From 9063bc8ed2fbb18422de6407e22756121a573c4f Mon Sep 17 00:00:00 2001
From: rds <rds>
Date: Fri, 8 May 2009 15:08:18 +0000
Subject: [PATCH] some cleaning up, some factorising functions and data
structures. trying to find initial bump issues...
---
src/zmapWindow/zmapWindowColBump.c | 1274 +++++++++-------------------
1 file changed, 408 insertions(+), 866 deletions(-)
diff --git a/src/zmapWindow/zmapWindowColBump.c b/src/zmapWindow/zmapWindowColBump.c
index 121bae6cd..f176c32b6 100755
--- a/src/zmapWindow/zmapWindowColBump.c
+++ b/src/zmapWindow/zmapWindowColBump.c
@@ -27,9 +27,9 @@
*
* Exported functions: See zmapWindow_P.h
* HISTORY:
- * Last edited: May 1 13:18 2009 (rds)
+ * Last edited: May 7 22:33 2009 (rds)
* Created: Tue Sep 4 10:52:09 2007 (edgrif)
- * CVS info: $Id: zmapWindowColBump.c,v 1.40 2009-05-01 12:19:33 rds Exp $
+ * CVS info: $Id: zmapWindowColBump.c,v 1.41 2009-05-08 15:08:18 rds Exp $
*-------------------------------------------------------------------
*/
@@ -38,31 +38,32 @@
#include <ZMap/zmapGLibUtils.h>
#include <zmapWindow_P.h>
#include <zmapWindowContainer.h>
+#include <zmapWindowCanvasItem.h>
typedef struct
{
- GQuark style_id;
- ZMapStyleBumpMode bump_mode;
- ZMapStyleColumnDisplayState display_state;
- unsigned int match_threshold;
- gboolean bump_all;
-} StylePropertiesStruct;
+ ZMapWindow window;
+ ZMapWindowItemFeatureSetData set_data;
+ GQuark style_id;
+ ZMapStyleBumpMode overlap_mode;
+ ZMapStyleColumnDisplayState display_state;
+ unsigned int match_threshold;
+ gboolean bump_all;
+} BumpPropertiesStruct, *BumpProperties;
/* For straight forward bumping. */
typedef struct
{
- ZMapWindow window ;
- ZMapWindowItemFeatureSetData set_data ;
+ GHashTable *pos_hash ;
+ GList *pos_list ;
- GHashTable *pos_hash ;
- GList *pos_list ;
-
- double offset ;
- double incr ;
+ double offset;
+ double incr ;
- int start, end ;
+ int start;
+ int end ;
- StylePropertiesStruct style_prop;
+ BumpPropertiesStruct bump_prop_data;
} BumpColStruct, *BumpCol ;
@@ -94,35 +95,27 @@ typedef GList* (*GListTraverseFunc)(GList *list) ;
typedef struct
{
- ZMapWindow window ;
- FooCanvasGroup *column_group ;
- ZMapWindowItemFeatureSetData set_data ;
+ BumpProperties bump_properties;
+ GHashTable *name_hash ;
+ GList *bumpcol_list ;
+ double curr_offset ;
+ double incr ;
+ OverLapListFunc overlap_func ;
+ gboolean protein ;
+ GString *temp_buffer;
- gboolean bump_all ;
- GHashTable *name_hash ;
- GList *bumpcol_list ;
- double curr_offset ;
- double incr ;
- OverLapListFunc overlap_func ;
- gboolean protein ;
-
- unsigned int match_threshold;
- GQuark style_id;
} ComplexBumpStruct, *ComplexBump ;
typedef struct
{
- ZMapWindow window ;
- FooCanvasGroup *column_group ;
- ZMapWindowItemFeatureSetData set_data ;
-
- double incr ;
- double offset ;
- double width ;
- GList *feature_list ;
- unsigned int match_threshold;
+ BumpProperties bump_properties;
+ double incr ;
+ double offset ;
+ double width; /* this will be removed! */
+ GList *feature_list ;
+ ZMapWindowCanvasItem parent_item;
} ComplexColStruct, *ComplexCol ;
@@ -181,28 +174,15 @@ typedef struct
-typedef enum {COLINEAR_INVALID, COLINEAR_NOT, COLINEAR_IMPERFECT, COLINEAR_PERFECT} ColinearityType ;
-
-
-
-
static void bumpColCB(gpointer data, gpointer user_data) ;
static void compareListOverlapCB(gpointer data, gpointer user_data) ;
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-static void addToList(gpointer data, gpointer user_data);
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
static gboolean featureListCB(gpointer data, gpointer user_data) ;
static gint sortByScoreCB(gconstpointer a, gconstpointer b) ;
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-static gint sortBySpanCB(gconstpointer a, gconstpointer b) ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
static gint sortByStrandSpanCB(gconstpointer a, gconstpointer b) ;
static gint sortByOverlapCB(gconstpointer a, gconstpointer b, gpointer user_data) ;
static void bestFitCB(gpointer data, gpointer user_data) ;
@@ -218,15 +198,6 @@ static void setAllOffsetCB(gpointer data, gpointer user_data) ;
static void getMaxWidth(gpointer data, gpointer user_data) ;
static void sortListPosition(gpointer data, gpointer user_data) ;
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-static void addBackgrounds(gpointer data, gpointer user_data) ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-static void addMultiBackgrounds(gpointer data, gpointer user_data) ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
static void addGapsCB(gpointer data, gpointer user_data) ;
static void removeGapsCB(gpointer data, gpointer user_data) ;
@@ -257,11 +228,6 @@ static void setStyleBumpCB(ZMapFeatureTypeStyle style, gpointer user_data) ;
static gboolean bumpBackgroundEventCB(FooCanvasItem *item, GdkEvent *event, gpointer data) ;
static gboolean bumpBackgroundDestroyCB(FooCanvasItem *feature_item, gpointer data) ;
-
-
-#ifdef UNUSED_FUNCTIONS
-static gint compareNameToColumn(gconstpointer list_data, gconstpointer user_data) ;
-#endif
static gint findItemInQueueCB(gconstpointer a, gconstpointer b) ;
static void removeNonColinearExtensions(gpointer data, gpointer user_data) ;
@@ -322,9 +288,9 @@ void zmapWindowColumnBumpRange(FooCanvasItem *column_item, ZMapStyleBumpMode bum
{
BumpColStruct bump_data = {NULL} ;
FooCanvasGroup *column_features ;
- StylePropertiesStruct styles_prop = {0};
- ZMapWindowItemFeatureType feature_type ;
- ZMapContainerLevelType container_type ;
+ ZMapWindowItemFeatureType feature_type;
+ ZMapContainerLevelType container_type;
+ BumpPropertiesStruct bump_properties = {NULL};
FooCanvasGroup *column_group = NULL ;
ZMapWindowItemFeatureSetData set_data ;
ZMapStyleBumpMode historic_bump_mode;
@@ -358,12 +324,12 @@ void zmapWindowColumnBumpRange(FooCanvasItem *column_item, ZMapStyleBumpMode bum
set_data = g_object_get_data(G_OBJECT(column_group), ITEM_FEATURE_SET_DATA) ;
zMapAssert(set_data) ;
- bump_data.set_data = set_data ;
+ bump_properties.set_data = set_data ;
+ bump_properties.window = set_data->window;
+ bump_properties.overlap_mode = bump_mode;
zMapWindowBusy(set_data->window, TRUE) ;
- bump_data.window = set_data->window ;
-
/* Need to know if mark is set for limiting feature display for several modes/feature types. */
mark_set = zmapWindowMarkIsSet(set_data->window->mark) ;
@@ -404,14 +370,14 @@ void zmapWindowColumnBumpRange(FooCanvasItem *column_item, ZMapStyleBumpMode bum
* and features within the column, otherwise we just bump the specific features. */
if (column)
{
- styles_prop.bump_all = TRUE ;
- styles_prop.style_id = set_data->unique_id;
- styles_prop.display_state = zmapWindowItemFeatureSetGetDisplay(set_data);
-
- zmapWindowItemFeatureSetJoinAligns(set_data, &(styles_prop.match_threshold));
+ bump_properties.bump_all = TRUE ;
+ bump_properties.style_id = set_data->unique_id;
+ bump_properties.display_state = zmapWindowItemFeatureSetGetDisplay(set_data);
+
+ zmapWindowItemFeatureSetJoinAligns(set_data, &(bump_properties.match_threshold));
zmapWindowStyleTableForEach(set_data->style_table, setStyleBumpCB, GINT_TO_POINTER(bump_mode)) ;
- }
+ }
else
{
ZMapFeatureTypeStyle style;
@@ -420,25 +386,23 @@ void zmapWindowColumnBumpRange(FooCanvasItem *column_item, ZMapStyleBumpMode bum
feature = g_object_get_data(G_OBJECT(column_item), ITEM_FEATURE_DATA) ;
zMapAssert(feature) ;
- styles_prop.bump_all = FALSE;
- styles_prop.style_id = feature->style_id;
+ bump_properties.bump_all = FALSE;
+ bump_properties.style_id = feature->style_id;
