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Commit 90e9ed95 authored by edgrif's avatar edgrif
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Add code to match highlighting code to show if start and/or end of a set of HSP's is truncated.

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src/zmapWindow/zmapWindowDraw.c
+ 357
− 22
View file @ 90e9ed95
......@@ -28,9 +28,9 @@
*
* Exported functions: See zmapWindow_P.h
* HISTORY:
* Last edited: Dec 15 07:34 2006 (edgrif)
* Last edited: Dec 21 14:55 2006 (edgrif)
* Created: Thu Sep 8 10:34:49 2005 (edgrif)
* CVS info: $Id: zmapWindowDraw.c,v 1.51 2006-12-15 09:19:49 edgrif Exp $
* CVS info: $Id: zmapWindowDraw.c,v 1.52 2006-12-21 14:57:43 edgrif Exp $
*-------------------------------------------------------------------
*/
......@@ -172,7 +172,14 @@ static void makeNameListCB(gpointer data, gpointer user_data) ;
static void setOffsetCB(gpointer data, gpointer user_data) ;
static void sortListPosition(gpointer data, gpointer user_data) ;
static void addBackgrounds(gpointer data, gpointer user_data) ;
static void addMultiBackgrounds(gpointer data, gpointer user_data) ;
static void NEWaddMultiBackgrounds(gpointer data, gpointer user_data) ;
static FooCanvasItem *makeMatchItem(FooCanvasGroup *parent,
double x1, double y1, double x2, double y2,
GdkColor *colour, gpointer item_data, gpointer event_data) ;
static gboolean listsOverlap(GList *curr_features, GList *new_features) ;
static gboolean listsOverlapNoInterleave(GList *curr_features, GList *new_features) ;
static void reverseOffsets(GList *bumpcol_list) ;
......@@ -564,7 +571,13 @@ void zmapWindowColumnBump(FooCanvasItem *column_item, ZMapStyleOverlapMode bump_
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
g_list_foreach(complex.bumpcol_list, addBackgrounds, &set_data->extra_items) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
g_list_foreach(complex.bumpcol_list, addMultiBackgrounds, &set_data->extra_items) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
g_list_foreach(complex.bumpcol_list, NEWaddMultiBackgrounds, &set_data->extra_items) ;
}
/* Clear up. */
......@@ -797,7 +810,7 @@ void zmapWindowDrawZoom(ZMapWindow window)
/* Some features have different widths according to their score, this helps annotators
* gage whether something like an alignment is worth taking notice of.
* guage whether something like an alignment is worth taking notice of.
*
* Currently we only implement the algorithm given by acedb's Score_by_width but it maybe
* that we will need to do others to support their display.
......@@ -1616,6 +1629,249 @@ static void addBackgrounds(gpointer data, gpointer user_data)
}
/* GFunc() to add background items indicating goodness of match to each set of items in a list.
*
* THIS FUNCTION HAS SOME HARD CODED STUFF AND QUITE A BIT OF CODE THAT CAN BE REFACTORED TO
* SIMPLIFY THINGS, I'VE CHECKED IT IN NOW BECAUSE I WANT IT TO BE IN CVS OVER XMAS.
