From 0bc5d04b67a63df706accb9b476d523063e06920 Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Mon, 18 May 2009 14:55:05 +0000
Subject: [PATCH] add assembly path colours to style.
---
src/include/ZMap/zmapStyle.h | 8 +-
src/zmapFeature/zmapFeatureTypes.c | 10 ++-
src/zmapFeature/zmapStyle.c | 131 ++++++++++++++++++++++++++++-
src/zmapFeature/zmapStyleUtils.c | 13 ++-
src/zmapFeature/zmapStyle_I.h | 22 ++++-
5 files changed, 172 insertions(+), 12 deletions(-)
diff --git a/src/include/ZMap/zmapStyle.h b/src/include/ZMap/zmapStyle.h
index 9c2403009..8b51f071e 100755
--- a/src/include/ZMap/zmapStyle.h
+++ b/src/include/ZMap/zmapStyle.h
@@ -26,9 +26,9 @@
* Description: Style and Style set handling functions.
*
* HISTORY:
- * Last edited: May 15 11:29 2009 (edgrif)
+ * Last edited: May 18 15:17 2009 (edgrif)
* Created: Mon Feb 26 09:28:26 2007 (edgrif)
- * CVS info: $Id: zmapStyle.h,v 1.38 2009-05-15 15:28:06 edgrif Exp $
+ * CVS info: $Id: zmapStyle.h,v 1.39 2009-05-18 14:55:05 edgrif Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_STYLE_H
@@ -109,6 +109,9 @@
/* Text properties */
#define ZMAPSTYLE_PROPERTY_TEXT_FONT "text-font"
+/* Assembly path properties */
+#define ZMAPSTYLE_PROPERTY_ASSEMBLY_PATH_NON_COLOURS "non-assembly-colours"
+
/*
* The following are a series of enums that define various properties of a style.
* NOTE that it is imperative that each enum type has as it's first member
@@ -229,6 +232,7 @@ _(ZMAPSTYLE_COLOURTARGET_FRAME0, , "frame0", "Frame 1 colour ", "") \
_(ZMAPSTYLE_COLOURTARGET_FRAME1, , "frame1", "Frame 2 colour ", "") \
_(ZMAPSTYLE_COLOURTARGET_FRAME2, , "frame2", "Frame 3 colour ", "") \
_(ZMAPSTYLE_COLOURTARGET_CDS, , "cds", "Colour to apply to CDS ", "") \
+_(ZMAPSTYLE_COLOURTARGET_NON_ASSEMBLY_PATH, , "non-assembly_path", "Colour to non-path sections of assembly ", "") \
_(ZMAPSTYLE_COLOURTARGET_STRAND, , "strand", "Colour to apply to Strand ", "")
ZMAP_DEFINE_ENUM(ZMapStyleColourTarget, ZMAP_STYLE_COLOUR_TARGET_LIST) ;
diff --git a/src/zmapFeature/zmapFeatureTypes.c b/src/zmapFeature/zmapFeatureTypes.c
index ede790a28..282d20bbe 100755
--- a/src/zmapFeature/zmapFeatureTypes.c
+++ b/src/zmapFeature/zmapFeatureTypes.c
@@ -27,9 +27,9 @@
*
* Exported functions: See ZMap/zmapFeature.h
* HISTORY:
- * Last edited: Apr 28 14:24 2009 (edgrif)
