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Commit 670453e6 authored by edgrif's avatar edgrif
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remove any collectionfeature stuff, i.e. go back to where bump was before... 

remove any collectionfeature stuff, i.e. go back to where bump was before collectionfeatures were introduced.
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src/zmapWindow/zmapWindowColBump.c
+ 36
− 170
View file @ 670453e6
......@@ -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 ;
}
......
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