if((style = zmapWindowStyleTableFind(set_data->style_table, feature->style_id)))
{
g_object_get(G_OBJECT(style),
- ZMAPSTYLE_PROPERTY_DISPLAY_MODE, &(styles_prop.display_state),
+ ZMAPSTYLE_PROPERTY_DISPLAY_MODE, &(bump_properties.display_state),
NULL);
- zMapStyleGetJoinAligns(style, &(styles_prop.match_threshold));
-
+ zMapStyleGetJoinAligns(style, &(bump_properties.match_threshold));
+
zMapStyleSetBumpMode(style, bump_mode);
}
else
zMapLogCritical("Missing style '%s'", g_quark_to_string(feature->style_id));
}
- styles_prop.bump_mode = bump_mode;
-
/* If range set explicitly or a mark is set on the window, then only bump within the range of mark
* or the visible section of the window. */
if (compress_mode == ZMAPWINDOW_COMPRESS_INVALID)
@@ -448,7 +412,7 @@ void zmapWindowColumnBumpRange(FooCanvasItem *column_item, ZMapStyleBumpMode bum
else
{
start = set_data->window->min_coord ;
- end = set_data->window->max_coord ;
+ end = set_data->window->max_coord ;
}
}
else
@@ -486,19 +450,17 @@ void zmapWindowColumnBumpRange(FooCanvasItem *column_item, ZMapStyleBumpMode bum
}
bump_data.start = start ;
- bump_data.end = end ;
+ bump_data.end = end ;
- /* All bump modes except ZMAPBUMP_COMPLEX share common data/code as they are essentially
- * simple variants. The complex mode requires more processing so uses its own structs/lists. */
- width = zmapWindowItemFeatureSetGetWidth(set_data);
- bump_spacing = zmapWindowItemFeatureGetBumpSpacing(set_data) ;
-
-
- bump_data.style_prop = styles_prop; /* struct copy! */
-
+ width = zmapWindowItemFeatureSetGetWidth(set_data);
+ bump_spacing = zmapWindowItemFeatureGetBumpSpacing(set_data) ;
bump_data.incr = width + bump_spacing ;
+ bump_data.bump_prop_data = bump_properties; /* struct copy! */
+
+ /* All bump modes except ZMAPBUMP_COMPLEX share common data/code as they are essentially
+ * simple variants. The complex mode requires more processing so uses its own structs/lists. */
switch (bump_mode)
{
case ZMAPBUMP_UNBUMP:
@@ -530,24 +492,26 @@ void zmapWindowColumnBumpRange(FooCanvasItem *column_item, ZMapStyleBumpMode bum
GList *names_list = NULL ;
int list_length ;
- complex.bump_all = styles_prop.bump_all;
- complex.style_id = styles_prop.style_id;
- complex.match_threshold = 1; /* fix this! */
+ complex.temp_buffer = g_string_sized_new(255); /* Should be enough for most... */
+
+ complex.bump_properties = &(bump_data.bump_prop_data); /* point to the bump_properties */
/* Make a hash table of feature names which are hashed to lists of features with that name. */
- complex.name_hash = g_hash_table_new_full(NULL, NULL, /* NULL => use direct hash/comparison. */
- NULL, hashDataDestroyCB) ;
+ 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)
+ if (bump_mode == ZMAPBUMP_NAME_BEST_ENDS ||
+ bump_mode == ZMAPBUMP_NAME_COLINEAR ||
+ bump_mode == ZMAPBUMP_NAME_NO_INTERLEAVE)
g_list_foreach(column_features->item_list, makeNameListStrandedCB, &complex) ;
else
- g_list_foreach(column_features->item_list, makeNameListCB, &complex) ;
+ {
+ g_list_foreach(column_features->item_list, makeNameListCB, &complex) ;
+ }
zMapPrintTimer(NULL, "Made names list") ;
-
/* Extract the lists of features into a list of lists for sorting. */
g_hash_table_foreach(complex.name_hash, getListFromHash, &names_list) ;
@@ -564,12 +528,16 @@ void zmapWindowColumnBumpRange(FooCanvasItem *column_item, ZMapStyleBumpMode bum
/* Lets try different sorting for proteins vs. dna. */
if (complex.protein)
- names_list = g_list_sort(names_list, sortByScoreCB) ;
+ {
+ names_list = g_list_sort(names_list, sortByScoreCB) ;
+ }
else
+ {
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- names_list = g_list_sort(names_list, sortBySpanCB) ;
+ names_list = g_list_sort(names_list, sortBySpanCB) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
- names_list = g_list_sort(names_list, sortByStrandSpanCB) ;
+ names_list = g_list_sort(names_list, sortByStrandSpanCB) ;
+ }
zMapPrintTimer(NULL, "Sorted by score or strand") ;
@@ -580,16 +548,17 @@ void zmapWindowColumnBumpRange(FooCanvasItem *column_item, ZMapStyleBumpMode bum
|| (bump_mode == ZMAPBUMP_NAME_BEST_ENDS || bump_mode == ZMAPBUMP_NAME_COLINEAR))
{
RangeDataStruct range = {FALSE} ;
-
+
range.start = start ;
- range.end = end ;
+ range.end = end ;
names_list = g_list_sort_with_data(names_list, sortByOverlapCB, &range) ;
}
list_length = g_list_length(names_list) ;
- if ((compress_mode == ZMAPWINDOW_COMPRESS_VISIBLE || compress_mode == ZMAPWINDOW_COMPRESS_MARK))
+ if (compress_mode == ZMAPWINDOW_COMPRESS_VISIBLE ||
+ compress_mode == ZMAPWINDOW_COMPRESS_MARK)
{
if (removeNameListsByRange(&names_list, start, end))
set_data->hidden_bump_features = TRUE ;
@@ -602,7 +571,7 @@ void zmapWindowColumnBumpRange(FooCanvasItem *column_item, ZMapStyleBumpMode bum
/* There's a problem with logic here. see removeNonColinearExtensions! */
/* Remove non-colinear matches outside range if set. */
if (mark_set && bump_mode == ZMAPBUMP_NAME_COLINEAR
- && styles_prop.display_state != ZMAPSTYLE_COLDISPLAY_SHOW)
+ && bump_properties.display_state != ZMAPSTYLE_COLDISPLAY_SHOW)
g_list_foreach(names_list, removeNonColinearExtensions, &bump_data) ;
@@ -631,10 +600,6 @@ void zmapWindowColumnBumpRange(FooCanvasItem *column_item, ZMapStyleBumpMode bum
/* Merge the lists into the min. number of non-overlapping lists of features arranged
* by name and to some extent by score. */
- complex.window = set_data->window ;
- complex.column_group = column_group ;
- complex.set_data = set_data ;
-
complex.curr_offset = 0.0 ;
complex.incr = (width * COMPLEX_BUMP_COMPRESS) ;
@@ -690,7 +655,6 @@ void zmapWindowColumnBumpRange(FooCanvasItem *column_item, ZMapStyleBumpMode bum
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
g_list_foreach(complex.bumpcol_list, NEWaddMultiBackgrounds, set_data) ;
-
zMapPrintTimer(NULL, "added inter align bars etc.") ;
}
@@ -765,7 +729,6 @@ static void bumpColCB(gpointer data, gpointer user_data)
{
FooCanvasItem *item = (FooCanvasItem *)data ;
BumpCol bump_data = (BumpCol)user_data ;
- FooCanvasGroup *column_group = NULL ;
ZMapWindowItemFeatureSetData set_data ;
ZMapFeatureTypeStyle style ;
ZMapWindowItemFeatureType item_feature_type ;
@@ -776,192 +739,197 @@ static void bumpColCB(gpointer data, gpointer user_data)
double offset = 0.0, dx = 0.0 ;
ZMapStyleBumpMode bump_mode ;
gboolean ignore_mark;
+ gboolean proceed = FALSE;
- if(!(zmapWindowItemIsShown(item)))
- return ;
-
- item_feature_type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(item), ITEM_FEATURE_TYPE)) ;
- zMapAssert(item_feature_type == ITEM_FEATURE_SIMPLE || item_feature_type == ITEM_FEATURE_PARENT) ;
+ proceed = zmapWindowItemIsShown(item);
- feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA) ;
- zMapAssert(feature) ;
+ if(proceed)
+ {
+ /* Get what we need. */
+ item_feature_type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(item), ITEM_FEATURE_TYPE)) ;
- bump_mode = bump_data->style_prop.bump_mode ;
+ if(!(item_feature_type == ITEM_FEATURE_SIMPLE || item_feature_type == ITEM_FEATURE_PARENT))
+ proceed = FALSE;
- if (bump_data->style_prop.display_state == ZMAPSTYLE_COLDISPLAY_SHOW)
- ignore_mark = TRUE ;
- else
- ignore_mark = FALSE ;
+ feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA) ;
+ if(!feature)
+ proceed = FALSE;
+ bump_mode = bump_data->bump_prop_data.overlap_mode ;
+ set_data = bump_data->bump_prop_data.set_data;
+ style = zmapWindowItemFeatureSetStyleFromID(set_data, feature->style_id) ;
+ }
- /* try a range restriction... */