*
* */
static void NEWaddMultiBackgrounds(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. */
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 ;
GList *backgrounds = NULL ;
GList *list_item ;
double mid, half_width = COLUMN_BACKGROUND_SPACING ;
FooCanvasItem *item ;
FooCanvasItem *background ;
ZMapFeature prev_feature = NULL, curr_feature = NULL ;
ZMapFeatureTypeStyle prev_style = NULL, curr_style = NULL ;
GQuark prev_id = 0, curr_id = 0 ;
int prev_end = 0, curr_start = 0 ;
double x1, prev_y1, x2, prev_y2, curr_y1, curr_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 ;
}
/* Get the first item. */
list_item = g_list_first(name_list) ;
item = (FooCanvasItem *)list_item->data ;
foo_canvas_item_get_bounds(item, &x1, &curr_y1, &x2, &curr_y2) ;
curr_feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA) ;
zMapAssert(curr_feature) ;
curr_id = curr_feature->original_id ;
curr_style = curr_feature->style ;
/* Calculate mid point of this column of matches from the first item,
* N.B. this works because the items have already been positioned in the column. */
mid = (x2 + x1) * 0.5 ;
/* 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... */
do
{
unsigned int match_threshold ;
GdkColor *box_colour ;
ZMapWindowItemFeatureBumpData bump_data ;
int start, end ;
/* mark start of curr item if its incomplete. */
if (curr_feature->type == ZMAPFEATURE_ALIGNMENT)
{
if (curr_feature->feature.homol.y1 > curr_feature->feature.homol.y2)
{
start = curr_feature->feature.homol.y2 ;
end = curr_feature->feature.homol.y1 ;
}
else
{
start = curr_feature->feature.homol.y1 ;
end = curr_feature->feature.homol.y2 ;
}
if (start > 1)
{
bump_data = g_new0(ZMapWindowItemFeatureBumpDataStruct, 1) ;
bump_data->feature_id = curr_id ;
bump_data->style = curr_style ;
box_colour = &noncolinear ;
background = makeMatchItem(FOO_CANVAS_GROUP(item->parent),
(mid - (3 * half_width)), curr_y1,
(mid + (3 * half_width)), (curr_y1 + 10),
box_colour, bump_data, col_data->window) ;
backgrounds = g_list_append(backgrounds, background) ;
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
zmapWindowLongItemCheck(col_data->window->long_items, background, curr_y2, curr_y1) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
extra_items = g_list_append(extra_items, background) ;
}
}
/* make curr in to prev item */
prev_feature = curr_feature ;
prev_id = curr_feature->original_id ;
prev_end = curr_feature->feature.homol.y2 ;
prev_style = curr_feature->style ;
prev_y2 = curr_y2 ;
/* Mark in between matches for their colinearity. */
while ((list_item = g_list_next(list_item)))
{
/* get new curr item */
item = (FooCanvasItem *)list_item->data ;
foo_canvas_item_get_bounds(item, NULL, &curr_y1, NULL, &curr_y2);
curr_feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA) ;
zMapAssert(curr_feature) ;
curr_id = curr_feature->original_id ;
curr_start = curr_feature->feature.homol.y1 ;
curr_style = curr_feature->style ;
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
printf("%s : %d, %d\n", g_quark_to_string(feature->original_id), feature->x1, feature->x2) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
/* We only do aligns (remember that there can be different types in a single col)
* and only those for which joining of homols was requested. */
if (curr_feature->type != ZMAPFEATURE_ALIGNMENT
|| !(zMapStyleGetJoinAligns(curr_style, &match_threshold)))
continue ;
/* If we've changed to a new match then break, otherwise mark for colinearity. */
if (curr_id != prev_id)
break ;
else
{
int diff ;
/* Peverse stuff...only draw the box if the matches do not overlap, it can happen
* that there can be overlapping matches for a single piece of evidence....sigh... */
if (curr_y1 > prev_y2)
{
bump_data = g_new0(ZMapWindowItemFeatureBumpDataStruct, 1) ;
bump_data->feature_id = prev_id ;
bump_data->style = prev_style ;
diff = abs(prev_end - curr_start) ;
if (diff > match_threshold)
{
if (curr_start < prev_end)
box_colour = &noncolinear ;