+ * Last edited: May 18 13:11 2009 (edgrif)
* Created: Tue Dec 14 13:15:11 2004 (edgrif)
- * CVS info: $Id: zmapFeatureTypes.c,v 1.80 2009-04-28 14:29:49 edgrif Exp $
+ * CVS info: $Id: zmapFeatureTypes.c,v 1.81 2009-05-18 14:55:05 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -1206,10 +1206,11 @@ GData *zMapStyleGetAllPredefined(void)
curr = zMapStyleCreate(ZMAP_FIXED_STYLE_ASSEMBLY_PATH_NAME,
ZMAP_FIXED_STYLE_ASSEMBLY_PATH_TEXT) ;
{
- char *colours = "normal fill blue ; normal draw black ; selected fill red ; selected draw black" ;
+ char *colours = "normal fill blue ; normal border black ; selected fill red ; selected border black" ;
+ char *non_path_colours = "normal fill yellow ; normal border black ; selected fill red ; selected border black" ;
g_object_set(G_OBJECT(curr),
- ZMAPSTYLE_PROPERTY_MODE, ZMAPSTYLE_MODE_BASIC,
+ ZMAPSTYLE_PROPERTY_MODE, ZMAPSTYLE_MODE_ASSEMBLY_PATH,
ZMAPSTYLE_PROPERTY_DISPLAYABLE, TRUE,
ZMAPSTYLE_PROPERTY_DISPLAY_MODE, ZMAPSTYLE_COLDISPLAY_SHOW,
ZMAPSTYLE_PROPERTY_WIDTH, 10.0,
@@ -1217,6 +1218,7 @@ GData *zMapStyleGetAllPredefined(void)
ZMAPSTYLE_PROPERTY_DEFAULT_BUMP_MODE, ZMAPBUMP_ALTERNATING,
ZMAPSTYLE_PROPERTY_BUMP_FIXED, TRUE,
ZMAPSTYLE_PROPERTY_COLOURS, colours,
+ ZMAPSTYLE_PROPERTY_ASSEMBLY_PATH_NON_COLOURS, non_path_colours,
NULL);
}
g_datalist_id_set_data(&style_list, curr->unique_id, curr);
diff --git a/src/zmapFeature/zmapStyle.c b/src/zmapFeature/zmapStyle.c
index 41532bbba..87df5a357 100755
--- a/src/zmapFeature/zmapStyle.c
+++ b/src/zmapFeature/zmapStyle.c
@@ -28,9 +28,9 @@
*
* Exported functions: See ZMap/zmapStyle.h
* HISTORY:
- * Last edited: May 8 14:59 2009 (rds)
+ * Last edited: May 18 15:17 2009 (edgrif)
* Created: Mon Feb 26 09:12:18 2007 (edgrif)
- * CVS info: $Id: zmapStyle.c,v 1.32 2009-05-08 14:21:15 rds Exp $
+ * CVS info: $Id: zmapStyle.c,v 1.33 2009-05-18 14:55:05 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -39,6 +39,20 @@
#include <zmapStyle_P.h>
+/*
+ * PLEASE READ THIS......
+ *
+ * The g_object/paramspec stuff all needs redoing so that it's table driven
+ * otherwise we will all go mad.....it is way too error prone......
+ *
+ * but it needs to be done carefully, we need the "set" flags to support
+ * inheritance....and they g_object copy/set/get code in glib all expects
+ * paramspecs etc so it's not straight forward...
