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Commit e38fdbfe authored by edgrif's avatar edgrif
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fix bugs in 'incomplete alignment' markers.

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src/zmapWindow/items/zmapWindowCollectionFeature.c
+ 101
− 182
View file @ e38fdbfe
......@@ -27,9 +27,9 @@
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Aug 28 09:12 2009 (edgrif)
* Last edited: Jan 27 13:55 2010 (edgrif)
* Created: Wed Dec 3 10:02:22 2008 (rds)
* CVS info: $Id: zmapWindowCollectionFeature.c,v 1.12 2010-01-11 16:50:20 mh17 Exp $
* CVS info: $Id: zmapWindowCollectionFeature.c,v 1.13 2010-01-27 14:00:19 edgrif Exp $
*-------------------------------------------------------------------
*/
......@@ -41,6 +41,8 @@
#include <zmapWindowLongItem.h>
typedef enum {FIRST_MATCH, LAST_MATCH} MatchType ;
typedef struct
{
ZMapWindowCanvasItem parent;
......@@ -92,10 +94,9 @@ static double get_glyph_mid_point(FooCanvasItem *item, double glyph_width,
double *x2_out, double *y2_out);
static void group_remove(gpointer data, gpointer user_data);
static void add_colinear_lines(gpointer data, gpointer user_data);
static gboolean first_match_incomplete(ZMapFeature curr_feature,
gboolean revcomped_features);
static gboolean last_match_incomplete(ZMapFeature prev_feature,
gboolean revcomped_features);
static void markMatchIfIncomplete(ZMapWindowCanvasItem collection,
ZMapStrand ref_strand, MatchType match_type,
FooCanvasItem *item, ZMapFeature feature) ;
static gboolean fragments_splice(char *fragment_a, char *fragment_b);
static void process_feature(ZMapFeature prev_feature);
......@@ -290,99 +291,44 @@ ZMapStyleGlyphType zmapWindowCanvasItemGetGlyph(ZMapWindowCanvasItem collection)
void zMapWindowCollectionFeatureAddIncompleteMarkers(ZMapWindowCanvasItem collection,
gboolean revcomped_features)
{
// char *noncolinear_colour = ZMAP_WINDOW_MATCH_NOTCOLINEAR ;
FooCanvasGroup *group;
GdkColor *marker_fill=NULL,*marker_draw=NULL,*marker_border=NULL;
GdkColor fill,outline;
double width;
gboolean incomplete ;
ZMapStyleGlyphType glyph_style; // = ZMAP_GLYPH_ITEM_STYLE_DIAMOND;
ZMapFeatureTypeStyle style;
glyph_style = zmapWindowCanvasItemGetGlyph(collection); // get from style, default to previous hard coded value ('6')
group = FOO_CANVAS_GROUP(collection);
/* mark start of curr item if its incomplete. */
incomplete = FALSE ;
/* From style? */
style = (ZMAP_CANVAS_ITEM_GET_CLASS(collection)->get_style)(collection);
if(!zMapStyleGetColoursGlyphDefault(style,&marker_fill,&marker_draw,&marker_border))
{
gdk_color_parse("red",&fill);
gdk_color_parse("black",&outline);
marker_fill = &fill;
marker_border = &outline;
}
if(group->item_list)
if ((group = FOO_CANVAS_GROUP(collection)) && (group->item_list))
{
ZMapWindowCanvasItem canvas_item;
FooCanvasItem *first_item, *last_item;
ZMapFeature curr_feature;
width = 6.0;
ZMapWindowCanvasItem canvas_item ;
FooCanvasItem *first_item, *last_item ;
ZMapFeature first_feature, last_feature ;
ZMapStrand ref_strand ;
/* Assume that match is forward so first match is first item, last match is last item. */
first_item = FOO_CANVAS_ITEM(group->item_list->data);
canvas_item = ZMAP_CANVAS_ITEM(first_item);
