diff --git a/src/zmapWindow/zmapWindowColBump.c b/src/zmapWindow/zmapWindowColBump.c
index d969ad62d4841338179b1b48ae2c7b818d99ca7e..8f1e33ad595eec95d91423531f20a5aebb37ef78 100755
--- a/src/zmapWindow/zmapWindowColBump.c
+++ b/src/zmapWindow/zmapWindowColBump.c
@@ -27,9 +27,9 @@
*
* Exported functions: See zmapWindow_P.h
* HISTORY:
- * Last edited: Apr 29 09:24 2010 (edgrif)
+ * Last edited: May 24 16:01 2010 (edgrif)
* Created: Tue Sep 4 10:52:09 2007 (edgrif)
- * CVS info: $Id: zmapWindowColBump.c,v 1.72 2010-04-30 08:37:15 edgrif Exp $
+ * CVS info: $Id: zmapWindowColBump.c,v 1.73 2010-05-24 15:02:39 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -112,6 +112,8 @@ typedef struct
gboolean protein ;
GString *temp_buffer;
+ ZMapWindowContainerFeatureSet feature_set ;
+
} ComplexBumpStruct, *ComplexBump ;
@@ -121,8 +123,8 @@ typedef struct
double incr ;
double offset ;
double width; /* this will be removed! */
- GList *feature_list ;
- ZMapWindowCanvasItem parent_item;
+ GList *feature_list ;
+ ZMapWindowContainerFeatureSet feature_set ;
} ComplexColStruct, *ComplexCol ;
@@ -217,11 +219,6 @@ static gboolean getFeatureFromListItem(GList *list_item, FooCanvasItem **item_ou
static gboolean findRangeListItems(GList *search_start, int seq_start, int seq_end,
GList **first_out, GList **last_out) ;
static GList *removeNonColinear(GList *first_list_item, ZMapGListDirection direction, BumpCol bump_data) ;
-
-static gboolean column_clear_collections(FooCanvasGroup *column_features) ;
-static void make_parent_item_cb(gpointer data, gpointer user_data) ;
-
-
static ColinearityType featureHomolIsColinear(ZMapWindow window, unsigned int match_threshold,
ZMapFeature feat_1, ZMapFeature feat_2) ;
@@ -230,7 +227,6 @@ static void printChild(gpointer data, gpointer user_data) ;
static void printQuarks(gpointer data, gpointer user_data) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
static ZMapStyleBumpMode hack_initial_mode(ZMapFeatureTypeStyle style);
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
@@ -353,10 +349,11 @@ void zmapWindowColumnBumpRange(FooCanvasItem *bump_item, ZMapStyleBumpMode bump_
if(historic_bump_mode > ZMAPBUMP_UNBUMP && historic_bump_mode != bump_mode && bump_mode != ZMAPBUMP_UNBUMP)
zmapWindowColumnBumpRange(bump_item,ZMAPBUMP_UNBUMP,compress_mode);
+
column_features = (FooCanvasGroup *)zmapWindowContainerGetFeatures((ZMapWindowContainerGroup)container) ;
/* always reset the column */
- column_clear_collections(column_features);
+ zMapWindowContainerFeatureSetRemoveSubFeatures(ZMAP_CONTAINER_FEATURESET(container)) ;
zmapWindowContainerShowAllHiddenFeatures(container);
@@ -520,7 +517,6 @@ void zmapWindowColumnBumpRange(FooCanvasItem *bump_item, ZMapStyleBumpMode bump_
complex.name_hash = g_hash_table_new_full(NULL, NULL, /* NULL => use direct hash/comparison. */
NULL, hashDataDestroyCB) ;
-
if (bump_mode == ZMAPBUMP_NAME_BEST_ENDS ||
bump_mode == ZMAPBUMP_NAME_COLINEAR ||
bump_mode == ZMAPBUMP_NAME_NO_INTERLEAVE)
@@ -632,6 +628,8 @@ void zmapWindowColumnBumpRange(FooCanvasItem *bump_item, ZMapStyleBumpMode bump_
complex.curr_offset = 0.0 ;
complex.incr = (width * COMPLEX_BUMP_COMPRESS) ;
+ complex.feature_set = container ;
+
if (bump_mode == ZMAPBUMP_NAME_INTERLEAVE)
complex.overlap_func = listsOverlap ;
else if (bump_mode == ZMAPBUMP_NAME_NO_INTERLEAVE || bump_mode == ZMAPBUMP_NAME_BEST_ENDS
@@ -645,45 +643,26 @@ void zmapWindowColumnBumpRange(FooCanvasItem *bump_item, ZMapStyleBumpMode bump_
zMapPrintTimer(NULL, "offsets set for subsets of features") ;
-
-
/* we reverse the offsets for reverse strand cols so as to mirror the forward strand. */
if (zmapWindowContainerFeatureSetGetStrand(container) == ZMAPSTRAND_REVERSE)
reverseOffsets(complex.bumpcol_list) ;
- g_list_foreach(complex.bumpcol_list, make_parent_item_cb, column_features);
-
/* Bump all the features to their correct offsets. */
g_list_foreach(complex.bumpcol_list, moveItemsCB, NULL) ;
zMapPrintTimer(NULL, "bumped features to offsets") ;