- if (bump_mode != ZMAPBUMP_UNBUMP && !(ignore_mark))
+ if(proceed)
{
- if (feature->x2 < bump_data->start || feature->x1 > bump_data->end)
+ if (bump_data->bump_prop_data.display_state == ZMAPSTYLE_COLDISPLAY_SHOW)
+ ignore_mark = TRUE ;
+ else
+ ignore_mark = FALSE ;
+
+ /* try a range restriction... */
+ if (bump_mode != ZMAPBUMP_UNBUMP && !(ignore_mark))
{
- bump_data->set_data->hidden_bump_features = TRUE ;
-
- foo_canvas_item_hide(item) ;
-
- return ;
+ if (feature->x2 < bump_data->start || feature->x1 > bump_data->end)
+ {
+ set_data->hidden_bump_features = TRUE ;
+
+ foo_canvas_item_hide(item) ;
+
+ proceed = FALSE;
+ }
}
- }
-
-
- /* If we not bumping all features, then only bump the features who have the bumped style. */
- column_group = zmapWindowContainerGetParentContainerFromItem(item) ;
-
- set_data = g_object_get_data(G_OBJECT(column_group), ITEM_FEATURE_SET_DATA) ;
- zMapAssert(set_data) ;
-
- style = zmapWindowItemFeatureSetStyleFromID(set_data, feature->style_id) ;
-
- if (!(bump_data->style_prop.bump_all) && bump_data->style_prop.style_id != feature->style_id)
- return ;
+ if (!(bump_data->bump_prop_data.bump_all) &&
+ !(bump_data->bump_prop_data.style_id == feature->style_id))
+ proceed = FALSE;
+ }
- /* x1, x2 always needed so might as well get y coords as well because foocanvas will have
- * calculated them anyway. */
- foo_canvas_item_get_bounds(item, &x1, &y1, &x2, &y2) ;
-
- switch (bump_mode)
+ if(proceed)
{
- case ZMAPBUMP_START_POSITION:
- {
- /* Bump features over if they have the same start coord. */
-
- y1_ptr = GINT_TO_POINTER((int)y1) ;
+ /* x1, x2 always needed so might as well get y coords as well because foocanvas will have
+ * calculated them anyway. */
+ foo_canvas_item_get_bounds(item, &x1, &y1, &x2, &y2) ;
- if (g_hash_table_lookup_extended(bump_data->pos_hash, y1_ptr, &key, &value))
+ switch (bump_mode)
+ {
+ case ZMAPBUMP_START_POSITION:
{
- offset = *(double *)value + bump_data->incr ;
+ /* Bump features over if they have the same start coord. */
- *(double *)value = offset ;
+ y1_ptr = GINT_TO_POINTER((int)y1) ;
+
+ if (g_hash_table_lookup_extended(bump_data->pos_hash, y1_ptr, &key, &value))
+ {
+ offset = *(double *)value + bump_data->incr ;
+
+ *(double *)value = offset ;
+ }
+ else
+ {
+ value = g_new(double, 1) ;
+ *(double *)value = offset ;
+
+ g_hash_table_insert(bump_data->pos_hash, y1_ptr, value) ;
+ }
+
+ break ;
}
- else
+ case ZMAPBUMP_OVERLAP:
{
- value = g_new(double, 1) ;
- *(double *)value = offset ;
+ /* Bump features over if they overlap at all. */
+ BumpColRange new_range ;
+
+ new_range = g_new0(BumpColRangeStruct, 1) ;
+ new_range->y1 = y1 ;
+ new_range->y2 = y2 ;
+ new_range->offset = 0.0 ;
+ new_range->incr = bump_data->incr ;
+
+ g_list_foreach(bump_data->pos_list, compareListOverlapCB, new_range) ;
+
+ bump_data->pos_list = g_list_append(bump_data->pos_list, new_range) ;
- g_hash_table_insert(bump_data->pos_hash, y1_ptr, value) ;
+ offset = new_range->offset ;
+
+ break ;
}
-
- break ;
- }
-
-
- case ZMAPBUMP_OVERLAP:
- {
- /* Bump features over if they overlap at all. */
- BumpColRange new_range ;
-
- new_range = g_new0(BumpColRangeStruct, 1) ;
- new_range->y1 = y1 ;
- new_range->y2 = y2 ;
- new_range->offset = 0.0 ;
- new_range->incr = bump_data->incr ;
-
- g_list_foreach(bump_data->pos_list, compareListOverlapCB, new_range) ;
-
- bump_data->pos_list = g_list_append(bump_data->pos_list, new_range) ;
-
- offset = new_range->offset ;
-
- break ;
- }
- case ZMAPBUMP_NAME:
- {
- /* Bump features that have the same name, i.e. are the same feature, so that each
- * vertical subcolumn is composed of just one feature in different positions. */
- ZMapFeature feature ;
-
- feature = (ZMapFeature)(g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA)) ;
-
- if (g_hash_table_lookup_extended(bump_data->pos_hash,
- GINT_TO_POINTER(feature->original_id), &key, &value))
+ case ZMAPBUMP_NAME:
{
- offset = *(double *)value ;
+ /* Bump features that have the same name, i.e. are the same feature, so that each
+ * vertical subcolumn is composed of just one feature in different positions. */
+ ZMapFeature feature ;
+
+ feature = (ZMapFeature)(g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA)) ;
+
+ if (g_hash_table_lookup_extended(bump_data->pos_hash,
+ GINT_TO_POINTER(feature->original_id), &key, &value))
+ {
+ offset = *(double *)value ;
+ }
+ else
+ {
+ offset = bump_data->offset ;
+
+ value = g_new(double, 1) ;
+ *(double *)value = offset ;
+
+ g_hash_table_insert(bump_data->pos_hash, GINT_TO_POINTER(feature->original_id), value) ;
+
+ bump_data->offset += bump_data->incr ;
+ }
+
+ break ;
}
- else
+ case ZMAPBUMP_UNBUMP:
+ case ZMAPBUMP_ALL:
{
offset = bump_data->offset ;
-
- value = g_new(double, 1) ;
- *(double *)value = offset ;
-
- g_hash_table_insert(bump_data->pos_hash, GINT_TO_POINTER(feature->original_id), value) ;
-
bump_data->offset += bump_data->incr ;
+
+ break ;
}
-
- break ;
- }
- case ZMAPBUMP_UNBUMP:
- case ZMAPBUMP_ALL:
- {
- offset = bump_data->offset ;
- bump_data->offset += bump_data->incr ;
-
- break ;
- }
- case ZMAPBUMP_NAVIGATOR:
- {
- /* Bump features over if they overlap at all. */
- BumpColRange new_range ;
-
- new_range = g_new0(BumpColRangeStruct, 1) ;
- new_range->y1 = y1 ;
- new_range->y2 = y2 ;
- new_range->offset = 0.0 ;
- new_range->incr = x2 - x1 + 1.0;//bump_data->incr ;
-
- g_list_foreach(bump_data->pos_list, compareListOverlapCB, new_range) ;
-
- bump_data->pos_list = g_list_append(bump_data->pos_list, new_range) ;
-
- offset = new_range->offset ;
-
- break ;
- }
- break;
- case ZMAPBUMP_ALTERNATING:
- {
- /* first time through ->offset == 0.0 this is where we need to draw _this_ feature.*/
- /* next time needs to be bumped to the next column (width of _this_ feature) */
- if((offset = bump_data->offset) == 0.0)
- bump_data->offset = x2 - x1 + 1.0;
- else
- bump_data->offset = 0.0; /* back to the first column */
- }
- break;
- default:
- zMapAssertNotReached() ;
- break ;
+ case ZMAPBUMP_NAVIGATOR:
+ {
+ /* Bump features over if they overlap at all. */
+ BumpColRange new_range ;
+
+ new_range = g_new0(BumpColRangeStruct, 1) ;
+ new_range->y1 = y1 ;
+ new_range->y2 = y2 ;
+ new_range->offset = 0.0 ;
+ new_range->incr = x2 - x1 + 1.0;
+
+ g_list_foreach(bump_data->pos_list, compareListOverlapCB, new_range) ;
+
+ bump_data->pos_list = g_list_append(bump_data->pos_list, new_range) ;
+
+ offset = new_range->offset ;
+
+ break ;
+ }
+ break;
+ case ZMAPBUMP_ALTERNATING:
+ {
+ /* first time through ->offset == 0.0 this is where we need to draw _this_ feature.*/
+ /* next time needs to be bumped to the next column (width of _this_ feature) */
+ if((offset = bump_data->offset) == 0.0)
+ bump_data->offset = x2 - x1 + 1.0;
+ else
+ bump_data->offset = 0.0; /* back to the first column */
+ }
+ break;
+ default:
+ zMapAssertNotReached() ;
+ break ;
+ } /* switch(bump_mode) */
+
}
- if (feature->type != ZMAPSTYLE_MODE_GRAPH)
+ if(proceed)
{
- /* Some features are drawn with different widths to indicate things like score. In this case
- * their offset needs to be corrected to place them centrally. (We always do this which
- * seems inefficient but its a toss up whether it would be quicker to test (dx == 0). */
- dx = (zMapStyleGetWidth(style) - (x2 - x1)) / 2 ;
- offset += dx ;
- }
-
- /* Not having something like this appears to be part of the cause of the oddness. Not all though */
- if (offset < 0.0)
- offset = 0.0;
-
- /* This does a item_get_bounds... don't we already have them?
