diff --git a/src/include/ZMap/zmapStyle.h b/src/include/ZMap/zmapStyle.h
index 8bfee98f6d4d4ead26fe3ee65b64ff912d48f37c..651fadf964ec3d58373f8dc77457c2b9571671eb 100755
--- a/src/include/ZMap/zmapStyle.h
+++ b/src/include/ZMap/zmapStyle.h
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: Jul 29 09:27 2009 (edgrif)
* Created: Mon Feb 26 09:28:26 2007 (edgrif)
- * CVS info: $Id: zmapStyle.h,v 1.44 2010-01-06 15:58:00 mh17 Exp $
+ * CVS info: $Id: zmapStyle.h,v 1.45 2010-01-11 16:50:20 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_STYLE_H
@@ -97,6 +97,7 @@
/* glyph properties. */
#define ZMAPSTYLE_PROPERTY_GLYPH_MODE "glyph-mode"
+#define ZMAPSTYLE_PROPERTY_GLYPH_TYPE "glyph-type"
/* alignment properties */
#define ZMAPSTYLE_PROPERTY_ALIGNMENT_PARSE_GAPS "alignment-parse-gaps"
@@ -204,13 +205,19 @@ _(ZMAPSTYLE_GRAPH_HISTOGRAM, , "histogram", "Usual blocky like graph." , "")
ZMAP_DEFINE_ENUM(ZMapStyleGraphMode, ZMAP_STYLE_GRAPH_MODE_LIST);
-/* Specifies the style of glyph. */
+/* Specifies the sub-mode of glyph.
+ * SPLICE is partly hard coded due the nature of the data
+ * MARKER can be attached to any data via style mode=glyph and glyph type defined as in GLYPH_TYPE below
+ */
+
#define ZMAP_STYLE_GLYPH_MODE_LIST(_) \
_(ZMAPSTYLE_GLYPH_INVALID, , "invalid", "Initial setting. ", "") \
-_(ZMAPSTYLE_GLYPH_SPLICE, , "splice" , "" , "")
+_(ZMAPSTYLE_GLYPH_SPLICE, , "splice" , "" , "") \
+_(ZMAPSTYLE_GLYPH_MARKER, , "marker" , "Zoom free marker" , "")
ZMAP_DEFINE_ENUM(ZMapStyleGlyphMode, ZMAP_STYLE_GLYPH_MODE_LIST);
+
/* Specifies the style of glyph for an incomplete alignment marker. (not a free standing glyph) */
// refer to enum in zmapWindowGlyphItem.h
#define ZMAP_STYLE_GLYPH_TYPE_LIST(_) \
@@ -394,9 +401,15 @@ double zMapStyleGetMinScore(ZMapFeatureTypeStyle style) ;
gboolean zMapStyleGetShowWhenEmpty(ZMapFeatureTypeStyle style);
gboolean zMapStyleGetColours(ZMapFeatureTypeStyle style, ZMapStyleColourTarget target, ZMapStyleColourType type,
GdkColor **fill, GdkColor **draw, GdkColor **border) ;
+gboolean zMapStyleGetColoursDefault(ZMapFeatureTypeStyle style,
+ GdkColor **background, GdkColor **foreground, GdkColor **outline);
char *zMapStyleGetDescription(ZMapFeatureTypeStyle style) ;
double zMapStyleGetWidth(ZMapFeatureTypeStyle style) ;
+ZMapStyleGlyphType zMapStyleGlyphType(ZMapFeatureTypeStyle style);
+ZMapStyleGlyphType zMapStyleGlyphMode(ZMapFeatureTypeStyle style);
+
+