curr_feature = canvas_item->feature;
incomplete = first_match_incomplete(curr_feature, revcomped_features);
if (incomplete)
{
double x_coord, y_coord;
x_coord = get_glyph_mid_point(first_item, width,
NULL, &y_coord, NULL, NULL);
y_coord = ceil(y_coord); /* line_thickness */
y_coord = curr_feature->x1 - ((FooCanvasGroup *)collection)->ypos - 1.0; /* Ext2Zero */
foo_canvas_item_new(FOO_CANVAS_GROUP(collection->items[WINDOW_ITEM_OVERLAY]),
zMapWindowGlyphItemGetType(),
"x", x_coord,
"y", y_coord,
"width", width,
"height", width,
"glyph_style", glyph_style,
"line_width", 1,
"fill_color_gdk", marker_fill,
"outline_color_gdk", marker_border,
NULL);
}
first_feature = canvas_item->feature;
last_item = FOO_CANVAS_ITEM(group->item_list_end->data);
canvas_item = ZMAP_CANVAS_ITEM(last_item);
curr_feature = canvas_item->feature;
incomplete = last_match_incomplete(curr_feature, revcomped_features);
last_feature = canvas_item->feature;
/* Now we have a feature we can retrieve which strand of the reference sequence the
* alignment is to. */
ref_strand = first_feature->strand ;
if(incomplete)
/* If the alignment is to the reverse strand of the reference sequence then swop first and last. */
if (ref_strand == ZMAPSTRAND_REVERSE)
{
double x_coord, y_coord;
x_coord = get_glyph_mid_point(last_item, width,
NULL, NULL, NULL, &y_coord);
y_coord = floor(y_coord); /* line_thickness */
y_coord = curr_feature->x2 - ((FooCanvasGroup *)collection)->ypos;
if(((FooCanvasGroup *)(collection->items[WINDOW_ITEM_OVERLAY]))->ypos != 0.0)
g_warning("non zero group!");
foo_canvas_item_new(FOO_CANVAS_GROUP(collection->items[WINDOW_ITEM_OVERLAY]),
zMapWindowGlyphItemGetType(),
"x", x_coord,
"y", y_coord,
"width", width,
"height", width,
"glyph_style", glyph_style,
"line_width", 1,
"fill_color_gdk", marker_fill,
"outline_color_gdk", marker_border,
NULL);
last_item = FOO_CANVAS_ITEM(group->item_list->data);
canvas_item = ZMAP_CANVAS_ITEM(last_item);
last_feature = canvas_item->feature;
first_item = FOO_CANVAS_ITEM(group->item_list_end->data);
canvas_item = ZMAP_CANVAS_ITEM(first_item);
first_feature = canvas_item->feature;
}
/* If either the first or last match features are truncated then add the incomplete marker. */
markMatchIfIncomplete(collection, ref_strand, FIRST_MATCH, first_item, first_feature) ;
markMatchIfIncomplete(collection, ref_strand, LAST_MATCH, last_item, last_feature) ;
}
......@@ -489,6 +435,18 @@ void zMapWindowCollectionFeatureAddSpliceMarkers(ZMapWindowCanvasItem collection
return ;
}
/*
* Internal routines.
*/
static FooCanvasItem *zmap_window_collection_feature_add_interval(ZMapWindowCanvasItem collection,
ZMapFeatureSubPartSpan unused,
double top, double bottom,
......@@ -846,125 +804,86 @@ static void add_colinear_lines(gpointer data, gpointer user_data)
}
static gboolean first_match_incomplete(ZMapFeature curr_feature,
gboolean revcomped_features)
{
gboolean incomplete = FALSE;
int query_seq_end, align_end ;
/* THIS NEEDS CHANGING TOOO.......y1 < y2 ALWAYS....FROM NOW ON.... */
/* Mark a first or last feature in a series of alignment features as incomplete.
* The first feature is incomplete if it's start > 1, the last is incomplete
* if it's end < homol_length.