+ *
+ */
+
+
+
enum
{
@@ -107,6 +121,9 @@ enum
STYLE_PROP_ALIGNMENT_NONCOLINEAR_COLOURS,
STYLE_PROP_TRANSCRIPT_CDS_COLOURS,
+
+ STYLE_PROP_ASSEMBLY_PATH_NON_COLOURS,
+
STYLE_PROP_TEXT_FONT,
};
@@ -645,6 +662,12 @@ gboolean zMapStyleIsPropertySet(ZMapFeatureTypeStyle style, char *property_name,
break;
}
+ case STYLE_PROP_ASSEMBLY_PATH_NON_COLOURS:
+ {
+ is_set = isColourSet(style, pspec->param_id, property_subpart) ;
+
+ break;
+ }
default:
{
G_OBJECT_WARN_INVALID_PROPERTY_ID(style, pspec->param_id, pspec);
@@ -780,6 +803,7 @@ gboolean zMapStyleIsTrueFeature(ZMapFeatureTypeStyle style)
case ZMAPSTYLE_MODE_ALIGNMENT:
case ZMAPSTYLE_MODE_RAW_SEQUENCE:
case ZMAPSTYLE_MODE_PEP_SEQUENCE:
+ case ZMAPSTYLE_MODE_ASSEMBLY_PATH:
{
valid = TRUE ;
break ;
@@ -845,6 +869,7 @@ gboolean zMapStyleIsDrawable(ZMapFeatureTypeStyle style, GError **error)
case ZMAPSTYLE_MODE_BASIC:
case ZMAPSTYLE_MODE_TRANSCRIPT:
case ZMAPSTYLE_MODE_ALIGNMENT:
+ case ZMAPSTYLE_MODE_ASSEMBLY_PATH:
case ZMAPSTYLE_MODE_RAW_SEQUENCE:
case ZMAPSTYLE_MODE_PEP_SEQUENCE:
{
@@ -902,6 +927,7 @@ gboolean zMapStyleIsDrawable(ZMapFeatureTypeStyle style, GError **error)
case ZMAPSTYLE_MODE_BASIC:
case ZMAPSTYLE_MODE_TRANSCRIPT:
case ZMAPSTYLE_MODE_ALIGNMENT:
+ case ZMAPSTYLE_MODE_ASSEMBLY_PATH:
{
if (!(style->colours.normal.fields_set.fill) && !(style->colours.normal.fields_set.border))
{
@@ -1049,6 +1075,7 @@ gboolean zMapStyleMakeDrawable(ZMapFeatureTypeStyle style)
switch (style->mode)
{
+ case ZMAPSTYLE_MODE_ASSEMBLY_PATH:
case ZMAPSTYLE_MODE_PEP_SEQUENCE:
case ZMAPSTYLE_MODE_RAW_SEQUENCE:
case ZMAPSTYLE_MODE_TEXT:
@@ -1203,6 +1230,9 @@ gboolean zMapStyleSetColours(ZMapFeatureTypeStyle style, ZMapStyleColourTarget t
case ZMAPSTYLE_COLOURTARGET_CDS:
full_colour = &(style->mode_data.transcript.CDS_colours) ;
break ;
+ case ZMAPSTYLE_COLOURTARGET_NON_ASSEMBLY_PATH:
+ full_colour = &(style->mode_data.assembly_path.non_path_colours) ;
+ break ;
case ZMAPSTYLE_COLOURTARGET_STRAND:
full_colour = &(style->strand_rev_colours);
break;
@@ -1265,6 +1295,9 @@ gboolean zMapStyleGetColours(ZMapFeatureTypeStyle style, ZMapStyleColourTarget t
case ZMAPSTYLE_COLOURTARGET_CDS:
full_colour = &(style->mode_data.transcript.CDS_colours) ;
break ;
+ case ZMAPSTYLE_COLOURTARGET_NON_ASSEMBLY_PATH:
+ full_colour = &(style->mode_data.assembly_path.non_path_colours) ;
+ break ;
case ZMAPSTYLE_COLOURTARGET_STRAND:
full_colour = &(style->strand_rev_colours) ;
break ;
@@ -1997,6 +2030,10 @@ static void set_implied_mode(ZMapFeatureTypeStyle style, guint param_id)
if(style->implied_mode == ZMAPSTYLE_MODE_INVALID)
style->implied_mode = ZMAPSTYLE_MODE_TRANSCRIPT;
break;
+ case STYLE_PROP_ASSEMBLY_PATH_NON_COLOURS:
+ if(style->implied_mode == ZMAPSTYLE_MODE_INVALID)
+ style->implied_mode = ZMAPSTYLE_MODE_ASSEMBLY_PATH;
+ break;
default:
break;
}
