From a60c633569cda8d6ef061a99c38735cbdc11a38c Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Thu, 29 Jul 2010 10:17:37 +0000
Subject: [PATCH] fix whole load of coord problems with displaying peptides.
fix memory free bug. Add missing deselect calls.
---
.../items/zmapWindowSequenceFeature.c | 267 ++++++++++++------
.../items/zmapWindowSequenceFeature.h | 20 +-
.../items/zmapWindowSequenceFeature_I.h | 27 +-
3 files changed, 203 insertions(+), 111 deletions(-)
diff --git a/src/zmapWindow/items/zmapWindowSequenceFeature.c b/src/zmapWindow/items/zmapWindowSequenceFeature.c
index 20136fedb..baf8af2db 100755
--- a/src/zmapWindow/items/zmapWindowSequenceFeature.c
+++ b/src/zmapWindow/items/zmapWindowSequenceFeature.c
@@ -22,30 +22,29 @@
*
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk,
- * Malcolm Hinsley (Sanger Institute, UK) mh17@sanger.ac.uk
+ * Malcolm Hinsley (Sanger Institute, UK) mh17@sanger.ac.uk
*
- * Description:
+ * Description: Function/methods for object representing either a
+ * DNA or a Peptide sequence. Handles display, coords,
+ * highlighting.
*
- * Exported functions: See XXXXXXXXXXXXX.h
+ * Exported functions: See zmapWindowSequenceFeature.h
* HISTORY:
- * Last edited: Feb 16 10:07 2010 (edgrif)
+ * Last edited: Jul 29 11:15 2010 (edgrif)
* Created: Fri Jun 12 10:01:17 2009 (rds)
- * CVS info: $Id: zmapWindowSequenceFeature.c,v 1.12 2010-06-14 15:40:18 mh17 Exp $
+ * CVS info: $Id: zmapWindowSequenceFeature.c,v 1.13 2010-07-29 10:17:37 edgrif Exp $
*-------------------------------------------------------------------
*/
#include <ZMap/zmap.h>
-
-
-
-
-
-
#include <ZMap/zmapPeptide.h>
+#include <ZMap/zmapSequence.h>
#include <zmapWindowSequenceFeature_I.h>
#include <zmapWindowSequenceFeatureCMarshal.h>
#include <zmapWindowTextItem.h>
+
+
enum
{
PROP_0,
@@ -57,8 +56,6 @@ enum
PROP_FLOAT_MAX_Y,
PROP_FLOAT_AXIS,
-
-
PROP_LAST,
};
@@ -120,7 +117,6 @@ static double zmap_window_sequence_feature_point (FooCanvasItem *item,
#ifdef RDS_DONT_INCLUDE
static void zmap_window_sequence_feature_destroy (GtkObject *gtkobject);
#endif /* RDS_DONT_INCLUDE */
-
static gboolean zmap_window_sequence_feature_selected_signal(ZMapWindowSequenceFeature sequence_feature,
int text_first_char, int text_final_char);
@@ -137,21 +133,30 @@ static gboolean feature_exons_world2canvas_text(ZMapFeature feature,
FooCanvasItem *item,
GList **list_out) ;
static void get_detailed_exons(gpointer exon_data, gpointer user_data) ;
-static char *zMapFeatureTranscriptTranslation(ZMapFeature feature, int *length) ;
-static char *zMapFeatureTranslation(ZMapFeature feature, int *length) ;
static ZMapFullExon zmapExonCreate(void) ;
+static void exonListFree(gpointer data, gpointer user_data_unused) ;
static void zmapExonDestroy(ZMapFullExon exon) ;
-static FooCanvasItemClass *canvas_parent_class_G;
-static FooCanvasItemClass *group_parent_class_G;
+static char *zMapFeatureTranscriptTranslation(ZMapFeature feature, int *length) ;
+static char *zMapFeatureTranslation(ZMapFeature feature, int *length) ;
+
+static void coordsDNA2Pep(ZMapFeature feature, int *start_inout, int *end_inout) ;
+/* globals. */
+static FooCanvasItemClass *canvas_parent_class_G ;
+static FooCanvasItemClass *group_parent_class_G ;
+/*
+ * External interface.