void zMapStyleGetGappedAligns(ZMapFeatureTypeStyle style, gboolean *parse_gaps, gboolean *show_gaps) ;
double zMapStyleGetBumpWidth(ZMapFeatureTypeStyle style) ;
diff --git a/src/zmapConfig/zmapConfigLoader.c b/src/zmapConfig/zmapConfigLoader.c
index f8594fb121247506d3dc49e842aab532ca2a0aee..9d3f9dba1bc79b6fd313ce38d267f66b43649733 100644
--- a/src/zmapConfig/zmapConfigLoader.c
+++ b/src/zmapConfig/zmapConfigLoader.c
@@ -31,7 +31,7 @@
* HISTORY:
* Last edited: Nov 6 13:34 2009 (edgrif)
* Created: Thu Sep 25 14:12:05 2008 (rds)
- * CVS info: $Id: zmapConfigLoader.c,v 1.4 2010-01-06 15:58:01 mh17 Exp $
+ * CVS info: $Id: zmapConfigLoader.c,v 1.5 2010-01-11 16:50:20 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -785,6 +785,7 @@ static gpointer create_config_style()
{ ZMAPSTYLE_PROPERTY_GRAPH_BASELINE, FALSE, ZMAPCONF_DOUBLE, {FALSE}, ZMAPCONV_NONE, {NULL} },
{ ZMAPSTYLE_PROPERTY_GLYPH_MODE, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2ENUM, {(ZMapConfStr2EnumFunc)zMapStyleStr2GlyphMode} },
+ { ZMAPSTYLE_PROPERTY_GLYPH_TYPE, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2ENUM, {(ZMapConfStr2EnumFunc)zMapStyleStr2GlyphType} },
{ ZMAPSTYLE_PROPERTY_ALIGNMENT_PARSE_GAPS, FALSE, ZMAPCONF_BOOLEAN, {FALSE}, ZMAPCONV_NONE, {NULL} },
{ ZMAPSTYLE_PROPERTY_ALIGNMENT_SHOW_GAPS, FALSE, ZMAPCONF_BOOLEAN, {FALSE}, ZMAPCONV_NONE, {NULL} },
@@ -893,7 +894,7 @@ static ZMapConfigIniContextKeyEntry get_style_group_data(char **stanza_name, cha
{ ZMAPSTYLE_PROPERTY_GRAPH_BASELINE, G_TYPE_DOUBLE, style_set_property, FALSE },
{ ZMAPSTYLE_PROPERTY_GLYPH_MODE, G_TYPE_STRING, style_set_property, FALSE },
-
+ { ZMAPSTYLE_PROPERTY_GLYPH_TYPE, G_TYPE_STRING, style_set_property, FALSE },
{ ZMAPSTYLE_PROPERTY_ALIGNMENT_PARSE_GAPS, G_TYPE_BOOLEAN, style_set_property, FALSE },
{ ZMAPSTYLE_PROPERTY_ALIGNMENT_SHOW_GAPS, G_TYPE_BOOLEAN, style_set_property, FALSE },
diff --git a/src/zmapDraw/zmapDraw.c b/src/zmapDraw/zmapDraw.c
index 6e722afc835ce7ece1d83aaec0f5ce4bef2af820..415eaf645dca70cc3c16baa22b31ad07da9e4684 100755
--- a/src/zmapDraw/zmapDraw.c
+++ b/src/zmapDraw/zmapDraw.c
@@ -30,7 +30,7 @@
* HISTORY:
* Last edited: Dec 2 15:02 2008 (rds)
* Created: Wed Oct 20 09:19:16 2004 (edgrif)
- * CVS info: $Id: zmapDraw.c,v 1.66 2008-12-02 15:04:33 rds Exp $
+ * CVS info: $Id: zmapDraw.c,v 1.67 2010-01-11 16:50:20 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -288,6 +288,7 @@ void zMapDrawBoxChangeSize(FooCanvasItem *box,
*
* @return Returns a pointer to the new canvas item representing the glyph.