- /* TRY JUST ADDING GAPS IF A MARK IS SET */
- if ((mark_set || zmapWindowContainerFeatureSetGetBumpUnmarked(container)) && bump_mode != ZMAPBUMP_NAME_INTERLEAVE)
+ if ((mark_set || zmapWindowContainerFeatureSetGetBumpUnmarked(container))
+ && bump_mode != ZMAPBUMP_NAME_INTERLEAVE)
{
/* NOTE THERE IS AN ISSUE HERE...WE SHOULD ADD COLINEAR STUFF FOR ALIGN FEATURES
* THIS IS NOT EXPLICIT IN THE CODE WHICH IS NOT CORRECT....NEED TO THINK THIS
* THROUGH, DON'T JUST MAKE THESE COMPLEX BUMP MODES SPECIFIC TO ALIGNMENTS,
* ITS MORE COMPLICATED THAN THAT... */
-
- /* for no interleave add background items.... */
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- g_list_foreach(complex.bumpcol_list, addBackgrounds, &container->extra_items) ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- g_list_foreach(complex.bumpcol_list, addMultiBackgrounds, &container->extra_items) ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
/* WE SHOULD ONLY BE DOING THIS FOR ALIGN FEATURES...TEST AT THIS LEVEL.... */
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- g_list_foreach(complex.bumpcol_list, NEWaddMultiBackgrounds, &container->extra_items) ;
- g_list_foreach(complex.bumpcol_list, NEWaddMultiBackgrounds, container) ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
g_list_foreach(complex.bumpcol_list, collection_add_colinear_cb, &complex);
zMapPrintTimer(NULL, "added inter align bars etc.") ;
@@ -773,23 +752,6 @@ void zmapWindowColumnUnbumpAll(FooCanvasItem *column_item)
-static void make_parent_item_cb(gpointer data, gpointer user_data)
-{
- ComplexCol column_data = (ComplexCol)data;
- FooCanvasGroup *column_features = FOO_CANVAS_GROUP(user_data);
- ZMapFeature feature;
-
- if((column_data->feature_list) &&
- (column_data->feature_list->data) &&
- (feature = zMapWindowCanvasItemGetFeature(FOO_CANVAS_ITEM(column_data->feature_list->data))))
- {
- if (feature->type == ZMAPSTYLE_MODE_ALIGNMENT)
- column_data->parent_item = zMapWindowCollectionFeatureCreate(column_features);
- }
-
- return ;
-}
-
static ColinearityType colinear_compare_features_cb(ZMapFeature feature_a,
ZMapFeature feature_b,
gpointer user_data)
@@ -801,60 +763,27 @@ static ColinearityType colinear_compare_features_cb(ZMapFeature feature_a,
column_data->bump_properties->match_threshold,
feature_a, feature_b);
- return type;
+ return type ;
}
static void collection_add_colinear_cb(gpointer data, gpointer user_data)
{
ComplexCol column_data = (ComplexCol)data;
-#ifdef RDS_UNUSED
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
ComplexBump bump_data = (ComplexBump)user_data;
-#endif
-
- if(column_data->parent_item)
- {
- zMapWindowCollectionFeatureAddColinearMarkers(column_data->parent_item,
- colinear_compare_features_cb,column_data);
- zMapWindowCollectionFeatureAddIncompleteMarkers(column_data->parent_item,
- column_data->bump_properties->window->revcomped_features);
- zMapWindowCollectionFeatureAddSpliceMarkers(column_data->parent_item);
- }
-
- return ;
-}
-
-static gboolean column_clear_collections(FooCanvasGroup *column_features)
- {
- GList *list, *next;
- gboolean result = FALSE;
-
- if((list = g_list_first(column_features->item_list)))
- {
- do
- {
- next = list->next;
- if(ZMAP_IS_WINDOW_COLLECTION_FEATURE(list->data))
- {
- ZMapWindowCanvasItem canvas_item;
-
- canvas_item = ZMAP_CANVAS_ITEM(list->data);
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
- zMapWindowCollectionFeatureRemoveSubFeatures(canvas_item, FALSE, TRUE);
+ zMapWindowContainerFeatureSetAddColinearMarkers(column_data->feature_set, column_data->feature_list,
+ colinear_compare_features_cb, column_data) ;
- zMapWindowCanvasItemClearOverlay(canvas_item);
- zMapWindowCanvasItemClearUnderlay(canvas_item);
+ zMapWindowContainerFeatureSetAddIncompleteMarkers(column_data->feature_set, column_data->feature_list,
+ column_data->bump_properties->window->revcomped_features) ;
- canvas_item = zMapWindowCanvasItemDestroy(canvas_item);
+ zMapWindowContainerFeatureSetAddSpliceMarkers(column_data->feature_set, column_data->feature_list) ;