+ */
+
+
GType zMapWindowSequenceFeatureGetType(void)
{
static GType group_type = 0;
@@ -180,18 +185,24 @@ GType zMapWindowSequenceFeatureGetType(void)
return group_type;
}
+
/*
- * \brief highlight/select the DNA
+ * highlight/select the DNA/Peptide
*/
+
+/* Highlight sequence corresponding to supplied feature, frame is needed for */
gboolean zMapWindowSequenceFeatureSelectByFeature(ZMapWindowSequenceFeature sequence_feature,
- ZMapFeature seed_feature,
- int select_flags_ignored_atm)
+ ZMapFeature seed_feature)
{
FooCanvasGroup *sequence_group;
GList *list;
gboolean result = TRUE;
+ ZMapWindowCanvasItem canvas_item ;
+ ZMapFeature feature ;
- sequence_group = FOO_CANVAS_GROUP(sequence_feature);
+ sequence_group = FOO_CANVAS_GROUP(sequence_feature) ;
+ canvas_item = ZMAP_CANVAS_ITEM(sequence_feature) ;
+ feature = canvas_item->feature ;
if ((list = sequence_group->item_list))
{
@@ -199,7 +210,7 @@ gboolean zMapWindowSequenceFeatureSelectByFeature(ZMapWindowSequenceFeature sequ
{
ZMapWindowTextItem text_item = (ZMapWindowTextItem)(list->data) ;
- /* There should only ever be one iteration here! */
+ /* There should only ever be one iteration here! UMMMM, SO WHY THIS COMMENT ?? */
switch(seed_feature->type)
{
case ZMAPSTYLE_MODE_TRANSCRIPT:
@@ -210,23 +221,36 @@ gboolean zMapWindowSequenceFeatureSelectByFeature(ZMapWindowSequenceFeature sequ
feature_exons_world2canvas_text(seed_feature, TRUE, NULL, &exon_list);
-
deselect = TRUE ; /* 1st time deselect any existing
highlight. */
event = FALSE ;
+
exon_list_member = g_list_first(exon_list);
do
{
+ int start, end ;
+
current_exon = (ZMapFullExon)(exon_list_member->data) ;
+ start = current_exon->exon_span.x1 ;
+ end = current_exon->exon_span.x2 ;
+
+ if (feature->type == ZMAPSTYLE_MODE_PEP_SEQUENCE)
+ coordsDNA2Pep(feature, &start, &end) ;
+
zMapWindowTextItemSelect(text_item,
- current_exon->exon_span.x1, current_exon->exon_span.x2,
+ start, end,
deselect, deselect) ;
deselect = FALSE ;
}
while((exon_list_member = g_list_next(exon_list_member)));
+ /* Free exons...?? */
+ g_list_foreach(exon_list, exonListFree, NULL) ;
+ g_list_free(exon_list) ;
+
+
break ;
}
@@ -234,8 +258,16 @@ gboolean zMapWindowSequenceFeatureSelectByFeature(ZMapWindowSequenceFeature sequ
{
if (ZMAP_IS_WINDOW_TEXT_ITEM(list->data))
{
+ int start, end ;
+
+ start = seed_feature->x1 ;
+ end = seed_feature->x2 ;
+
+ if (feature->type == ZMAPSTYLE_MODE_PEP_SEQUENCE)
+ coordsDNA2Pep(feature, &start, &end) ;
+
zMapWindowTextItemSelect(text_item,
- seed_feature->x1, seed_feature->x2,
+ start, end,
TRUE, TRUE) ;
}
break;
@@ -248,24 +280,26 @@ gboolean zMapWindowSequenceFeatureSelectByFeature(ZMapWindowSequenceFeature sequ
return result;
}
+
+/* Highlight a region in the sequence object, coord_type specifies whether region_start/end are
+ * sequence or peptide coords. */
gboolean zMapWindowSequenceFeatureSelectByRegion(ZMapWindowSequenceFeature sequence_feature,