- * Might be missing something though. Why doesn't the "Bump" bit calculate offsets? */
- my_foo_canvas_item_goto(item, &(offset), NULL) ;
-
+ if (feature->type != ZMAPSTYLE_MODE_GRAPH)
+ {
+ /* Some features are drawn with different widths to indicate things like score. In this case
+ * their offset needs to be corrected to place them centrally. (We always do this which
+ * seems inefficient but its a toss up whether it would be quicker to test (dx == 0). */
+ dx = (zMapStyleGetWidth(style) - (x2 - x1)) / 2 ;
+ offset += dx ;
+ }
+
+ /* Not having something like this appears to be part of the cause of the oddness. Not all though */
+ if (offset < 0.0)
+ offset = 0.0;
+
+ /* This does a item_get_bounds... don't we already have them?
+ * Might be missing something though. Why doesn't the "Bump" bit calculate offsets? */
+ my_foo_canvas_item_goto(item, &(offset), NULL) ;
+ }
return ;
}
-
/* GDestroyNotify() function for freeing the data part of a hash association. */
static void hashDataDestroyCB(gpointer data)
{
@@ -998,45 +966,6 @@ static void listDataDestroyCB(gpointer data, gpointer user_data)
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-static void printItem(FooCanvasItem *item, int indent, char *prefix)
-{
- int i ;
-
- for (i = 0 ; i < indent ; i++)
- {
- printf(" ") ;
- }
- printf("%s", prefix) ;
-
- zmapWindowPrintItemCoords(item) ;
-
- return ;
-}
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
-
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-/* UNUSED */
-static void addToList(gpointer data, gpointer user_data)
-{
- FooCanvasGroup *grp = FOO_CANVAS_GROUP(data);
- GList **list = (GList **)user_data;
- *list = g_list_append(*list, grp);
- return ;
-}
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
-
-
-
-
/*
* Functions for the complex bump...
*
@@ -1045,62 +974,16 @@ static void addToList(gpointer data, gpointer user_data)
* pointer itself.
*
*/
-
-/* Is called once for each item in a column and constructs a hash table in which each entry
- * is a list of all the features with the same name. */
-static void makeNameListCB(gpointer data, gpointer user_data)
+static void make_or_append_in_hash(GHashTable *name_hash, GQuark name_quark, FooCanvasItem *item)
{
- FooCanvasItem *item = (FooCanvasItem *)data ;
- ComplexBump complex = (ComplexBump)user_data ;
- GHashTable *name_hash = complex->name_hash ;
- ZMapWindowItemFeatureType item_feature_type ;
- ZMapFeature feature ;
gpointer key = NULL, value = NULL ;
GList **feature_list_ptr ;
GList *feature_list ;
- /* don't bother if something is not displayed. */
- if(!(zmapWindowItemIsShown(item)))
- return ;
-
- item_feature_type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(item), ITEM_FEATURE_TYPE)) ;
- zMapAssert(item_feature_type == ITEM_FEATURE_SIMPLE || item_feature_type == ITEM_FEATURE_PARENT) ;
-
- feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA) ;
- zMapAssert(feature) ;
-
- /* If we are not bumping all the features then only bump those for the specified style. */
- {
- FooCanvasGroup *column_group = NULL ;
- ZMapWindowItemFeatureSetData set_data ;
- ZMapFeatureTypeStyle style ;
-
- column_group = zmapWindowContainerGetParentContainerFromItem(item) ;
-
- set_data = g_object_get_data(G_OBJECT(column_group), ITEM_FEATURE_SET_DATA) ;
- zMapAssert(set_data) ;
-
- if (!(complex->bump_all) && complex->style_id != feature->style_id)
- return ;
-
- if(!complex->bump_all &&
- (style = zmapWindowItemFeatureSetStyleFromID(set_data, feature->style_id)))
- {
- /* Try doing this here.... */
- if (zMapStyleGetMode(style) == ZMAPSTYLE_MODE_ALIGNMENT
- && feature->feature.homol.type == ZMAPHOMOL_X_HOMOL)
- complex->protein = TRUE ;
- }
- }
-
-
-
-
-
/* If a list of features with this features name already exists in the hash then simply
* add this feature to it. Otherwise make a new entry in the hash. */
if (g_hash_table_lookup_extended(name_hash,
- GINT_TO_POINTER(feature->original_id), &key, &value))
+ GINT_TO_POINTER(name_quark), &key, &value))
{
feature_list_ptr = (GList **)value ;
@@ -1120,98 +1003,91 @@ static void makeNameListCB(gpointer data, gpointer user_data)
*feature_list_ptr = feature_list ;
- g_hash_table_insert(name_hash, GINT_TO_POINTER(feature->original_id), feature_list_ptr) ;
+ g_hash_table_insert(name_hash, GINT_TO_POINTER(name_quark), feature_list_ptr) ;
}
-
return ;
}
-
-
-static void makeNameListStrandedCB(gpointer data, gpointer user_data)
+static gboolean can_bump_item(FooCanvasItem *item, ComplexBump complex, ZMapFeature *feature_out)
{
- FooCanvasItem *item = (FooCanvasItem *)data ;
- ComplexBump complex = (ComplexBump)user_data ;
- GHashTable *name_hash = complex->name_hash ;
- ZMapWindowItemFeatureType item_feature_type ;
- ZMapFeature feature ;
- gpointer key = NULL, value = NULL ;
- GList **feature_list_ptr ;
- GList *feature_list ;
- char *feature_strand_name = NULL ;
- GQuark name_quark ;
+ gboolean bump_me = TRUE;
/* don't bother if something is not displayed. */
- if(!(zmapWindowItemIsShown(item)))
- return ;
-
- item_feature_type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(item), ITEM_FEATURE_TYPE)) ;
- zMapAssert(item_feature_type == ITEM_FEATURE_SIMPLE || item_feature_type == ITEM_FEATURE_PARENT) ;
-
- feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA) ;
- zMapAssert(feature) ;
-
- /* If we not bumping all features, then only bump the features who have the bumped style. */
- {
- FooCanvasGroup *column_group = NULL ;
- ZMapWindowItemFeatureSetData set_data ;
- ZMapFeatureTypeStyle style ;
+ if(zmapWindowItemIsShown(item))
+ {
+ ZMapWindowItemFeatureType item_feature_type ;
+ ZMapWindowItemFeatureSetData set_data ;
+ ZMapFeatureTypeStyle style ;
+ ZMapFeature feature ;
- column_group = zmapWindowContainerGetParentContainerFromItem(item) ;
+ item_feature_type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(item), ITEM_FEATURE_TYPE)) ;
+ zMapAssert(item_feature_type == ITEM_FEATURE_SIMPLE || item_feature_type == ITEM_FEATURE_PARENT) ;