- result = TRUE;
- }
- }
- while((list = next));
- }
-
- return result;
- }
+ return ;
+}
#warning this_needs_to_go
@@ -1731,17 +1660,6 @@ static gint sortByOverlapCB(gconstpointer a, gconstpointer b, gpointer user_data
strand_1 = feature->strand ;
bot_1 = feature->x2 ;
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- feature_list_1 = g_list_last(feature_list_1) ;
- item = (FooCanvasItem *)feature_list_1->data ;
- feature = zmapWindowItemGetFeature(item);
- zMapAssert(feature) ;
- bot_1 = feature->x2 ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
feature_list_2 = g_list_first(feature_list_2) ;
item = (FooCanvasItem *)feature_list_2->data ;
feature = zmapWindowItemGetFeature(item);
@@ -1750,17 +1668,6 @@ static gint sortByOverlapCB(gconstpointer a, gconstpointer b, gpointer user_data
strand_2 = feature->strand ;
bot_2 = feature->x2 ;
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- feature_list_2 = g_list_last(feature_list_2) ;
- item = (FooCanvasItem *)feature_list_2->data ;
- feature = zmapWindowItemGetFeature(item);
- zMapAssert(feature) ;
- bot_2 = feature->x2 ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
/* Strand first, then overlap. */
if (strand_1 < strand_2)
result = -1 ;
@@ -1865,28 +1772,25 @@ static void bestFitCB(gpointer data, gpointer user_data)
static ComplexCol ComplexBumpComplexColCreate(ComplexBump complex, GList *name_list)
{
- ComplexCol col = NULL;
+ ComplexCol col ;
+ OffsetWidthStruct x1_width = {G_MAXDOUBLE, 0.0};
- if((col = g_new0(ComplexColStruct, 1)))
- {
- OffsetWidthStruct x1_width = {G_MAXDOUBLE, 0.0};
+ col = g_new0(ComplexColStruct, 1) ;
- col->bump_properties = complex->bump_properties;
- col->offset = complex->curr_offset ;
- col->feature_list = name_list ;
+ col->bump_properties = complex->bump_properties ;
+ col->offset = complex->curr_offset ;
+ col->feature_list = name_list ;
+ col->feature_set = complex->feature_set ;
- g_list_foreach(name_list, getMaxWidth, &x1_width) ;
+ g_list_foreach(name_list, getMaxWidth, &x1_width) ;
- complex->bumpcol_list = g_list_append(complex->bumpcol_list, col) ;
- complex->curr_offset += x1_width.width ;
+ complex->bumpcol_list = g_list_append(complex->bumpcol_list, col) ;
+ complex->curr_offset += x1_width.width ;
- if(x1_width.x != G_MAXDOUBLE)
- col->offset -= x1_width.x;
- }
- else
- zMapLogCritical("%s", "Failed to allocate");
+ if(x1_width.x != G_MAXDOUBLE)
+ col->offset -= x1_width.x ;
- return col;
+ return col ;
}
/* GFunc() to try to combine lists of features, if the lists have any overlapping features,
@@ -2121,15 +2025,7 @@ static void reverseOffsets(GList *bumpcol_list)
return ;
}
-static void reparentItemCB(gpointer data, gpointer user_data)
-{
- ComplexCol col_data = (ComplexCol)user_data;
-
- zMapWindowCollectionFeatureStaticReparent(ZMAP_CANVAS_ITEM(data),
- ZMAP_CANVAS_ITEM(col_data->parent_item));
- return ;
-}
/* These two callbacks go through the list of lists of features moving all their canvas items
* into the correct place within their columns. */
@@ -2137,37 +2033,7 @@ static void moveItemsCB(gpointer data, gpointer user_data)
{
ComplexCol col_data = (ComplexCol)data ;
- if(!col_data->parent_item)
- g_list_foreach(col_data->feature_list, moveItemCB, col_data) ;
- else
- {
- FooCanvasItem *first_item;
- double x, y;
-
- if((col_data->feature_list) && (col_data->feature_list->data))
- {
- /* Firstly we need to move the parent_item to the same coords as
- * the first item in feature_list */
-
- first_item = FOO_CANVAS_ITEM(col_data->feature_list->data);
-
- g_object_get(G_OBJECT(first_item),
- "x", &x,
- "y", &y,
- NULL);
-
- foo_canvas_item_set(FOO_CANVAS_ITEM(col_data->parent_item),
- "x", x,
- "y", y,
- NULL);
-
- g_list_foreach(col_data->feature_list, reparentItemCB, col_data);
-
- foo_canvas_item_set(FOO_CANVAS_ITEM(col_data->parent_item),
- "x", x + col_data->offset,
- NULL);
- }
- }
+ g_list_foreach(col_data->feature_list, moveItemCB, col_data) ;
return ;
}