- int region_start, int region_end,
- int select_flags_ignored_atm)
+ ZMapSequenceType coord_type, int region_start, int region_end)
{
- FooCanvasGroup *sequence_group;
- GList *list;
- gboolean result = TRUE;
+ gboolean result = TRUE ;
+ FooCanvasGroup *sequence_group ;
+ GList *list ;
- sequence_group = FOO_CANVAS_GROUP(sequence_feature);
- foo_canvas_item_request_update((FooCanvasItem *)sequence_feature);
+ sequence_group = FOO_CANVAS_GROUP(sequence_feature);
if((list = sequence_group->item_list))
{
do
{
- /* There should only ever be one iteration here! */
- if(ZMAP_IS_WINDOW_TEXT_ITEM(list->data))
+ /* There should only ever be one iteration here! IS THIS BECAUSE THERE SHOULD ONLY BE
+ ONE TEXT ITEM ???? */
+ if (ZMAP_IS_WINDOW_TEXT_ITEM(list->data))
{
ZMapWindowTextItem text_item = (ZMapWindowTextItem)(list->data);
@@ -277,10 +311,36 @@ gboolean zMapWindowSequenceFeatureSelectByRegion(ZMapWindowSequenceFeature seque
while((list = list->next));
}
- return result;
+ return result ;
}
+gboolean zMapWindowSequenceDeSelect(ZMapWindowSequenceFeature sequence_feature)
+{
+ gboolean result = FALSE;
+ FooCanvasGroup *sequence_group ;
+ GList *list ;
+
+ sequence_group = FOO_CANVAS_GROUP(sequence_feature);
+
+ if((list = sequence_group->item_list))
+ {
+ do
+ {
+ /* There should only ever be one iteration here! IS THIS BECAUSE THERE SHOULD ONLY BE
+ ONE TEXT ITEM ???? */
+ if (ZMAP_IS_WINDOW_TEXT_ITEM(list->data))
+ {
+ ZMapWindowTextItem text_item = (ZMapWindowTextItem)(list->data);
+
+ zMapWindowTextItemDeselect(text_item, TRUE) ;
+ }
+ }
+ while((list = list->next));
+ }
+
+ return result;
+}
static gboolean feature_exons_world2canvas_text(ZMapFeature feature,
@@ -336,11 +396,12 @@ static gboolean feature_exons_world2canvas_text(ZMapFeature feature,
/* In case there are no exons */
result = full_data.result;
- if(result && full_data.phase_length < full_data.cds_coord_counter)
+ if (result && full_data.phase_length < full_data.cds_coord_counter)
{
ZMapFullExon last_exon;
GList *last;
- if((last = g_list_last(*(full_data.full_exons))))
+
+ if ((last = g_list_last(*(full_data.full_exons))))
{
char *updated_pep;
last_exon = (ZMapFullExon)(last->data);
@@ -376,8 +437,7 @@ static void get_detailed_exons(gpointer exon_data, gpointer user_data)
/* chop out the correct bit of sequence */
- if(!(tr_start > exon_span->x2 ||
- tr_end < exon_span->x1))
+ if (!(tr_start > exon_span->x2 || tr_end < exon_span->x1))
{
/* translate able exon i.e. not whole UTR exon. */
int pep_start, pep_length, phase_length;
@@ -387,14 +447,14 @@ static void get_detailed_exons(gpointer exon_data, gpointer user_data)
ex1 = exon_span->x1;
ex2 = exon_span->x2;
- if(ex1 < tr_start)
+ if (ex1 < tr_start)
{
/* exon is part utr */
ex1 = tr_start;
if(feature->feature.transcript.flags.start_not_found)
full_exon->phase = (feature->feature.transcript.start_phase - 1);
}
- else if(ex1 == tr_start)