* */
+// mh17: this function is never called
FooCanvasItem *zMapDrawGlyph(FooCanvasGroup *group, double x, double y,
ZMapDrawGlyphType glyph_type,
GdkColor *colour, double width, guint line_width)
diff --git a/src/zmapFeature/zmapStyle.c b/src/zmapFeature/zmapStyle.c
index a0d17f79566ee0d9a34141745dbd89108bfbedd3..1af90e3e03133fa18d79771c3b0ba88690012621 100755
--- a/src/zmapFeature/zmapStyle.c
+++ b/src/zmapFeature/zmapStyle.c
@@ -30,7 +30,7 @@
* HISTORY:
* Last edited: Jul 29 09:27 2009 (edgrif)
* Created: Mon Feb 26 09:12:18 2007 (edgrif)
- * CVS info: $Id: zmapStyle.c,v 1.37 2010-01-11 11:29:16 mh17 Exp $
+ * CVS info: $Id: zmapStyle.c,v 1.38 2010-01-11 16:50:20 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -1441,7 +1441,7 @@ GdkColor *zMapStyleGetColour(ZMapFeatureTypeStyle style, ZMapStyleDrawContext co
-/* I NOW THINK THIS FUNCTION IS REDUNDANT.... */
+/* I NOW THINK THIS FUNCTION IS REDUNDANT.... mh17: not true it has a new lease of life */
/* As for zMapStyleGetColours() but defaults colours that are not set in the style according
* to the style mode e.g. rules may be different for Transcript as opposed to Basic mode.
*
@@ -1459,14 +1459,14 @@ gboolean zMapStyleGetColoursDefault(ZMapFeatureTypeStyle style,
case ZMAPSTYLE_MODE_TRANSCRIPT:
case ZMAPSTYLE_MODE_ALIGNMENT:
case ZMAPSTYLE_MODE_TEXT:
+ case ZMAPSTYLE_MODE_GLYPH:
case ZMAPSTYLE_MODE_GRAPH:
{
/* Our rule is that missing colours will default to the fill colour so if the fill colour
* is missing there is nothing we can do. */
if (style->colours.normal.fields_set.fill)
{
- result = TRUE ; /* We know we can default to fill
- colour. */
+ result = TRUE ; /* We know we can default to fill colour. */
if (background)
{
@@ -1965,6 +1965,27 @@ double zMapStyleBaseline(ZMapFeatureTypeStyle style)
return baseline ;
}
+ZMapStyleGlyphType zMapStyleGlyphMode(ZMapFeatureTypeStyle style)
+{
+ int glyph_mode = ZMAPSTYLE_GLYPH_INVALID;
+
+ g_object_get(style,
+ ZMAPSTYLE_PROPERTY_GLYPH_MODE, &glyph_mode,
+ NULL) ;
+
+ return glyph_mode ;
+}
+
+ZMapStyleGlyphType zMapStyleGlyphType(ZMapFeatureTypeStyle style)
+{
+ int glyph_type = ZMAPSTYLE_GLYPH_TYPE_INVALID;
+
+ g_object_get(style,
+ ZMAPSTYLE_PROPERTY_GLYPH_TYPE, &glyph_type,
+ NULL) ;
+
+ return glyph_type ;
+}
diff --git a/src/zmapFeature/zmapStyle_I.h b/src/zmapFeature/zmapStyle_I.h
index e3cf5c22ef046f0f36bd417aa03e207f715ae61d..48d9dec952f55553583f2bc92c631ae726c4fd64 100755
--- a/src/zmapFeature/zmapStyle_I.h
+++ b/src/zmapFeature/zmapStyle_I.h
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: Jul 29 09:43 2009 (edgrif)
* Created: Mon Feb 26 09:13:30 2007 (edgrif)
- * CVS info: $Id: zmapStyle_I.h,v 1.13 2010-01-06 15:58:02 mh17 Exp $
+ * CVS info: $Id: zmapStyle_I.h,v 1.14 2010-01-11 16:50:20 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -180,10 +180,12 @@ typedef struct
struct
{
unsigned int mode : 1 ;
+ unsigned int type : 1 ;
} fields_set ; /*!< Fields set. */
