemTextIndex2Item(overlay_item, index2, &last[0]);
-
- if(first_found && last_found)
- {
- double minx, maxx;
- foo_canvas_item_get_bounds(overlay_item, &minx, NULL, &maxx, NULL);
-
- points = foo_canvas_points_new(8);
-
- zmapWindowItemTextOverlayFromCellBounds(points,
- &first[0],
- &last[0],
- minx, maxx);
- zmapWindowItemTextOverlayText2Overlay(overlay_item, points);
-
- /* set the points */
- if(points_out)
- {
- *points_out = points;
- /* record such */
- redraw = TRUE;
- }
- else
- foo_canvas_points_free(points);
- }
- }
-
- return redraw;
-}
-
/* item_to_char_cell_coords: This is a ZMapWindowOverlaySizeRequestCB callback
* The overlay code calls this function to request whether to draw an overlay
* on a region and specifically where to draw it. returns TRUE to make the
@@ -2103,13 +1922,12 @@ static FooCanvasItem *drawSimpleGraphFeature(RunSet run_data, ZMapFeature featur
ZMapFeatureTypeStyle style)
{
ZMapWindowFToIFactory factory = run_data->factory ;
- gboolean status ;
FooCanvasGroup *parent = run_data->container ;
FooCanvasItem *feature_item ;
- GdkColor *outline = NULL, *foreground = NULL, *background = NULL ;
guint line_width ;
double numerator, denominator, dx ;
double width, max_score, min_score ;
+ ZMapWindowCanvasItem canvas_item;
width = zMapStyleGetWidth(style) ;
min_score = zMapStyleGetMinScore(style) ;
@@ -2119,10 +1937,6 @@ static FooCanvasItem *drawSimpleGraphFeature(RunSet run_data, ZMapFeature featur
zmapWindowSeq2CanOffset(&y1, &y2, feature_offset) ; /* Make sure we cover the whole last base. */
- status = zMapStyleGetColours(style, ZMAPSTYLE_COLOURTARGET_NORMAL, ZMAPSTYLE_COLOURTYPE_NORMAL,
- &background, &foreground, &outline) ;
- zMapAssert(status) ;
-
numerator = feature->score - min_score ;
denominator = max_score - min_score ;
@@ -2155,16 +1969,12 @@ static FooCanvasItem *drawSimpleGraphFeature(RunSet run_data, ZMapFeature featur
x2 = tmp ;
}
- {
- ZMapWindowCanvasItem canvas_item;
-
- canvas_item = zMapWindowCanvasItemCreate(parent, y1, feature, style);
-
- zMapWindowCanvasItemAddInterval(canvas_item, NULL, 0.0, y2 - y1, x1, x2);
-
- feature_item = (FooCanvasItem *)canvas_item;
- }
+ canvas_item = zMapWindowCanvasItemCreate(parent, y1, feature, style);
+ zMapWindowCanvasItemAddInterval(canvas_item, NULL, 0.0, y2 - y1, x1, x2);
+
+ feature_item = (FooCanvasItem *)canvas_item;
+
return feature_item ;
}
@@ -2400,17 +2210,6 @@ static FooCanvasItem *invalidFeature(RunSet run_data, ZMapFeature feature,
return NULL;
}
-static void null_item_created(FooCanvasItem *new_item,
- ZMapWindowItemFeatureType new_item_type,
- ZMapFeature full_feature,
- ZMapWindowItemFeature sub_feature,
- double new_item_y1,
- double new_item_y2,
- gpointer handler_data)
-{
- return ;
-}
-
static gboolean null_top_item_created(FooCanvasItem *top_item,
ZMapFeatureContext context,
ZMapFeatureAlignment align,
diff --git a/src/zmapWindow/zmapWindowItemFactory.h b/src/zmapWindow/zmapWindowItemFactory.h