+ else if (ex1 == tr_start)
{
if(feature->feature.transcript.flags.start_not_found)
full_exon->phase = (feature->feature.transcript.start_phase - 1);
@@ -406,7 +466,7 @@ static void get_detailed_exons(gpointer exon_data, gpointer user_data)
coord_length = (ex2 - ex1 + 1);
- if(ex2 > tr_end)
+ if (ex2 > tr_end)
{
/* exon is part utr */
ex2 = tr_end;
@@ -414,7 +474,9 @@ static void get_detailed_exons(gpointer exon_data, gpointer user_data)
coord_length = (ex2 - ex1 + 1);
}
else
- full_exon->end_phase = (full_exon->phase + coord_length) % 3;
+ {
+ full_exon->end_phase = (full_exon->phase + coord_length) % 3 ;
+ }
start = full_data->cds_coord_counter + 1;
full_exon->cds_span.x1 = start;
@@ -449,10 +511,7 @@ static void get_detailed_exons(gpointer exon_data, gpointer user_data)
full_exon->peptide = NULL;
}
-
-
- *(full_data->full_exons) = g_list_append(*(full_data->full_exons),
- full_exon);
+ *(full_data->full_exons) = g_list_append(*(full_data->full_exons), full_exon) ;
/* what more can we do? */
full_data->result = TRUE;
@@ -543,6 +602,20 @@ static ZMapFullExon zmapExonCreate(void)
return exon ;
}
+
+/* A GFunc() callback to free each exon element of the exons list. */
+static void exonListFree(gpointer data, gpointer user_data_unused)
+{
+ ZMapFullExon exon = (ZMapFullExon)data ;
+
+ zmapExonDestroy(exon) ;
+
+ return ;
+}
+
+
+
+
static void zmapExonDestroy(ZMapFullExon exon)
{
zMapAssert(exon);
@@ -598,8 +671,9 @@ static gboolean sequence_feature_selection_proxy_cb(ZMapWindowTextItem text,
current_index = index2 + first_char_index;
/* this is needed to fix up what is probably unavoidable from the text item... [-ve coords] */
- if(origin_index < 1)
+ if (origin_index < 1)
origin_index = 1;
+
/* this is needed to fix up what is probably unavoidable from the text item... [too long coords] */
if(current_index > feature->feature.sequence.length)
current_index = feature->feature.sequence.length;
@@ -621,12 +695,6 @@ static FooCanvasItem *zmap_window_sequence_feature_add_interval(ZMapWindowCanvas
FooCanvasItem *item = NULL;
ZMapFeatureTypeStyle style;
ZMapFeature feature;
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- /* NO....BREAKS EVERYTHING....FONT FOUND BUT NOT MONOSPACE.... */
- char *font_name = "Lucida Console";
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
char *font_name = "monospace" ;
@@ -637,8 +705,6 @@ static FooCanvasItem *zmap_window_sequence_feature_add_interval(ZMapWindowCanvas
-
-
group = FOO_CANVAS_GROUP(sequence);
if (!(group->item_list))
@@ -649,17 +715,6 @@ static FooCanvasItem *zmap_window_sequence_feature_add_interval(ZMapWindowCanvas
feature = sequence->feature ;
style = (ZMAP_CANVAS_ITEM_GET_CLASS(sequence)->get_style)(sequence) ;
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- /* I'm not at all too sure this is a great idea...allowing fonts other than
- * monospace breaks everything so where's the value in allowing this flexibility.