@@ -2371,6 +2408,13 @@ static void zmap_feature_type_style_class_init(ZMapFeatureTypeStyleClass style_c
"Colour used to CDS section of a transcript.",
"", ZMAP_PARAM_STATIC_RW));
+ /* Assembly path colours. */
+ g_object_class_install_property(gobject_class,
+ STYLE_PROP_ASSEMBLY_PATH_NON_COLOURS,
+ g_param_spec_string(ZMAPSTYLE_PROPERTY_ASSEMBLY_PATH_NON_COLOURS, "non-path colours",
+ "Colour used for unused part of an assembly path sequence.",
+ "", ZMAP_PARAM_STATIC_RW));
+
/* Text Font. */
g_object_class_install_property(gobject_class,
STYLE_PROP_TEXT_FONT,
@@ -2934,6 +2978,38 @@ static void zmap_feature_type_style_set_property(GObject *gobject,
} /* case STYLE_PROP_ALIGNMENT_PARSE_GAPS..STYLE_PROP_ALIGNMENT_NONCOLINEAR_COLOURS */
+ case STYLE_PROP_ASSEMBLY_PATH_NON_COLOURS:
+ {
+ /* Handle all assembly path specific options. */
+
+ if (style->implied_mode != ZMAPSTYLE_MODE_ASSEMBLY_PATH)
+ {
+ if (!copy_style)
+ {
+ badPropertyForMode(style, ZMAPSTYLE_MODE_ASSEMBLY_PATH, "set", pspec) ;
+ result = FALSE ;
+ }
+ }
+ else
+ {
+ switch(param_id)
+ {
+ case STYLE_PROP_ASSEMBLY_PATH_NON_COLOURS:
+ result = parseColours(style, copy_style, param_id, (GValue *)value) ;
+
+ break ;
+
+ default:
+ G_OBJECT_WARN_INVALID_PROPERTY_ID(gobject, param_id, pspec);
+ result = FALSE ;
+
+ break;
+ }
+ }
+
+ break;
+ }
+
case STYLE_PROP_TRANSCRIPT_CDS_COLOURS:
{
/* Handle all transcript specific options. */
@@ -3633,6 +3709,52 @@ static void zmap_feature_type_style_get_property(GObject *gobject,
}
break;
}
+
+ /* assembly path mode_data access */
+ case STYLE_PROP_ASSEMBLY_PATH_NON_COLOURS:
+ {
+ /* Handle all assembly path specific options. */
+
+ if (style->implied_mode != ZMAPSTYLE_MODE_ASSEMBLY_PATH)
+ {
+ if (!copy)
+ {
+ badPropertyForMode(style, ZMAPSTYLE_MODE_ASSEMBLY_PATH, "get", pspec) ;
+ result = FALSE ;
+ }
+ }
+ else
+ {
+ /* We allocate memory here to hold the colour string, it's g_object_get caller's
+ * responsibility to g_free the string... */
+ ZMapStyleFullColour this_colour = NULL ;
+ GString *colour_string = NULL ;
+
+ colour_string = g_string_sized_new(500) ;
+
+ switch(param_id)
+ {
+ case STYLE_PROP_ASSEMBLY_PATH_NON_COLOURS:
+ this_colour = &(style->mode_data.assembly_path.non_path_colours) ;
+ break;
+ default:
+ G_OBJECT_WARN_INVALID_PROPERTY_ID(gobject, param_id, pspec);
+ break;
+ }
+
+ formatColours(colour_string, "normal", &(this_colour->normal)) ;
+ formatColours(colour_string, "selected", &(this_colour->selected)) ;
+
+ if (colour_string->len)
+ g_value_set_string(value, g_string_free(colour_string, FALSE)) ;
+ else
+ {
+ g_string_free(colour_string, TRUE) ;
+ result = FALSE ;
+ }
+ }
+ break;
+ }
case STYLE_PROP_TEXT_FONT:
{
/* Handle all text specific options. */
@@ -3810,6 +3932,11 @@ static gboolean parseColours(ZMapFeatureTypeStyle style, ZMapFeatureTypeStyle co
if (copy_style)
copy_full_colour = &(copy_style->mode_data.transcript.CDS_colours) ;