+
+ feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA) ;
+ zMapAssert(feature) ;
+
+ set_data = complex->bump_properties->set_data;
+ style = zmapWindowStyleTableFind(set_data->style_table, feature->style_id) ;
- set_data = g_object_get_data(G_OBJECT(column_group), ITEM_FEATURE_SET_DATA) ;
- zMapAssert(set_data) ;
+ if ((!complex->bump_properties->bump_all) && (complex->bump_properties->style_id != feature->style_id))
+ bump_me = FALSE;
+
+ /* Try doing this here.... */
+ if((zMapStyleGetMode(style) == ZMAPSTYLE_MODE_ALIGNMENT) &&
+ (feature->feature.homol.type == ZMAPHOMOL_X_HOMOL))
+ complex->protein = TRUE ;
- if (!(complex->bump_all) && complex->style_id != feature->style_id)
- return ;
- if(!complex->bump_all &&
- (style = zmapWindowItemFeatureSetStyleFromID(set_data, feature->style_id)))
- {
- /* Try doing this here.... */
- if (zMapStyleGetMode(style) == ZMAPSTYLE_MODE_ALIGNMENT
- && feature->feature.homol.type == ZMAPHOMOL_X_HOMOL)
- complex->protein = TRUE ;
- }
- }
+ if(bump_me && feature_out)
+ *feature_out = feature;
+ }
+ else
+ bump_me = FALSE;
- /* Make a stranded name... */
- feature_strand_name = g_strdup_printf("%s-%s",
- g_quark_to_string(feature->original_id),
- (feature->strand == ZMAPSTRAND_NONE ? "none"
- : feature->strand == ZMAPSTRAND_FORWARD ? "+"
- : "-")) ;
- name_quark = g_quark_from_string(feature_strand_name) ;
+ return bump_me;
+}
+/* Is called once for each item in a column and constructs a hash table in which each entry
+ * is a list of all the features with the same name. */
+static void makeNameListCB(gpointer data, gpointer user_data)
+{
+ FooCanvasItem *item = (FooCanvasItem *)data ;
+ ComplexBump complex = (ComplexBump)user_data ;
+ GHashTable *name_hash = complex->name_hash ;
+ ZMapFeature feature ;
- /* If a list of features with this features name already exists in the hash then simply
- * add this feature to it. Otherwise make a new entry in the hash. */
- if (g_hash_table_lookup_extended(name_hash,
- GINT_TO_POINTER(name_quark), &key, &value))
- {
- feature_list_ptr = (GList **)value ;
+ if(!can_bump_item(item, complex, &feature))
+ return ;
- feature_list = *feature_list_ptr ;
+ make_or_append_in_hash(name_hash, feature->original_id, item);
- feature_list = g_list_append(feature_list, item) ;
+ return ;
+}
- *feature_list_ptr = feature_list ;
- }
- else
- {
- feature_list_ptr = (GList **)g_malloc0(sizeof(GList **)) ;
+static void makeNameListStrandedCB(gpointer data, gpointer user_data)
+{
+ FooCanvasItem *item = (FooCanvasItem *)data ;
+ ComplexBump complex = (ComplexBump)user_data ;
+ GHashTable *name_hash = complex->name_hash ;
+ ZMapFeature feature ;
+ GQuark name_quark ;
- feature_list = NULL ;
+ if(!can_bump_item(item, complex, &feature))
+ return ;
- feature_list = g_list_append(feature_list, item) ;
+ /* Make a stranded name... */
+ g_string_append_printf(complex->temp_buffer, "%s-%c",
+ g_quark_to_string(feature->original_id),
+ (feature->strand == ZMAPSTRAND_NONE ? '.'
+ : feature->strand == ZMAPSTRAND_FORWARD ? '+'
+ : '-')) ;
- *feature_list_ptr = feature_list ;
+ name_quark = g_quark_from_string(complex->temp_buffer->str) ;
- g_hash_table_insert(name_hash, GINT_TO_POINTER(name_quark), feature_list_ptr) ;
- }
+ make_or_append_in_hash(name_hash, name_quark, item);
- g_free(feature_strand_name) ;
+ g_string_truncate(complex->temp_buffer, 0);
return ;
@@ -1304,167 +1180,31 @@ static gboolean removeNameListsByRange(GList **names_list, int start, int end)
/* GFunc() to test whether a set of features overlaps the range given in user_data, sets
* TRUE when an overlap is detected. Features that don't ovelap are hidden. */
-static void testRangeCB(gpointer data, gpointer user_data)
-{
- FooCanvasItem *item = (FooCanvasItem *)data ;
- RangeData range_data = (RangeData)user_data ;
- ZMapFeature feature ;
-
- feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA) ;
- zMapAssert(feature) ;
-
- if (!(feature->x1 > range_data->end || feature->x2 < range_data->start))
- range_data->overlap = TRUE ;
-
- return ;
-}
-
-
-/* GFunc() to hide all items in a list. */
-static void hideItemsCB(gpointer data, gpointer user_data_unused)
-{
- FooCanvasItem *item = (FooCanvasItem *)data ;
-
- foo_canvas_item_hide(item) ;
-
- return ;
-}
-
-
-
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-/* UNUSED */
-/* GFunc() to add a background item to each set of items in a list. */
-static void addBackgrounds(gpointer data, gpointer user_data)
-{
- ComplexCol col_data = (ComplexCol)data ;
- GList **extras_ptr = (GList **)user_data ;
- GList *extra_items = *extras_ptr ;
- GList *name_list = col_data->feature_list ; /* Single list of named features. */
- GList *first, *last ;
- FooCanvasItem *first_item, *last_item, *background ;
- static gboolean colour_init = FALSE ;
- static GdkColor perfect, colinear, noncolinear ;
- char *perfect_colour = ZMAP_WINDOW_MATCH_PERFECT ;
- char *colinear_colour = ZMAP_WINDOW_MATCH_COLINEAR ;
- char *noncolinear_colour = ZMAP_WINDOW_MATCH_NOTCOLINEAR ;
- double x1, y1, x2, y2 ;
-
- if (!colour_init)
- {
- gdk_color_parse(perfect_colour, &perfect) ;
- gdk_color_parse(colinear_colour, &colinear) ;
- gdk_color_parse(noncolinear_colour, &noncolinear) ;
-
- colour_init = TRUE ;
- }
-
-
- /* SHOULD FILTER ON TYPE AS WELL...WE DON'T WANT ALL TYPES TO HAVE BACKGROUNDS....???? */
- if (g_list_length(name_list) > 1)
- {
- GList *backgrounds = NULL ;
- GList *list_item ;
- GQuark first_id = 0 ;
- ZMapFeatureTypeStyle first_style = NULL ;
- double mid, half_width = COLUMN_BACKGROUND_SPACING ;
-
- first = last = NULL ;
- list_item = g_list_first(name_list) ;
-
- while (list_item)
- {
- FooCanvasItem *item ;
- ZMapFeature feature ;
- GQuark feature_id = 0 ;
-
- item = (FooCanvasItem *)list_item->data ;
- feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA) ;
- zMapAssert(feature) ;
- feature_id = feature->original_id ;
-