- * We would need to check it was monospace and then default to monospace if it wasn't. */
- g_object_get(G_OBJECT(style),
- "text-font", &tmp_font,
- NULL);
- if (tmp_font != NULL)
- font_name = tmp_font ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
item = foo_canvas_item_new(group, ZMAP_TYPE_WINDOW_TEXT_ITEM,
"x", left,
"y", top,
@@ -672,16 +727,15 @@ static FooCanvasItem *zmap_window_sequence_feature_add_interval(ZMapWindowCanvas
/* Selection highlighting takes its colour from the style "select" fill colour. */
zMapStyleGetColours(style, STYLE_PROP_COLOURS, ZMAPSTYLE_COLOURTYPE_SELECTED,
&fill, &draw, &border) ;
+
if (fill)
g_object_set(G_OBJECT(item),
"select-color-gdk", fill,
NULL) ;
-
g_signal_connect(G_OBJECT(item), "text-selected",
G_CALLBACK(sequence_feature_selection_proxy_cb),
sequence);
-
}
return item;
@@ -692,7 +746,7 @@ static void zmap_window_sequence_feature_bounds (FooCanvasItem *item,
double *x2, double *y2)
{
- if(canvas_parent_class_G->bounds)
+ if (canvas_parent_class_G->bounds)
(canvas_parent_class_G->bounds)(item, x1, y1, x2, y2);
return ;
@@ -784,7 +838,7 @@ static void zmap_window_sequence_feature_class_init (ZMapWindowSequenceFeatureC
return ;
}
-static void zmap_window_sequence_feature_init (ZMapWindowSequenceFeature sequence)
+static void zmap_window_sequence_feature_init(ZMapWindowSequenceFeature sequence)
{
ZMapWindowCanvasItem canvas_item;
FooCanvasItem *item;
@@ -901,13 +955,15 @@ static void invoke_zeroing_update(gpointer item_data, gpointer unused_data)
return ;
}
-static void zmap_window_sequence_feature_update (FooCanvasItem *item,
- double i2w_dx, double i2w_dy,
- int flags)
+static void zmap_window_sequence_feature_update(FooCanvasItem *item,
+ double i2w_dx, double i2w_dy,
+ int flags)
{
ZMapWindowSequenceFeature seq_feature;
FooCanvasItem *parent;
FooCanvasGroup *group;
+ ZMapWindowCanvasItem canvas_item ;
+ ZMapFeature feature ;
double x1, x2, y1, y2;
double xpos, ypos;
double scr_x1, scr_y1, scr_x2, scr_y2;
@@ -915,6 +971,9 @@ static void zmap_window_sequence_feature_update (FooCanvasItem *item,
seq_feature = ZMAP_WINDOW_SEQUENCE_FEATURE(item);
group = FOO_CANVAS_GROUP (item);
+ canvas_item = ZMAP_CANVAS_ITEM(seq_feature) ;
+ feature = canvas_item->feature ;
+
xpos = group->xpos;
ypos = group->ypos;
@@ -941,14 +1000,14 @@ static void zmap_window_sequence_feature_update (FooCanvasItem *item,
foo_canvas_item_w2i(item, &scr_x1, &scr_y1);
foo_canvas_item_w2i(item, &scr_x2, &scr_y2);
- if(seq_feature->float_flags.float_axis & ZMAP_FLOAT_AXIS_X)
+ if (seq_feature->float_flags.float_axis & ZMAP_FLOAT_AXIS_X)
{
xpos = x1;
- if(scr_x1 >= x1 && scr_x1 < x2)
+ if (scr_x1 >= x1 && scr_x1 < x2)
xpos = scr_x1;
}