break;
+ case STYLE_PROP_ASSEMBLY_PATH_NON_COLOURS:
+ full_colour = &(style->mode_data.assembly_path.non_path_colours) ;
+ if (copy_style)
+ copy_full_colour = &(copy_style->mode_data.assembly_path.non_path_colours) ;
+ break;
default:
zMapAssertNotReached() ;
break;
diff --git a/src/zmapFeature/zmapStyleUtils.c b/src/zmapFeature/zmapStyleUtils.c
index cfb42c111..16d94e18d 100755
--- a/src/zmapFeature/zmapStyleUtils.c
+++ b/src/zmapFeature/zmapStyleUtils.c
@@ -28,9 +28,9 @@
* Exported functions: See ZMap/zmapStyle.h
*
* HISTORY:
- * Last edited: Apr 27 14:10 2009 (edgrif)
+ * Last edited: May 18 14:53 2009 (edgrif)
* Created: Thu Oct 30 10:24:35 2008 (edgrif)
- * CVS info: $Id: zmapStyleUtils.c,v 1.4 2009-04-28 14:29:49 edgrif Exp $
+ * CVS info: $Id: zmapStyleUtils.c,v 1.5 2009-05-18 14:55:05 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -491,6 +491,15 @@ void zMapStylePrint(ZMapIOOut dest, ZMapFeatureTypeStyle style, char *prefix, gb
indent = "\t\t" ;
PRINTFULLCOLOUR(dest, mode_data.transcript.CDS_colours, "CDS") ;
+ break ;
+ }
+ case ZMAPSTYLE_MODE_ASSEMBLY_PATH:
+ {
+ zMapOutWriteFormat(dest, "%sAssembly_path Mode -\n", indent) ;
+
+ indent = "\t\t" ;
+ PRINTFULLCOLOUR(dest, mode_data.assembly_path.non_path_colours, "Non-assembly") ;
+
break ;
}
default:
diff --git a/src/zmapFeature/zmapStyle_I.h b/src/zmapFeature/zmapStyle_I.h
index f44e40a88..f95d9f0a7 100755
--- a/src/zmapFeature/zmapStyle_I.h
+++ b/src/zmapFeature/zmapStyle_I.h
@@ -26,9 +26,9 @@
* Description: Private header for style.
*
* HISTORY:
- * Last edited: Apr 27 14:30 2009 (edgrif)
+ * Last edited: May 18 14:48 2009 (edgrif)
* Created: Mon Feb 26 09:13:30 2007 (edgrif)
- * CVS info: $Id: zmapStyle_I.h,v 1.10 2009-04-28 14:29:49 edgrif Exp $
+ * CVS info: $Id: zmapStyle_I.h,v 1.11 2009-05-18 14:55:05 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -253,6 +253,23 @@ typedef struct
} ZMapStyleTranscriptStruct, *ZMapStyleTranscript ;
+/*! @struct ZMapStyleAssemblyPath zmapStyle_P.h
+ * @brief AssemblyPath feature
+ *
+ * Draws an assembly path as a series of boxes placed alternately to form a tiling path. */
+typedef struct
+{
+ struct
+ {
+ unsigned int unused : 1 ;
+ } fields_set ; /*!< Fields set. */
+
+
+ ZMapStyleFullColourStruct non_path_colours ; /*!< Colour for non-assembly part of feature. */
+
+} ZMapStyleAssemblyPathStruct, *ZMapStyleAssemblyPath ;
+
+
/* THIS STRUCT NEEDS A MAGIC PTR, ONCE IT HAS ONE THEN ADD A TEST TO zmapStyleIsValid() FOR IT.... */
/*! @struct ZMapFeatureTypeStyle zmapStyle_P.h
@@ -414,6 +431,7 @@ typedef struct _zmapFeatureTypeStyleStruct
ZMapStyleSequenceStruct sequence ;
ZMapStyleTextStruct text ;
ZMapStyleTranscriptStruct transcript ;
+ ZMapStyleAssemblyPathStruct assembly_path ;
ZMapStyleAlignmentStruct alignment ;
ZMapStyleGraphStruct graph ;
ZMapStyleGlyphStruct glyph ;
--
GitLab