- if (!first)
- {
- first = last = list_item ;
- first_item = (FooCanvasItem *)first->data ;
-
- /* N.B. this works because the items have already been positioned in the column. */
- foo_canvas_item_get_bounds(first_item, &x1, &y1, &x2, NULL) ;
- mid = (x2 + x1) * 0.5 ;
-
- first_id = feature_id ;
- first_style = feature->style ;
- list_item = g_list_next(list_item) ;
- }
- else
- {
- if (feature_id == first_id)
- {
- last = list_item ;
- list_item = g_list_next(list_item) ;
- }
-
- if (feature_id != first_id || !list_item)
- {
- /* Only do boxes where there is more than one item. */
- if (first != last)
- {
- ZMapWindowItemFeatureBumpData bump_data ;
-
- last_item = (FooCanvasItem *)last->data ;
-
- foo_canvas_item_get_bounds(last_item, NULL, NULL, NULL, &y2);
-
- bump_data = g_new0(ZMapWindowItemFeatureBumpDataStruct, 1) ;
- bump_data->first_item = first_item ;
- bump_data->feature_id = first_id ;
- bump_data->style = first_style ;
-
- background = zMapDrawBox(FOO_CANVAS_GROUP(first_item->parent),
- (mid - half_width), y1, (mid + half_width), y2,
- &perfect, &perfect, 0.0) ;
-
- zmapWindowLongItemCheck(col_data->window->long_items, background, y1, y2) ;
-
- extra_items = g_list_append(extra_items, background) ;
-
- g_object_set_data(G_OBJECT(background), ITEM_FEATURE_TYPE,
- GINT_TO_POINTER(ITEM_FEATURE_GROUP_BACKGROUND)) ;
- g_object_set_data(G_OBJECT(background), ITEM_FEATURE_BUMP_DATA, bump_data) ;
- g_signal_connect(GTK_OBJECT(background), "event",
- GTK_SIGNAL_FUNC(bumpBackgroundEventCB), col_data->window) ;
- g_signal_connect(GTK_OBJECT(background), "destroy",
- GTK_SIGNAL_FUNC(bumpBackgroundDestroyCB), col_data->window) ;
-
-
- /* Make sure these backgrounds are drawn behind the features items. */
- foo_canvas_item_lower_to_bottom(background) ;
-
- backgrounds = g_list_append(backgrounds, background) ;
- }
-
- /* N.B. ensure we don't move on in the list so that we pick up this item
- * as the next "first" item... */
- first = NULL ;
- }
+static void testRangeCB(gpointer data, gpointer user_data)
+{
+ FooCanvasItem *item = (FooCanvasItem *)data ;
+ RangeData range_data = (RangeData)user_data ;
+ ZMapFeature feature ;
- }
- }
+ feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA) ;
+ zMapAssert(feature) ;
+ if (!(feature->x1 > range_data->end || feature->x2 < range_data->start))
+ range_data->overlap = TRUE ;
- /* Need to add all backgrounds to col list here and lower them in group.... */
- name_list = g_list_concat(name_list, backgrounds) ;
+ return ;
+}
- col_data->feature_list = name_list ;
+/* GFunc() to hide all items in a list. */
+static void hideItemsCB(gpointer data, gpointer user_data_unused)
+{
+ FooCanvasItem *item = (FooCanvasItem *)data ;
- *extras_ptr = extra_items ;
- }
+ foo_canvas_item_hide(item) ;
return ;
}
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
/* Draw any items that have gaps but were drawn as a simple block as a series
@@ -1653,7 +1393,7 @@ static void removeNonColinearExtensions(gpointer data, gpointer user_data)
return ;
}
-
+//#ifdef RDS_COLLECTION_FEATURES_INSTEAD
/*
* There was/is a problem with this function. Before FooCanvasItems
* are mapped calling foo_canvas_item_get_bounds will return 0.0 for
@@ -1696,7 +1436,7 @@ static void NEWaddMultiBackgrounds(gpointer data, gpointer user_data)
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
ZMapWindowItemFeatureSetData set_data = (ZMapWindowItemFeatureSetData)user_data ;
GList *extra_items = set_data->extra_items ;
-
+ ZMapWindow window;
GList *name_list = col_data->feature_list ; /* Single list of named features. */
static gboolean colour_init = FALSE ;
static GdkColor perfect, colinear, noncolinear ;
@@ -1761,6 +1501,7 @@ static void NEWaddMultiBackgrounds(gpointer data, gpointer user_data)
half_width = width * 0.5 ;
col_data->width = width ;
+ window = col_data->bump_properties->window;
/* CODE HERE WORKS BUT IS NOT CORRECT IN THAT IT IS USING THE CANVAS BOX COORDS WHEN IT
* SHOULD BE USING THE FEATURE->X1/X2 COORDS...i'LL FIX IT LATER... */
@@ -1776,7 +1517,7 @@ static void NEWaddMultiBackgrounds(gpointer data, gpointer user_data)
incomplete = FALSE ;
if (curr_feature->feature.homol.y1 > curr_feature->feature.homol.y2)
{
- if (col_data->window->revcomped_features)
+ if (window->revcomped_features)
{
query_seq_end = 1 ;
align_end = curr_feature->feature.homol.y2 ;
@@ -1795,7 +1536,7 @@ static void NEWaddMultiBackgrounds(gpointer data, gpointer user_data)
}
else
{
- if (col_data->window->revcomped_features)
+ if (window->revcomped_features)
{
query_seq_end = curr_feature->feature.homol.length ;
align_end = curr_feature->feature.homol.y2 ;
@@ -1835,11 +1576,11 @@ static void NEWaddMultiBackgrounds(gpointer data, gpointer user_data)
box_end = curr_y1 + 10 ;
box_colour = &noncolinear ;
- background = makeMatchItem(col_data->window->long_items,
+ background = makeMatchItem(window->long_items,
FOO_CANVAS_GROUP(item->parent), ZMAPDRAW_OBJECT_BOX,
mid - 1, box_start,
mid + 1, box_end,
- box_colour, bump_data, col_data->window) ;
+ box_colour, bump_data, window) ;
backgrounds = g_list_append(backgrounds, background) ;
@@ -1851,7 +1592,7 @@ static void NEWaddMultiBackgrounds(gpointer data, gpointer user_data)
prev_feature = curr_feature ;
prev_id = curr_feature->original_id ;
- if (col_data->window->revcomped_features)
+ if (window->revcomped_features)
prev_end = curr_feature->feature.homol.y1 ;
else
prev_end = curr_feature->feature.homol.y2 ;
@@ -1881,7 +1622,7 @@ static void NEWaddMultiBackgrounds(gpointer data, gpointer user_data)
curr_y1 = curr_feature->x1 + 1;
curr_y2 = curr_feature->x2;
- if (col_data->window->revcomped_features)
+ if (window->revcomped_features)
curr_start = curr_feature->feature.homol.y2 ;
else
curr_start = curr_feature->feature.homol.y1 ;
@@ -1904,7 +1645,7 @@ static void NEWaddMultiBackgrounds(gpointer data, gpointer user_data)
/* Checks that adjacent matches do not overlap and then checks for colinearity.