index bf8fc78107e35307fd22a853899264ad891648d0..d3d02e1f46e63326631d0465e14bf1fc5531a5f2 100755
--- a/src/zmapWindow/zmapWindowItemFactory.h
+++ b/src/zmapWindow/zmapWindowItemFactory.h
@@ -27,9 +27,9 @@
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
- * Last edited: Dec 10 10:43 2008 (rds)
+ * Last edited: Jun 19 13:37 2009 (rds)
* Created: Mon Sep 25 09:09:52 2006 (rds)
- * CVS info: $Id: zmapWindowItemFactory.h,v 1.7 2009-06-05 13:35:05 rds Exp $
+ * CVS info: $Id: zmapWindowItemFactory.h,v 1.8 2009-07-27 03:15:13 rds Exp $
*-------------------------------------------------------------------
*/
@@ -41,13 +41,6 @@
-typedef void (*ZMapWindowFToIFactoryItemCreated)(FooCanvasItem *new_item,
- ZMapWindowItemFeatureType new_item_type,
- ZMapFeature full_feature,
- ZMapWindowItemFeature sub_feature,
- double new_item_y1,
- double new_item_y2,
- gpointer handler_data);
typedef gboolean (*ZMapWindowFToIFactoryTopItemCreated)(FooCanvasItem *top_item,
ZMapFeatureContext context,
@@ -64,7 +57,6 @@ typedef gboolean (*ZMapWindowFToIFactoryItemFeatureSizeRequest)(ZMapFeature feat
typedef struct
{
- ZMapWindowFToIFactoryItemCreated item_created;
ZMapWindowFToIFactoryTopItemCreated top_item_created;
ZMapWindowFToIFactoryItemFeatureSizeRequest feature_size_request;
}ZMapWindowFToIFactoryProductionTeamStruct, *ZMapWindowFToIFactoryProductionTeam;
diff --git a/src/zmapWindow/zmapWindowItemHash.c b/src/zmapWindow/zmapWindowItemHash.c
index 6938a366b48e2220c72b7ac80c89f4bae7efdce3..260aac9b3874e861c41676e7d410b99eba647876 100755
--- a/src/zmapWindow/zmapWindowItemHash.c
+++ b/src/zmapWindow/zmapWindowItemHash.c
@@ -29,9 +29,9 @@
*
* Exported functions: See zMapWindow_P.h
* HISTORY:
- * Last edited: Jun 12 09:21 2009 (rds)
+ * Last edited: Jul 3 15:19 2009 (rds)
* Created: Mon Jun 13 10:06:49 2005 (edgrif)
- * CVS info: $Id: zmapWindowItemHash.c,v 1.44 2009-06-19 11:16:09 rds Exp $
+ * CVS info: $Id: zmapWindowItemHash.c,v 1.45 2009-07-27 03:15:13 rds Exp $
*-------------------------------------------------------------------
*/
@@ -39,6 +39,7 @@
#include <ZMap/zmapUtils.h>
#include <ZMap/zmapFeature.h>
#include <zmapWindow_P.h>
+#include <zmapWindowCanvasItem.h> /* zMapWindowCanvasItemIntevalGetData() */
#define zmapWindowFToIFindAlignById(FTOI_HASH, ID) \
@@ -1160,24 +1161,20 @@ static void childSearchCB(gpointer data, gpointer user_data)
{
FooCanvasItem *item = (FooCanvasItem *)data ;
ChildSearch child_search = (ChildSearch)user_data ;
- ZMapWindowItemFeatureType item_feature_type ;
/* We take the first match we find so this function does nothing if we have already
* found matching child item. */
if (!(child_search->child_item))
{
- item_feature_type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(item),
- ITEM_FEATURE_TYPE)) ;
- if (item_feature_type == ITEM_FEATURE_CHILD)
+ ZMapFeatureSubPartSpan item_subfeature_data ;
+
+ if((item_subfeature_data = zMapWindowCanvasItemIntervalGetData(item)))