*
* Code is complicated by markers/coord testing needing to be reversed for
* alignments to reverse strand. */
static void markMatchIfIncomplete(ZMapWindowCanvasItem collection,
ZMapStrand ref_strand, MatchType match_type,
FooCanvasItem *item, ZMapFeature feature)
{
int start, end ;
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
if (curr_feature->feature.homol.y1 > curr_feature->feature.homol.y2)
if (match_type == FIRST_MATCH)
{
if (revcomped_features)
{
query_seq_end = 1 ;
align_end = curr_feature->feature.homol.y2 ;
if (query_seq_end < align_end)
incomplete = TRUE ;
}
else
{
query_seq_end = curr_feature->feature.homol.length ;
align_end = curr_feature->feature.homol.y1 ;
if (query_seq_end > align_end)
incomplete = TRUE ;
}
start = 1 ;
end = feature->feature.homol.y1 ;
}
else
{
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
if (revcomped_features)
{
query_seq_end = curr_feature->feature.homol.length ;
align_end = curr_feature->feature.homol.y2 ;
if (query_seq_end > align_end)
incomplete = TRUE ;
}
else
{
query_seq_end = 1 ;
align_end = curr_feature->feature.homol.y1 ;
if (query_seq_end < align_end)
incomplete = TRUE ;
}
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
start = feature->feature.homol.y2 ;
end = feature->feature.homol.length ;
}
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
return incomplete;
}
static gboolean last_match_incomplete(ZMapFeature prev_feature,
gboolean revcomped_features)
{
gboolean incomplete = FALSE;
int query_seq_end, align_end ;
if (start < end)
{
double x_coord, y_coord, y_coord_start, y_coord_end ;
double width = 6.0 ;
GdkColor *marker_fill=NULL,*marker_draw=NULL,*marker_border=NULL ;
GdkColor fill,outline ;
ZMapStyleGlyphType glyph_style ;
ZMapFeatureTypeStyle style ;
/* THIS NEEDS CHANGING TOO !!! */
/* get from style, default to previous hard coded value ('6') */
glyph_style = zmapWindowCanvasItemGetGlyph(collection);
/* From style? */
style = (ZMAP_CANVAS_ITEM_GET_CLASS(collection)->get_style)(collection) ;
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
if (prev_feature->feature.homol.y1 > prev_feature->feature.homol.y2)
{
if (revcomped_features)
if (!zMapStyleGetColoursGlyphDefault(style,&marker_fill,&marker_draw,&marker_border))
{
query_seq_end = prev_feature->feature.homol.length ;
align_end = prev_feature->feature.homol.y1 ;
if (query_seq_end > align_end)
incomplete = TRUE ;
gdk_color_parse("red", &fill) ;
gdk_color_parse("black", &outline) ;
marker_fill = &fill ;
marker_border = &outline ;
}
else
{
query_seq_end = 1 ;
align_end = prev_feature->feature.homol.y2 ;
if (query_seq_end < align_end)
incomplete = TRUE ;
}
}
else
{
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
if (revcomped_features)
x_coord = get_glyph_mid_point(item, width,
NULL, &y_coord_start, NULL, &y_coord_end) ;
if ((match_type == FIRST_MATCH && ref_strand == ZMAPSTRAND_FORWARD)
|| (match_type == LAST_MATCH && ref_strand == ZMAPSTRAND_REVERSE))
{
query_seq_end = 1 ;
align_end = prev_feature->feature.homol.y1 ;
if (query_seq_end < align_end)
incomplete = TRUE ;
y_coord = ceil(y_coord_start); /* line_thickness */
y_coord = feature->x1 - ((FooCanvasGroup *)collection)->ypos - 1.0 ; /* Ext2Zero */
}
else
{
query_seq_end = prev_feature->feature.homol.length ;
align_end = prev_feature->feature.homol.y2 ;
if (query_seq_end > align_end)
incomplete = TRUE ;
y_coord = floor(y_coord_end); /* line_thickness */
y_coord = feature->x2 - ((FooCanvasGroup *)collection)->ypos;
}
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
foo_canvas_item_new(FOO_CANVAS_GROUP(collection->items[WINDOW_ITEM_OVERLAY]),
zMapWindowGlyphItemGetType(),
"x", x_coord,
"y", y_coord,
"width", width,
"height", width,
"glyph_style", glyph_style,
"line_width", 1,
"fill_color_gdk", marker_fill,
"outline_color_gdk", marker_border,
NULL);
}
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
return incomplete;
return ;
}
static gboolean fragments_splice(char *fragment_a, char *fragment_b)
{
gboolean splice = FALSE;
......
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