- ZMapStyleGlyphMode mode ; /*!< Glyph style. */
-
+ ZMapStyleGlyphMode mode ; /*!< Glyph mode. eg splice or marker*/
+ ZMapStyleGlyphMode type ; /*!< Glyph type. eg diamond or circle */
+
} ZMapStyleGlyphStruct, *ZMapStyleGlyph ;
diff --git a/src/zmapWindow/items/zmapWindowBasicFeature.c b/src/zmapWindow/items/zmapWindowBasicFeature.c
index 01424080d68c9c647d0f8e19bd75fe3f5a2abdec..cd724d52bb26989da664dac67c161f324222dbe0 100755
--- a/src/zmapWindow/items/zmapWindowBasicFeature.c
+++ b/src/zmapWindow/items/zmapWindowBasicFeature.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Jul 3 17:07 2009 (rds)
* Created: Wed Dec 3 10:02:22 2008 (rds)
- * CVS info: $Id: zmapWindowBasicFeature.c,v 1.8 2009-07-27 03:13:28 rds Exp $
+ * CVS info: $Id: zmapWindowBasicFeature.c,v 1.9 2010-01-11 16:50:20 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -104,6 +104,8 @@ static FooCanvasItem *zmap_window_basic_feature_add_interval(ZMapWindowCanvasIte
ZMapFeatureTypeStyle style;
ZMapFeature feature;
gboolean interval_type_from_feature_type = TRUE; /* for now */
+ GdkColor fill,outline;
+ GdkColor *pfill = &fill,*poutline = &outline;
feature = basic->feature;
style = (ZMAP_CANVAS_ITEM_GET_CLASS(basic)->get_style)(basic);
@@ -127,29 +129,55 @@ static FooCanvasItem *zmap_window_basic_feature_add_interval(ZMapWindowCanvasIte
case ZMAP_WINDOW_BASIC_GLYPH:
{
/* where do we do the points calculation? */
- /* Should it be here from the left, right, top, bottom coords? */
+ /* Should it be here from the left, right, top, bottom cogreenords? */
/* Should the glyph code do it? */
/* intron/gaps are done at this level... */
int type = 0;
-
- if(feature->strand == ZMAPSTRAND_FORWARD)
- type = ZMAP_GLYPH_ITEM_STYLE_TRIANGLE;
- else
- type = ZMAP_GLYPH_ITEM_STYLE_TRIANGLE;
+ int mode = zMapStyleGlyphMode(style);
+
+ switch(mode)
+ {
+ case ZMAPSTYLE_GLYPH_SPLICE: // hard coded on GF_Splice feature - should never be configured
+ if(feature->strand == ZMAPSTRAND_FORWARD)
+ type = ZMAP_GLYPH_ITEM_STYLE_TRIANGLE;
+ else
+ type = ZMAP_GLYPH_ITEM_STYLE_TRIANGLE; // mh17: (sic)
+
+ gdk_color_parse("#0000ff",&fill);
+ gdk_color_parse("#000000",&outline);
+ pfill = &fill;
+ poutline = &outline;
+ break;
+
+ case ZMAPSTYLE_GLYPH_MARKER:
+ type = zMapStyleGlyphType(style);
+ if(!zMapStyleGetColoursDefault(style,&pfill,NULL,&poutline))
+ {
+ gdk_color_parse("#00ff00",&fill);
+ gdk_color_parse("#000000",&outline);
+ pfill = &fill;
+ poutline = &outline;
+ }
+
+ break;
+ }
+
basic->auto_resize_background = 1;
item = foo_canvas_item_new(FOO_CANVAS_GROUP(basic),
- ZMAP_TYPE_WINDOW_GLYPH_ITEM,
- "glyph_style", type,
- "x", 0.0,
- "y", 0.0,
- "width", right,
- "height", right,
- "line-width", 1,
- "join_style", GDK_JOIN_BEVEL,
- "cap_style", GDK_CAP_BUTT,
- NULL);
+ ZMAP_TYPE_WINDOW_GLYPH_ITEM,
+ "glyph_style", type,
+ "x", 0.0,
+ "y", 0.0,
+ "width", right,
+ "height", right, // mh17: gross!.. right being the width of the column? so this means square??