{
- ZMapWindowItemFeature item_subfeature_data ;
-
- item_subfeature_data = (ZMapWindowItemFeature)g_object_get_data(G_OBJECT(item),
- ITEM_SUBFEATURE_DATA) ;
-
- if (item_subfeature_data->start == child_search->child_start
- && item_subfeature_data->end == child_search->child_end)
- child_search->child_item = item ;
+ if (item_subfeature_data->start == child_search->child_start &&
+ item_subfeature_data->end == child_search->child_end)
+ {
+ child_search->child_item = item ;
+ }
}
}
diff --git a/src/zmapWindow/zmapWindowItemText.c b/src/zmapWindow/zmapWindowItemText.c
index c3d9bb7f38ccb7e06aa46beacbf2d2ec6218764c..1c142630bd6035388c38ecfba0cb244402afdc6f 100755
--- a/src/zmapWindow/zmapWindowItemText.c
+++ b/src/zmapWindow/zmapWindowItemText.c
@@ -27,9 +27,9 @@
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
- * Last edited: Jun 12 09:24 2009 (rds)
+ * Last edited: Jun 25 08:56 2009 (rds)
* Created: Mon Apr 2 09:35:42 2007 (rds)
- * CVS info: $Id: zmapWindowItemText.c,v 1.21 2009-06-19 11:16:17 rds Exp $
+ * CVS info: $Id: zmapWindowItemText.c,v 1.22 2009-07-27 03:15:13 rds Exp $
*-------------------------------------------------------------------
*/
@@ -1271,31 +1271,20 @@ static FooCanvasItem *draw_show_translation(FooCanvasGroup *container_features,
&text_width,
&text_height);
}
-
- if((item = foo_canvas_item_new(FOO_CANVAS_GROUP(feature_parent),
- foo_canvas_zmap_text_get_type(),
- "x", 0.0,
- "y", 0.0,
- "anchor", GTK_ANCHOR_NW,
- "font_desc", font_desc,
- "full-width", 30.0 + SHOW_TRANSLATION_COUNTER_LENGTH,
- "wrap-mode", PANGO_WRAP_CHAR,
- "fill_color_gdk", foreground,
- "allocate_func", canvas_allocate_show_translation_cb,
- "fetch_text_func", canvas_fetch_show_transaltion_text_cb,
- "callback_data", feature,
- NULL)))
- {
- ZMapWindowItemFeature sub_feature = NULL;
-#ifdef RDS_DONT_INCLUDE
- g_object_set_data(G_OBJECT(item), ITEM_FEATURE_TYPE,
- GINT_TO_POINTER(ITEM_FEATURE_CHILD)) ;
- g_object_set_data(G_OBJECT(item), ITEM_FEATURE_DATA,
- feature) ;
-#endif
- if(sub_feature != NULL)
- g_object_set_data(G_OBJECT(item), ITEM_SUBFEATURE_DATA, sub_feature);
- }
+#warning should use zmapwindowcanvasitem code
+ item = foo_canvas_item_new(FOO_CANVAS_GROUP(feature_parent),
+ foo_canvas_zmap_text_get_type(),
+ "x", 0.0,
+ "y", 0.0,
+ "anchor", GTK_ANCHOR_NW,
+ "font_desc", font_desc,
+ "full-width", 30.0 + SHOW_TRANSLATION_COUNTER_LENGTH,
+ "wrap-mode", PANGO_WRAP_CHAR,
+ "fill_color_gdk", foreground,
+ "allocate_func", canvas_allocate_show_translation_cb,
+ "fetch_text_func", canvas_fetch_show_transaltion_text_cb,
+ "callback_data", feature,
+ NULL);
return item;
}
diff --git a/src/zmapWindow/zmapWindowMenus.c b/src/zmapWindow/zmapWindowMenus.c
index d0be8b6416009d24744358568931562c22f4aac0..ffe1761761f1411acf74c817c207a38d1acca79f 100755
--- a/src/zmapWindow/zmapWindowMenus.c
+++ b/src/zmapWindow/zmapWindowMenus.c
@@ -27,9 +27,9 @@