* Note that matches are most likely to overlap where a false end to an HSP has been made. */
- colinearity = featureHomolIsColinear(col_data->window, col_data->match_threshold,
+ colinearity = featureHomolIsColinear(window, col_data->bump_properties->match_threshold,
prev_feature, curr_feature) ;
if (colinearity != COLINEAR_INVALID)
@@ -1931,10 +1672,10 @@ static void NEWaddMultiBackgrounds(gpointer data, gpointer user_data)
/* Make line... */
- background = makeMatchItem(col_data->window->long_items,
+ background = makeMatchItem(window->long_items,
FOO_CANVAS_GROUP(item->parent), ZMAPDRAW_OBJECT_LINE,
mid, real_start, mid, real_end,
- box_colour, bump_data, col_data->window) ;
+ box_colour, bump_data, window) ;
extra_items = g_list_append(extra_items, background) ;
@@ -1948,11 +1689,11 @@ static void NEWaddMultiBackgrounds(gpointer data, gpointer user_data)
bump_data->feature_id = prev_id ;
bump_data->style = prev_style ;
- background = makeMatchItem(col_data->window->long_items,
+ background = makeMatchItem(window->long_items,
FOO_CANVAS_GROUP(item->parent), ZMAPDRAW_OBJECT_BOX,
(mid - half_width), real_start, (mid + half_width), real_end,
NULL,
- bump_data, col_data->window) ;
+ bump_data, window) ;
extra_items = g_list_append(extra_items, background) ;
@@ -1965,7 +1706,7 @@ static void NEWaddMultiBackgrounds(gpointer data, gpointer user_data)
prev_feature = curr_feature ;
prev_id = curr_feature->original_id ;
- if (col_data->window->revcomped_features)
+ if (window->revcomped_features)
prev_end = curr_feature->feature.homol.y1 ;
else
prev_end = curr_feature->feature.homol.y2 ;
@@ -1984,9 +1725,10 @@ static void NEWaddMultiBackgrounds(gpointer data, gpointer user_data)
/* Mark start/end of final feature if its incomplete. */
incomplete = FALSE ;
+
if (prev_feature->feature.homol.y1 > prev_feature->feature.homol.y2)
{
- if (col_data->window->revcomped_features)
+ if (window->revcomped_features)
{
query_seq_end = prev_feature->feature.homol.length ;
align_end = prev_feature->feature.homol.y1 ;
@@ -2006,7 +1748,7 @@ static void NEWaddMultiBackgrounds(gpointer data, gpointer user_data)
}
else
{
- if (col_data->window->revcomped_features)
+ if (window->revcomped_features)
{
query_seq_end = 1 ;
align_end = prev_feature->feature.homol.y1 ;
@@ -2044,11 +1786,11 @@ static void NEWaddMultiBackgrounds(gpointer data, gpointer user_data)
mid = end_x1 + ((end_x2 - end_x1) / 2) ;
box_colour = &noncolinear ;
- background = makeMatchItem(col_data->window->long_items,
+ background = makeMatchItem(window->long_items,
FOO_CANVAS_GROUP(item->parent), ZMAPDRAW_OBJECT_BOX,
mid - 1, box_start,
mid + 1, box_end,
- box_colour, bump_data, col_data->window) ;
+ box_colour, bump_data, window) ;
backgrounds = g_list_append(backgrounds, background) ;
@@ -2070,7 +1812,6 @@ static void NEWaddMultiBackgrounds(gpointer data, gpointer user_data)
-
static FooCanvasItem *makeMatchItem(ZMapWindowLongItems long_items,
FooCanvasGroup *parent, ZMapDrawObjectType shape,
double x1, double y1, double x2, double y2,
@@ -2106,6 +1847,7 @@ static FooCanvasItem *makeMatchItem(ZMapWindowLongItems long_items,
return match_item ;
}
+//#endif /* RDS_COLLECTION_FEATURES_INSTEAD */
static void freeExtraItems(gpointer data, gpointer user_data_unused)
@@ -2214,70 +1956,6 @@ static void listScoreCB(gpointer data, gpointer user_data)
}
-
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-/* UNUSED */
-/* GCompareFunc() to sort two lists of features by the overall span of all their features. */
-static gint sortBySpanCB(gconstpointer a, gconstpointer b)
-{
- gint result = 0 ; /* make a == b default. */
- GList **feature_list_out_1 = (GList **)a ;
- GList *feature_list_1 = *feature_list_out_1 ; /* Single list of named features. */
- GList **feature_list_out_2 = (GList **)b ;
- GList *feature_list_2 = *feature_list_out_2 ; /* Single list of named features. */
- FooCanvasItem *item ;
- ZMapWindowItemFeatureType item_feature_type ;
- ZMapFeature feature ;
- int list_span_1 = 0, list_span_2 = 0 ;
-
-
- feature_list_1 = g_list_first(feature_list_1) ;
- item = (FooCanvasItem *)feature_list_1->data ;
- item_feature_type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(item), ITEM_FEATURE_TYPE)) ;
- zMapAssert(item_feature_type == ITEM_FEATURE_SIMPLE || item_feature_type == ITEM_FEATURE_PARENT) ;
- feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA) ;
- zMapAssert(feature) ;
- list_span_1 = feature->x1 ;
-
- feature_list_1 = g_list_last(feature_list_1) ;
- item = (FooCanvasItem *)feature_list_1->data ;
- item_feature_type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(item), ITEM_FEATURE_TYPE)) ;
- zMapAssert(item_feature_type == ITEM_FEATURE_SIMPLE || item_feature_type == ITEM_FEATURE_PARENT) ;
- feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA) ;
- zMapAssert(feature) ;
- list_span_1 = feature->x1 - list_span_1 + 1 ;
-
-
- feature_list_2 = g_list_first(feature_list_2) ;
- item = (FooCanvasItem *)feature_list_2->data ;
- item_feature_type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(item), ITEM_FEATURE_TYPE)) ;
- zMapAssert(item_feature_type == ITEM_FEATURE_SIMPLE || item_feature_type == ITEM_FEATURE_PARENT) ;
- feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA) ;
- zMapAssert(feature) ;
- list_span_2 = feature->x1 ;
-
- feature_list_2 = g_list_last(feature_list_2) ;
- item = (FooCanvasItem *)feature_list_2->data ;
- item_feature_type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(item), ITEM_FEATURE_TYPE)) ;
- zMapAssert(item_feature_type == ITEM_FEATURE_SIMPLE || item_feature_type == ITEM_FEATURE_PARENT) ;
- feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA) ;
- zMapAssert(feature) ;
- list_span_2 = feature->x1 - list_span_2 + 1 ;
-
- /* Highest spans go first. */
- if (list_span_1 > list_span_2)
- result = -1 ;
- else if (list_span_1 < list_span_2)
- result = 1 ;
-
- return result ;
-}
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
-
/* GCompareFunc() to sort two lists of features by strand and then the overall span of all their features. */
static gint sortByStrandSpanCB(gconstpointer a, gconstpointer b)
{
@@ -2513,48 +2191,28 @@ static void bestFitCB(gpointer data, gpointer user_data)
return ;
}
-
-
-
-
-
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-/* GFunc() to return a features span. */
-static void listSpanCB(gpointer data, gpointer user_data)
+static ComplexCol ComplexBumpComplexColCreate(ComplexBump complex, GList *name_list)
{
- FooCanvasItem *item = (FooCanvasItem *)data ;
- double span = *((double *)user_data) ;
+ ComplexCol col = NULL;
- /* don't bother if something is not displayed. */
- if((zmapWindowItemIsShown(item)))
+ if((col = g_new0(ComplexColStruct, 1)))
{
- ZMapWindowItemFeatureType item_feature_type ;
- ZMapFeature feature ;
+ double max_width = 0.0 ;
- /* Sanity checks... */
- item_feature_type = GPOINTER_TO_INT(g_object_get_data(G_OBJECT(item), ITEM_FEATURE_TYPE)) ;
- zMapAssert(item_feature_type == ITEM_FEATURE_SIMPLE || item_feature_type == ITEM_FEATURE_PARENT) ;
+ col->bump_properties = complex->bump_properties;
+ col->offset = complex->curr_offset ;
+ col->feature_list = name_list ;
- feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA) ;
- zMapAssert(feature) ;
-
- /* Can only compare by span if features have a span... */
- if (feature->flags.has_score)
- {
- score += feature->score ;
-
- *((double *)user_data) = score ;
- }
+ g_list_foreach(name_list, getMaxWidth, &max_width) ;
+
+ complex->bumpcol_list = g_list_append(complex->bumpcol_list, col) ;
+ complex->curr_offset += max_width ;
}
+ else
+ zMapLogCritical("%s", "Failed to allocate");
- return ;
+ return col;
}
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
-
/* GFunc() to try to combine lists of features, if the lists have any overlapping features,
* then the new list must be placed at a new offset in the column. */
@@ -2573,22 +2231,7 @@ static void setOffsetCB(gpointer data, gpointer user_data)
if (!complex->bumpcol_list
|| zMap_g_list_cond_foreach(complex->bumpcol_list, featureListCB, &feature_data))
{
- ComplexCol col ;
- double max_width = 0.0 ;
-
- g_list_foreach(name_list, getMaxWidth, &max_width) ;
-
- col = g_new0(ComplexColStruct, 1) ;
- col->window = complex->window ;
- col->column_group = complex->column_group ;
- col->set_data = complex->set_data ;
- col->offset = complex->curr_offset ;
- col->feature_list = name_list ;
-
- complex->bumpcol_list = g_list_append(complex->bumpcol_list, col) ;
-
- complex->curr_offset += max_width ;
-
+ ComplexBumpComplexColCreate(complex, name_list);
}
return ;
@@ -2604,7 +2247,6 @@ static gboolean featureListCB(gpointer data, gpointer user_data)
FeatureData feature_data = (FeatureData)user_data ;
GList *name_list = *(feature_data->name_list) ;
-
if (!(feature_data->overlap_func)(col->feature_list, name_list))
{
col->feature_list = g_list_concat(col->feature_list, name_list) ;
@@ -2629,57 +2271,7 @@ static void setAllOffsetCB(gpointer data, gpointer user_data)
GList *name_list = *name_list_ptr ; /* Single list of named features. */
ComplexBump complex = (ComplexBump)user_data ;
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- FeatureDataStruct feature_data ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- feature_data.name_list = &name_list ;
- feature_data.overlap_func = complex->overlap_func ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
- /* If theres already a list of columns then try to add this set of name features to one of them
- * otherwise create a new column. */
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- if (!complex->bumpcol_list
- || zMap_g_list_cond_foreach(complex->bumpcol_list, feature2ListCB, &feature_data))
- {
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
- ComplexCol col ;
- double max_width = 0.0 ;
-
- g_list_foreach(name_list, getMaxWidth, &max_width) ;
-
-
- col = g_new0(ComplexColStruct, 1) ;
- col->window = complex->window ;
- col->column_group = complex->column_group ;
- col->set_data = complex->set_data ;
- col->offset = complex->curr_offset ;
- col->feature_list = name_list ;
-
- complex->bumpcol_list = g_list_append(complex->bumpcol_list, col) ;
-
-
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- complex->curr_offset += complex->incr ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
- complex->curr_offset += max_width ;
-
-
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- }
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
+ ComplexBumpComplexColCreate(complex, name_list);
return ;
}
@@ -2761,34 +2353,6 @@ static void getMaxWidth(gpointer data, gpointer user_data)
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-/* Check to see if two lists overlap, if they don't then merge the two lists.