- if(seq_feature->float_flags.float_axis & ZMAP_FLOAT_AXIS_Y)
+ if (seq_feature->float_flags.float_axis & ZMAP_FLOAT_AXIS_Y)
{
ypos = y1;
@@ -998,12 +1057,12 @@ static void zmap_window_sequence_feature_update (FooCanvasItem *item,
return ;
}
-static double zmap_window_sequence_feature_point (FooCanvasItem *item,
- double x,
- double y,
- int cx,
- int cy,
- FooCanvasItem **actual_item)
+static double zmap_window_sequence_feature_point(FooCanvasItem *item,
+ double x,
+ double y,
+ int cx,
+ int cy,
+ FooCanvasItem **actual_item)
{
double dist = 1.0;
@@ -1030,6 +1089,7 @@ static void zmap_window_sequence_feature_realize (FooCanvasItem *item)
(* canvas_parent_class_G->realize)(item);
}
+
static void zmap_window_sequence_feature_draw(FooCanvasItem *item,
GdkDrawable *drawable,
GdkEventExpose *expose)
@@ -1118,16 +1178,21 @@ static void save_scroll_region(FooCanvasItem *item)
static GType float_group_axis_get_type (void)
{
- static GType etype = 0;
- if (etype == 0) {
- static const GEnumValue values[] = {
- { ZMAP_FLOAT_AXIS_X, "ZMAP_FLOAT_AXIS_X", "x-axis" },
- { ZMAP_FLOAT_AXIS_Y, "ZMAP_FLOAT_AXIS_Y", "y-axis" },
- { 0, NULL, NULL }
- };
- etype = g_enum_register_static ("ZMapWindowFloatGroupAxis", values);
- }
- return etype;
+ static GType etype = 0 ;
+
+ if (etype == 0)
+ {
+ static const GEnumValue values[] =
+ {
+ { ZMAP_FLOAT_AXIS_X, "ZMAP_FLOAT_AXIS_X", "x-axis" },
+ { ZMAP_FLOAT_AXIS_Y, "ZMAP_FLOAT_AXIS_Y", "y-axis" },
+ { 0, NULL, NULL }
+ };
+
+ etype = g_enum_register_static ("ZMapWindowFloatGroupAxis", values);
+ }
+
+ return etype ;
}
@@ -1169,3 +1234,17 @@ static gboolean sequence_feature_emit_signal(ZMapWindowSequenceFeature sequence_
return TRUE;
}
+
+/* Convert coords from dna to pep, conversion is done on complete codons only. */
+static void coordsDNA2Pep(ZMapFeature feature, int *start_inout, int *end_inout)
+{
+ ZMapFrame frame = feature->feature.sequence.frame ;
+
+ /* If no frame we just default to frame 1 which seems sensible. */
+ if (!frame)
+ frame = ZMAPFRAME_0 ;
+
+ zMapSequenceDNA2Pep(start_inout, end_inout, frame) ;
+
+ return ;
+}
diff --git a/src/zmapWindow/items/zmapWindowSequenceFeature.h b/src/zmapWindow/items/zmapWindowSequenceFeature.h
index f3e9a28ff..7b471efe0 100755
--- a/src/zmapWindow/items/zmapWindowSequenceFeature.h
+++ b/src/zmapWindow/items/zmapWindowSequenceFeature.h
@@ -22,15 +22,16 @@
*
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk,
- * Malcolm Hinsley (Sanger Institute, UK) mh17@sanger.ac.uk
+ * Malcolm Hinsley (Sanger Institute, UK) mh17@sanger.ac.uk
*
- * Description:
+ * Description: External header for object representing either a
+ * DNA or a Peptide sequence. Handles display, coords,
+ * highlighting.