* Exported functions: ZMap/zmapWindows.h
*
* HISTORY:
- * Last edited: Jun 12 09:46 2009 (rds)
+ * Last edited: Jul 3 16:54 2009 (rds)
* Created: Thu Mar 10 07:56:27 2005 (edgrif)
- * CVS info: $Id: zmapWindowMenus.c,v 1.61 2009-06-19 11:16:43 rds Exp $
+ * CVS info: $Id: zmapWindowMenus.c,v 1.62 2009-07-27 03:15:13 rds Exp $
*-------------------------------------------------------------------
*/
@@ -1062,16 +1062,29 @@ static void blixemMenuCB(int menu_item_id, gpointer callback_data)
{
ItemMenuCBData menu_data = (ItemMenuCBData)callback_data ;
ZMapWindowCallbackCommandAlignStruct align ;
+ ZMapFeatureAny feature_any;
ZMapFeature feature ;
ZMapWindowCallbacks window_cbs_G = zmapWindowGetCBs() ;
- feature = zmapWindowItemGetFeature(menu_data->item);
- zMapAssert(feature) ; /* something badly wrong if no feature. */
- if(feature->struct_type == ZMAPFEATURE_STRUCT_FEATURESET)
+ feature_any = zmapWindowItemGetFeatureAny(menu_data->item);
+ zMapAssert(feature_any) ; /* something badly wrong if no feature. */
+
+ switch(feature_any->struct_type)
{
- /* need to fix implicit dec here! */
- feature = zMap_g_hash_table_nth(((ZMapFeatureSet)feature)->features, 0);
+ case ZMAPFEATURE_STRUCT_FEATURESET:
+ {
+ ZMapFeatureSet feature_set;
+ feature_set = (ZMapFeatureSet)feature_any;
+ /* need to fix implicit dec here! */
+ feature = zMap_g_hash_table_nth(feature_set->features, 0);
+ }
+ break;
+ case ZMAPFEATURE_STRUCT_FEATURE:
+ feature = (ZMapFeature)feature_any;
+ break;
+ default:
+ break;
}
align.cmd = ZMAPWINDOW_CMD_SHOWALIGN ;
diff --git a/src/zmapWindow/zmapWindowOverlays.c b/src/zmapWindow/zmapWindowOverlays.c
index f92f7465846d477cd649b4514e14e1b6f4542eb6..a6e9d47d2f9de0128740e97dd80e9f456f0dd728 100755
--- a/src/zmapWindow/zmapWindowOverlays.c
+++ b/src/zmapWindow/zmapWindowOverlays.c
@@ -27,9 +27,9 @@
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
- * Last edited: Jun 4 21:23 2009 (rds)
+ * Last edited: Jun 19 13:47 2009 (rds)
* Created: Mon Mar 12 12:28:18 2007 (rds)
- * CVS info: $Id: zmapWindowOverlays.c,v 1.11 2009-06-05 13:36:36 rds Exp $
+ * CVS info: $Id: zmapWindowOverlays.c,v 1.12 2009-07-27 03:15:13 rds Exp $
*-------------------------------------------------------------------
*/
@@ -39,7 +39,7 @@
#include <zmapWindowContainerUtils.h>
#include <ZMap/zmapUtils.h>
-#define OVERLAY_DEFAULT_ITEM_TYPE_MASK (ITEM_FEATURE_SIMPLE | ITEM_FEATURE_CHILD)
+#define OVERLAY_DEFAULT_ITEM_TYPE_MASK (1 | 2)//(ITEM_FEATURE_SIMPLE | ITEM_FEATURE_CHILD)
#define OVERLAY_DEFAULT_SUB_TYPE_MASK (ZMAPFEATURE_SUBPART_EXON_CDS | ZMAPFEATURE_SUBPART_EXON | ZMAPFEATURE_SUBPART_MATCH)
diff --git a/src/zmapWindow/zmapWindow_P.h b/src/zmapWindow/zmapWindow_P.h
index be977c58f77a8fb89eea1d4e43e7dca9af2aebf5..6a4937d44703541ee9403f26f82a737645668b8d 100755
--- a/src/zmapWindow/zmapWindow_P.h
+++ b/src/zmapWindow/zmapWindow_P.h
@@ -25,9 +25,9 @@
* Description: Defines internal interfaces/data structures of zMapWindow.