else
box_colour = &colinear ;
}
else
box_colour = &perfect ;
background = makeMatchItem(FOO_CANVAS_GROUP(item->parent),
(mid - half_width), prev_y2, (mid + half_width), curr_y1,
box_colour, bump_data, col_data->window) ;
zmapWindowLongItemCheck(col_data->window->long_items, background, prev_y2, curr_y1) ;
extra_items = g_list_append(extra_items, background) ;
/* Make sure these backgrounds are drawn behind the feature items. */
foo_canvas_item_lower_to_bottom(background) ;
backgrounds = g_list_append(backgrounds, background) ;
}
/* make curr into prev */
prev_feature = curr_feature ;
prev_id = curr_feature->original_id ;
prev_end = curr_feature->feature.homol.y2 ;
prev_style = curr_feature->style ;
prev_y2 = curr_y2 ;
}
}
/* mark end of prev item if premature ending. */
if (curr_feature->type == ZMAPFEATURE_ALIGNMENT)
{
if (prev_feature->feature.homol.y1 > prev_feature->feature.homol.y2)
{
start = prev_feature->feature.homol.y2 ;
end = prev_feature->feature.homol.y1 ;
printf("found one\n") ;
}
else
{
start = prev_feature->feature.homol.y1 ;
end = prev_feature->feature.homol.y2 ;
}
if (end < prev_feature->feature.homol.length)
{
bump_data = g_new0(ZMapWindowItemFeatureBumpDataStruct, 1) ;
bump_data->feature_id = prev_feature->original_id ;
bump_data->style = prev_feature->style ;
box_colour = &noncolinear ;
background = makeMatchItem(FOO_CANVAS_GROUP(item->parent),
(mid - (3 * half_width)), (prev_y2 - 10),
(mid + (3 * half_width)), prev_y2,
box_colour, bump_data, col_data->window) ;
backgrounds = g_list_append(backgrounds, background) ;
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
zmapWindowLongItemCheck(col_data->window->long_items, background, prev_y1, (prev_y1 + 10)) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
extra_items = g_list_append(extra_items, background) ;
}
}
} while (list_item) ;
/* Need to add all backgrounds to col list here and lower them in group.... */
name_list = g_list_concat(name_list, backgrounds) ;
col_data->feature_list = name_list ;
*extras_ptr = extra_items ;
return ;
}
/* GFunc() to add background items indicating goodness of match to each set of items in a list. */
static void addMultiBackgrounds(gpointer data, gpointer user_data)
{
......@@ -1629,6 +1885,7 @@ static void addMultiBackgrounds(gpointer data, gpointer user_data)
char *colinear_colour = ZMAP_WINDOW_MATCH_COLINEAR ;
char *noncolinear_colour = ZMAP_WINDOW_MATCH_NOTCOLINEAR ;
if (!colour_init)
{
gdk_color_parse(perfect_colour, &perfect) ;
......@@ -1639,7 +1896,7 @@ static void addMultiBackgrounds(gpointer data, gpointer user_data)
}
/* No point in doing lists that are only 1 long.... */
/* No point in doing lists that are only 1 long....actually not true if we want to mark start/end.... */
if (g_list_length(name_list) > 1)
{
GList *backgrounds = NULL ;
......@@ -1650,7 +1907,7 @@ static void addMultiBackgrounds(gpointer data, gpointer user_data)
int prev_end = 0, curr_start = 0 ;
FooCanvasItem *item ;
FooCanvasItem *background ;
ZMapFeature feature ;
ZMapFeature prev_feature, feature ;
GQuark prev_id = 0, curr_id = 0 ;
......@@ -1659,7 +1916,7 @@ static void addMultiBackgrounds(gpointer data, gpointer user_data)
item = (FooCanvasItem *)list_item->data ;
foo_canvas_item_get_bounds(item, &x1, &prev_y1, &x2, &prev_y2) ;
feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA) ;
prev_feature = feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA) ;
zMapAssert(feature) ;
prev_id = feature->original_id ;
prev_end = feature->feature.homol.y2 ;
......@@ -1679,6 +1936,8 @@ static void addMultiBackgrounds(gpointer data, gpointer user_data)
if ((list_item = g_list_next(list_item)))
{
unsigned int match_threshold ;
GdkColor *box_colour ;
ZMapWindowItemFeatureBumpData bump_data ;
item = (FooCanvasItem *)list_item->data ;
......@@ -1687,13 +1946,10 @@ static void addMultiBackgrounds(gpointer data, gpointer user_data)
feature = g_object_get_data(G_OBJECT(item), ITEM_FEATURE_DATA) ;