- * NOTE that this is non-destructive merge, features are not moved from one list to the
- * other, see the glib docs for _list_concat(). */
-static gboolean featureList2CB(gpointer data, gpointer user_data)
-{
- gboolean call_again = TRUE ;
- ComplexCol col = (ComplexCol)data ;
- FeatureData feature_data = (FeatureData)user_data ;
- GList *name_list = *(feature_data->name_list) ;
-
-
- if (!(feature_data->overlap_func)(col->feature_list, name_list))
- {
- col->feature_list = g_list_concat(col->feature_list, name_list) ;
-
- /* Having done the merge we _must_ resort the list by position otherwise subsequent
- * overlap tests will fail. */
- col->feature_list = zmapWindowItemSortByPostion(col->feature_list) ;
-
- call_again = FALSE ;
- }
-
- return call_again ;
-}
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
@@ -2936,8 +2500,16 @@ static void reverseOffsets(GList *bumpcol_list)
return ;
}
+static void reparentItemCB(gpointer data, gpointer user_data)
+{
+#ifdef RDS_NO
+ ComplexCol col_data = (ComplexCol)user_data;
-
+ zMapWindowCollectionFeatureStaticReparent(ZMAP_CANVAS_ITEM(data),
+ ZMAP_CANVAS_ITEM(col_data->parent_item));
+#endif
+ return ;
+}
/* These two callbacks go through the list of lists of features moving all their canvas items
* into the correct place within their columns. */
@@ -2945,7 +2517,37 @@ static void moveItemsCB(gpointer data, gpointer user_data)
{
ComplexCol col_data = (ComplexCol)data ;
- g_list_foreach(col_data->feature_list, moveItemCB, col_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);
+ }
+ }
return ;
}
@@ -2958,27 +2560,34 @@ static void moveItemCB(gpointer data, gpointer user_data)
ZMapFeature feature ;
double dx = 0.0, offset = 0.0 ;
double x1 = 0.0, x2 = 0.0, y1 = 0.0, y2 = 0.0 ;
+ double width, spacing;
ZMapFeatureTypeStyle style ;
feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA) ;
zMapAssert(feature) ;
/* Get hold of the style. */
- style = zmapWindowItemFeatureSetStyleFromID(col_data->set_data, feature->style_id) ;
+ style = zmapWindowItemFeatureSetStyleFromID(col_data->bump_properties->set_data, feature->style_id) ;
/* x1, x2 always needed so might as well get y coords as well because foocanvas will have
* calculated them anyway. */
foo_canvas_item_get_bounds(item, &x1, &y1, &x2, &y2) ;
+ zMapStyleGet(style,
+ ZMAPSTYLE_PROPERTY_BUMP_SPACING, &spacing,
+ ZMAPSTYLE_PROPERTY_WIDTH, &width,
+ NULL);
+
/* Some features are drawn with different widths to indicate things like score. In this case
* their offset needs to be corrected to place them centrally. (We always do this which
* seems inefficient but its a toss up whether it would be quicker to test (dx == 0). */
- dx = ((zMapStyleGetWidth(style) * COMPLEX_BUMP_COMPRESS) - (x2 - x1)) / 2 ;
+ dx = (((width) * COMPLEX_BUMP_COMPRESS) - (x2 - x1)) / 2 ;
offset = col_data->offset + dx ;
my_foo_canvas_item_goto(item, &offset, NULL) ;
+
return ;
}
@@ -2996,31 +2605,6 @@ static void setStyleBumpCB(ZMapFeatureTypeStyle style, gpointer user_data)
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-/* UNUSED */
-static gint compareNameToColumn(gconstpointer list_data, gconstpointer user_data)
-{
- gint result = -1 ;
- FooCanvasGroup *col_group = (FooCanvasGroup *)list_data ;
- GQuark col_name = GPOINTER_TO_INT(user_data) ;
- ZMapFeatureSet feature_set ;
-
- /* We can have empty columns with no feature set so maynot be able to get feature set name.... */
- if ((feature_set = (ZMapFeatureSet)g_object_get_data(G_OBJECT(col_group), ITEM_FEATURE_DATA)))
- {
- if (feature_set->unique_id == col_name)
- result = 0 ;
- }
-
- return result ;
-}
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
-
-
-
/*
* Functions to draw as "normal" (i.e. not read frame) the frame sensitive columns
* from the canvas.
@@ -3398,8 +2982,10 @@ static GList *removeNonColinear(GList *first_list_item, ZMapGListDirection direc
curr_feature = tmp ;
}
- colinearity = featureHomolIsColinear(bump_data->window, bump_data->style_prop.match_threshold,
+ colinearity = featureHomolIsColinear(bump_data->bump_prop_data.window,
+ bump_data->bump_prop_data.match_threshold,
prev_feature, curr_feature) ;
+
if (colinearity == COLINEAR_INVALID || colinearity == COLINEAR_NOT)
still_colinear = FALSE ;
@@ -3605,41 +3191,6 @@ gboolean featureHomolIsTruncated(ZMapWindow window, ZMapFeature feature, gboolea
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-/* We don't have enough state in the styles when it comes to bump mode.
- * Here I wanted to get the initial bump mode from the style as I don't
- * want to unbump the transcripts. */
-static ZMapStyleBumpMode hack_initial_mode(ZMapFeatureTypeStyle style)
-{
- ZMapStyleBumpMode initial_mode = ZMAPBUMP_UNBUMP;
- ZMapStyleMode style_mode = ZMAPSTYLE_MODE_INVALID;
-
- style_mode = zMapStyleGetMode(style);
-
- switch(style_mode)
- {
- case ZMAPSTYLE_MODE_TRANSCRIPT:
- initial_mode = zMapStyleGetBumpMode(style);
- break;
- case ZMAPSTYLE_MODE_INVALID:
- case ZMAPSTYLE_MODE_BASIC:
- case ZMAPSTYLE_MODE_ALIGNMENT:
- case ZMAPSTYLE_MODE_RAW_SEQUENCE:
- case ZMAPSTYLE_MODE_PEP_SEQUENCE:
- case ZMAPSTYLE_MODE_TEXT:
- case ZMAPSTYLE_MODE_GRAPH:
- case ZMAPSTYLE_MODE_GLYPH:
- case ZMAPSTYLE_MODE_META:
- default:
- initial_mode = ZMAPBUMP_UNBUMP;
- break;
- }
-
- return initial_mode;
-}
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
static void invoke_bump_to_initial(FooCanvasGroup *container, FooCanvasPoints *points,
ZMapContainerLevelType level, gpointer user_data)
{
@@ -3656,16 +3207,7 @@ static void invoke_bump_to_initial(FooCanvasGroup *container, FooCanvasPoints *p
current_mode = zmapWindowItemFeatureSetGetBumpMode(set_data);
default_mode = zmapWindowItemFeatureSetGetDefaultBumpMode(set_data);
-#warning DISCUSS_WITH_ED
-#warning NEED_INITIAL_BUMP_MODE
-#ifdef CHECK_THIS_OUT
- initial_mode = hack_initial_mode(style);
-#endif
-
- /* Probably need to zmapWIndowItemFeatureSetHackInitialBumpModes(set_data); */
-
-#warning HACKED_FOR_NOW_TRANSCRIPTS_WILL_UNBUMP_TOO
- initial_mode = current_mode;
+ initial_mode = default_mode;
zmapWindowColumnBumpRange(FOO_CANVAS_ITEM(container), initial_mode, ZMAPWINDOW_COMPRESS_ALL);
}
--
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