*
- * Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
- * Last edited: Feb 16 09:58 2010 (edgrif)
+ * Last edited: Jul 27 09:10 2010 (edgrif)
* Created: Wed Dec 3 08:44:06 2008 (rds)
- * CVS info: $Id: zmapWindowSequenceFeature.h,v 1.9 2010-06-14 15:40:18 mh17 Exp $
+ * CVS info: $Id: zmapWindowSequenceFeature.h,v 1.10 2010-07-29 10:17:37 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -44,6 +45,7 @@
#define ZMAP_TYPE_WINDOW_SEQUENCE_FEATURE (zMapWindowSequenceFeatureGetType())
+
#if GOBJ_CAST
#define ZMAP_WINDOW_SEQUENCE_FEATURE(obj) ((ZMapWindowSequenceFeature) obj)
#define ZMAP_WINDOW_SEQUENCE_FEATURE_CONST(obj) ((ZMapWindowSequenceFeature const) obj)
@@ -78,12 +80,12 @@ typedef gboolean (* ZMapWindowSequenceFeatureSelectionCB)(ZMapWindowSequenceFeat
GType zMapWindowSequenceFeatureGetType(void);
gboolean zMapWindowSequenceFeatureSelectByRegion(ZMapWindowSequenceFeature sequence_feature,
- int region_start, int region_end,
- int select_flags_ignored_atm);
+ ZMapSequenceType coord_type, int region_start, int region_end) ;
gboolean zMapWindowSequenceFeatureSelectByFeature(ZMapWindowSequenceFeature sequence_feature,
- ZMapFeature seed_feature,
- int select_flags_ignored_atm);
+ ZMapFeature seed_feature) ;
+
+gboolean zMapWindowSequenceDeSelect(ZMapWindowSequenceFeature sequence_feature) ;
#endif /* ZMAP_WINDOW_SEQUENCE_FEATURE_H */
diff --git a/src/zmapWindow/items/zmapWindowSequenceFeature_I.h b/src/zmapWindow/items/zmapWindowSequenceFeature_I.h
index d1df2b45c..030607be7 100755
--- a/src/zmapWindow/items/zmapWindowSequenceFeature_I.h
+++ b/src/zmapWindow/items/zmapWindowSequenceFeature_I.h
@@ -24,28 +24,33 @@
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk,
* Malcolm Hinsley (Sanger Institute, UK) mh17@sanger.ac.uk
*
- * Description:
+ * Description: Internal header for object representing either a
+ * DNA or a Peptide sequence. Handles display, coords,
+ * highlighting.
*
- * Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
- * Last edited: Feb 16 09:58 2010 (edgrif)
+ * Last edited: Jul 22 14:47 2010 (edgrif)
* Created: Wed Dec 3 08:25:28 2008 (rds)
- * CVS info: $Id: zmapWindowSequenceFeature_I.h,v 1.6 2010-06-14 15:40:18 mh17 Exp $
+ * CVS info: $Id: zmapWindowSequenceFeature_I.h,v 1.7 2010-07-29 10:17:37 edgrif Exp $
*-------------------------------------------------------------------
*/
-
#ifndef ZMAP_WINDOW_SEQUENCE_FEATURE_I_H
#define ZMAP_WINDOW_SEQUENCE_FEATURE_I_H
#include <zmapWindowSequenceFeature.h>
#include <zmapWindowCanvasItem_I.h>
+
+/* OH GOSH....WHAT IS SO WRONG WITH ADDING A FEW COMMENTS...THIS IS SO TEDIOUS NOW....Ed */
+
+
typedef enum
{
SEQUENCE_SELECTED_SIGNAL,
SEQUENCE_LAST_SIGNAL,
} ZMapWindowSequenceFeatureSignalType ;
+
typedef struct _zmapWindowSequenceFeatureClassStruct
{
zmapWindowCanvasItemClass __parent__;
@@ -55,16 +60,22 @@ typedef struct _zmapWindowSequenceFeatureClassStruct
guint signals[SEQUENCE_LAST_SIGNAL];
} zmapWindowSequenceFeatureClassStruct;
+
+
typedef struct _zmapWindowSequenceFeatureStruct
{
zmapWindowCanvasItem __parent__;
+ /* Frame is needed for 3 frame translation objects which display peptides in 3 frames. We need
+ * to know which frame we are !! */
+ ZMapFrame frame ;
+
struct
{
double zoom_x, zoom_y;
/* world coords scroll region, also sets min/max x/y positions */
double scr_x1, scr_y1, scr_x2, scr_y2;
- }float_settings;
+ } float_settings;
struct
{
@@ -74,9 +85,9 @@ typedef struct _zmapWindowSequenceFeatureStruct
unsigned int max_y_set : 1;
unsigned int float_axis : 2;
- }float_flags;
+ } float_flags;
-} zmapWindowSequenceFeatureStruct;
+} zmapWindowSequenceFeatureStruct ;
#endif /* ZMAP_WINDOW_SEQUENCE_FEATURE_I_H */
--
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