*
* HISTORY:
- * Last edited: Jun 12 13:50 2009 (rds)
+ * Last edited: Jul 15 08:13 2009 (rds)
* Created: Fri Aug 1 16:45:58 2003 (edgrif)
- * CVS info: $Id: zmapWindow_P.h,v 1.245 2009-06-12 12:51:02 rds Exp $
+ * CVS info: $Id: zmapWindow_P.h,v 1.246 2009-07-27 03:15:13 rds Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_WINDOW_P_H
@@ -192,29 +192,7 @@ typedef struct
#define ITEM_FEATURE_ITEM_STYLE ZMAP_WINDOW_P_H "item_feature_item_style"
#define ITEM_FEATURE_TYPE ZMAP_WINDOW_P_H "item_feature_type"
-#define ITEM_SUBFEATURE_DATA ZMAP_WINDOW_P_H "item_subfeature_data"
-#define ITEM_FEATURE_TEXT_DATA ZMAP_WINDOW_P_H "item_feature_text_data"
-
-#define ITEM_FEATURE_OVERLAY_DATA ZMAP_WINDOW_P_H "item_feature_overlay_data"
-
-typedef enum
- {
- ITEM_FEATURE_INVALID = 0,
-
- /* Item is a group of features. */
- ITEM_FEATURE_GROUP = 1 << 0, /* Parent group for features. */
- ITEM_FEATURE_GROUP_BACKGROUND = 1 << 1, /* background for group. */
-
- /* Item is the whole feature. */
- ITEM_FEATURE_SIMPLE = 1 << 2,
-
- /* Item is a compound feature composed of subparts, e.g. exons, introns etc. */
- ITEM_FEATURE_PARENT = 1 << 3, /* Item is parent group of compound feature. */
- ITEM_FEATURE_CHILD = 1 << 4, /* Item is child/subpart of feature. */
- ITEM_FEATURE_BOUNDING_BOX = 1 << 5 /* Item is invisible bounding box of
- feature or subpart of feature. */
- } ZMapWindowItemFeatureType ;
@@ -432,31 +410,6 @@ typedef struct
-/* Probably will need to expand this to be a union as we come across more features that need
- * different information recording about them.
- * The intent of this structure is to hold information for items that are subparts of features,
- * e.g. exons, where it is tedious/error prone to recover the information from the feature and
- * canvas item. */
-typedef struct
-{
-
- /* I'm not completely sure this is a good idea but somehow we do need to be able to find out
- * whether something is in intron/exon or whatever.... */
- ZMapFeatureSubpartType subpart ; /* Exon, Intron etc. */
-
- int start, end ; /* start/end of subpart in sequence coords. */
-
- int query_start, query_end ; /* For alignments. */
-
- FooCanvasItem *twin_item ; /* Some features need to be drawn with
- two canvas items, an example is
- introns which need an invisible
- bounding box for sensible user
- interaction. */
-
-} ZMapWindowItemFeatureStruct, *ZMapWindowItemFeature ;
-
-
typedef void (*ZMapWindowRulerCanvasCallback)(gpointer data,
gpointer user_data);
@@ -751,15 +704,6 @@ typedef GHashTable * (*ZMapWindowListGetFToIHash)(gpointer user_data);
typedef GList * (*ZMapWindowListSearchHashFunc)(GHashTable *hash_table, gpointer user_data);
-/* Handler to set stuff after an item has been drawn. */
-typedef void (*ZMapWindowFeaturePostItemDrawHandler)(FooCanvasItem *new_item,
- ZMapWindowItemFeatureType new_item_type,
- ZMapFeature full_feature,
- ZMapWindowItemFeature sub_feature,
- double new_item_y1,
- double new_item_y2,
- gpointer handler_data);
-
ZMapWindowCallbacks zmapWindowGetCBs() ;
@@ -941,7 +885,7 @@ FooCanvasGroup *zmapWindowItemGetParentContainer(FooCanvasItem *feature_item) ;
gboolean zmapWindowItemIsGetSize(FooCanvasItem *item) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-FooCanvasItem *zmapWindowItemGetDNAItem(ZMapWindow window, FooCanvasItem *item);
+FooCanvasItem *zmapWindowItemGetDNATextItem(ZMapWindow window, FooCanvasItem *item);
void zmapWindowItemHighlightDNARegion(ZMapWindow window, FooCanvasItem *any_item, int region_start, int region_end);
FooCanvasGroup *zmapWindowItemGetTranslationColumnFromBlock(ZMapWindow window, ZMapFeatureBlock block);
FooCanvasItem *zmapWindowItemGetTranslationItemFromItem(ZMapWindow window, FooCanvasItem *item);
@@ -1157,11 +1101,6 @@ ZMapFrame zmapWindowFeatureFrame(ZMapFeature feature) ;
FooCanvasItem *zmapWindowFeatureDraw(ZMapWindow window, ZMapFeatureTypeStyle style,
FooCanvasGroup *set_group, ZMapFeature feature) ;
-FooCanvasItem *zmapWindowFeatureDrawScaled(ZMapWindow window,
- FooCanvasGroup *set_group,
- ZMapFeature feature,
- double scale_factor,
- ZMapWindowFeaturePostItemDrawHandler handler);
char *zmapWindowFeatureSetDescription(ZMapFeatureSet feature_set) ;
char *zmapWindowFeatureSourceDescription(ZMapFeature feature) ;