zMapAssert(feature) ;
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
printf("%s : %d, %d\n", g_quark_to_string(feature->original_id), feature->x1, feature->x2) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
curr_id = feature->original_id ;
curr_style = feature->style ;
......@@ -1705,17 +1961,82 @@ static void addMultiBackgrounds(gpointer data, gpointer user_data)
if (curr_id != prev_id)
{
int start, end ;
if (prev_feature->feature.homol.y1 > prev_feature->feature.homol.y2)
{
start = prev_feature->feature.homol.y2 ;
end = prev_feature->feature.homol.y1 ;
}
else
{
start = prev_feature->feature.homol.y1 ;
end = prev_feature->feature.homol.y2 ;
}
if (end < prev_feature->feature.homol.length)
{
bump_data = g_new0(ZMapWindowItemFeatureBumpDataStruct, 1) ;
bump_data->feature_id = prev_id ;
bump_data->style = prev_style ;
box_colour = &noncolinear ;
background = makeMatchItem(FOO_CANVAS_GROUP(item->parent),
(mid - (3 * half_width)), (prev_y2 - 10),
(mid + (3 * half_width)), prev_y2,
box_colour, bump_data, col_data->window) ;
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
zmapWindowLongItemCheck(col_data->window->long_items, background, prev_y2, curr_y1) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
extra_items = g_list_append(extra_items, background) ;
}
prev_feature = feature ;
prev_id = curr_id ;
prev_style = curr_style ;
prev_y2 = curr_y2 ;
prev_end = feature->feature.homol.y2 ;
curr_id = 0 ;
if (feature->feature.homol.y1 > feature->feature.homol.y2)
{
start = feature->feature.homol.y2 ;
end = feature->feature.homol.y1 ;
printf("found one\n") ;
}
else
{
start = feature->feature.homol.y1 ;
end = feature->feature.homol.y2 ;
}
if (start > 1)
{
bump_data = g_new0(ZMapWindowItemFeatureBumpDataStruct, 1) ;
bump_data->feature_id = feature->original_id ;
bump_data->style = feature->style ;
box_colour = &noncolinear ;
background = makeMatchItem(FOO_CANVAS_GROUP(item->parent),
(mid - (3 * half_width)), curr_y1,
(mid + (3 * half_width)), (curr_y1 + 10),
box_colour, bump_data, col_data->window) ;
#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
zmapWindowLongItemCheck(col_data->window->long_items, background, prev_y2, curr_y1) ;
#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
extra_items = g_list_append(extra_items, background) ;
}
}
else
{
ZMapWindowItemFeatureBumpData bump_data ;
GdkColor *box_colour ;
int diff ;
curr_start = feature->feature.homol.y1 ;
......@@ -1739,22 +2060,14 @@ static void addMultiBackgrounds(gpointer data, gpointer user_data)
else
box_colour = &perfect ;
background = zMapDrawBox(FOO_CANVAS_GROUP(item->parent),
(mid - half_width), prev_y2, (mid + half_width), curr_y1,
box_colour, box_colour, 0.0) ;
background = makeMatchItem(FOO_CANVAS_GROUP(item->parent),
(mid - half_width), prev_y2, (mid + half_width), curr_y1,
box_colour, bump_data, col_data->window) ;
zmapWindowLongItemCheck(col_data->window->long_items, background, prev_y2, curr_y1) ;
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 feature items. */
foo_canvas_item_lower_to_bottom(background) ;
......@@ -1781,6 +2094,28 @@ static void addMultiBackgrounds(gpointer data, gpointer user_data)
}
static FooCanvasItem *makeMatchItem(FooCanvasGroup *parent,
double x1, double y1, double x2, double y2,
GdkColor *colour,
gpointer item_data, gpointer event_data)
{
FooCanvasItem *match_item ;
match_item = zMapDrawBox(parent,
x1, y1, x2, y2,
colour, colour, 0.0) ;
g_object_set_data(G_OBJECT(match_item), ITEM_FEATURE_TYPE,
GINT_TO_POINTER(ITEM_FEATURE_GROUP_BACKGROUND)) ;
g_object_set_data(G_OBJECT(match_item), ITEM_FEATURE_BUMP_DATA, item_data) ;
g_signal_connect(GTK_OBJECT(match_item), "event",
GTK_SIGNAL_FUNC(bumpBackgroundEventCB), event_data) ;
g_signal_connect(GTK_OBJECT(match_item), "destroy",
GTK_SIGNAL_FUNC(bumpBackgroundDestroyCB), event_data) ;
return match_item ;
}
static void freeExtraItems(gpointer data, gpointer user_data_unused)
{
......
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