+ "line-width", 1,
+ "join_style", GDK_JOIN_BEVEL,
+ "cap_style", GDK_CAP_BUTT,
+ "fill_color_gdk", pfill,
+ "outline_color_gdk", poutline,
+ NULL);
}
break;
case ZMAP_WINDOW_BASIC_BOX:
diff --git a/src/zmapWindow/items/zmapWindowCollectionFeature.c b/src/zmapWindow/items/zmapWindowCollectionFeature.c
index f42c0c97c26aa7278407bc9cdac100e60414b33d..87c24010e54f4ea22af8a36e10eaad9d248d9ba0 100755
--- a/src/zmapWindow/items/zmapWindowCollectionFeature.c
+++ b/src/zmapWindow/items/zmapWindowCollectionFeature.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Aug 28 09:12 2009 (edgrif)
* Created: Wed Dec 3 10:02:22 2008 (rds)
- * CVS info: $Id: zmapWindowCollectionFeature.c,v 1.11 2010-01-11 11:29:16 mh17 Exp $
+ * CVS info: $Id: zmapWindowCollectionFeature.c,v 1.12 2010-01-11 16:50:20 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -293,7 +293,7 @@ void zMapWindowCollectionFeatureAddIncompleteMarkers(ZMapWindowCanvasItem collec
// char *noncolinear_colour = ZMAP_WINDOW_MATCH_NOTCOLINEAR ;
FooCanvasGroup *group;
GdkColor *marker_fill=NULL,*marker_draw=NULL,*marker_border=NULL;
- GdkColor red;
+ GdkColor fill,outline;
double width;
gboolean incomplete ;
ZMapStyleGlyphType glyph_style; // = ZMAP_GLYPH_ITEM_STYLE_DIAMOND;
@@ -310,8 +310,10 @@ void zMapWindowCollectionFeatureAddIncompleteMarkers(ZMapWindowCanvasItem collec
style = (ZMAP_CANVAS_ITEM_GET_CLASS(collection)->get_style)(collection);
if(!zMapStyleGetColoursGlyphDefault(style,&marker_fill,&marker_draw,&marker_border))
{
- gdk_color_parse("red",&red);
- marker_fill = marker_border = &red;
+ gdk_color_parse("red",&fill);
+ gdk_color_parse("black",&outline);
+ marker_fill = &fill;
+ marker_border = &outline;
}
if(group->item_list)
diff --git a/src/zmapWindow/items/zmapWindowGlyphItem.c b/src/zmapWindow/items/zmapWindowGlyphItem.c
index e19a5873a69ad9103707c44681db0a235ca3003b..7dd3f73a6c2a145678646a412ee1e965394f4b2d 100755
--- a/src/zmapWindow/items/zmapWindowGlyphItem.c
+++ b/src/zmapWindow/items/zmapWindowGlyphItem.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Jun 3 09:51 2009 (rds)
* Created: Fri Jan 16 11:20:07 2009 (rds)
- * CVS info: $Id: zmapWindowGlyphItem.c,v 1.4 2010-01-06 15:58:02 mh17 Exp $
+ * CVS info: $Id: zmapWindowGlyphItem.c,v 1.5 2010-01-11 16:50:20 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -451,9 +451,9 @@ static void zmap_window_glyph_item_set_property (GObject *object,
switch(param_id)
{
- case PROP_FILL_COLOR:
- case PROP_FILL_COLOR_GDK:
- case PROP_FILL_COLOR_RGBA:
+ case PROP_OUTLINE_COLOR:
+ case PROP_OUTLINE_COLOR_GDK:
+ case PROP_OUTLINE_COLOR_RGBA:
{
glyph_item->line_set = glyph_set_color_property(glyph_item, param_id, value,
&(glyph_item->line_rgba),
@@ -462,10 +462,10 @@ static void zmap_window_glyph_item_set_property (GObject *object,
redraw = 1;
}
break;
-
- case PROP_OUTLINE_COLOR:
- case PROP_OUTLINE_COLOR_GDK:
- case PROP_OUTLINE_COLOR_RGBA:
+
+ case PROP_FILL_COLOR:
+ case PROP_FILL_COLOR_GDK:
+ case PROP_FILL_COLOR_RGBA:
{
glyph_item->area_set = glyph_set_color_property(glyph_item, param_id, value,
&(glyph_item->area_rgba),
@@ -489,6 +489,7 @@ static void zmap_window_glyph_item_set_property (GObject *object,
case PROP_HEIGHT_PIXELS:
glyph_item->ch = g_value_get_double(value);
coord_update = 1;
+
break;
case PROP_GLYPH_STYLE:
glyph_item->style = g_value_get_uint(value);