From 505a51056017bf07e3ed68c23297103385cdc208 Mon Sep 17 00:00:00 2001
From: mh17 <mh17>
Date: Tue, 20 Apr 2010 12:00:37 +0000
Subject: [PATCH] fixed for styles glyph-align, unmarked-colinear and some
other options
---
src/include/ZMap/zmapStyle.h | 7 +++-
src/zmapConfig/zmapConfigLoader.c | 13 +++++-
src/zmapFeature/zmapFeatureTypes.c | 10 ++++-
src/zmapFeature/zmapStyle.c | 5 ++-
src/zmapFeature/zmapStyleUtils.c | 4 +-
src/zmapFeature/zmapStyle_I.h | 6 +--
.../items/zmapWindowContainerFeatureSet.c | 40 ++++++++++++++++++-
.../items/zmapWindowContainerFeatureSet_I.h | 13 +++---
src/zmapWindow/zmapWindowColBump.c | 7 ++--
9 files changed, 83 insertions(+), 22 deletions(-)
diff --git a/src/include/ZMap/zmapStyle.h b/src/include/ZMap/zmapStyle.h
index c82bd06d0..cea6fac52 100755
--- a/src/include/ZMap/zmapStyle.h
+++ b/src/include/ZMap/zmapStyle.h
@@ -28,7 +28,7 @@
* HISTORY:
* Last edited: Jan 26 08:42 2010 (edgrif)
* Created: Mon Feb 26 09:28:26 2007 (edgrif)
- * CVS info: $Id: zmapStyle.h,v 1.55 2010-04-19 11:45:57 mh17 Exp $
+ * CVS info: $Id: zmapStyle.h,v 1.56 2010-04-20 12:00:37 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_STYLE_H
@@ -169,6 +169,7 @@ typedef enum
STYLE_PROP_ALIGNMENT_PERFECT_COLOURS,
STYLE_PROP_ALIGNMENT_COLINEAR_COLOURS,
STYLE_PROP_ALIGNMENT_NONCOLINEAR_COLOURS,
+ STYLE_PROP_ALIGNMENT_UNMARKED_COLINEAR,
STYLE_PROP_TRANSCRIPT_CDS_COLOURS,
@@ -265,7 +266,7 @@ typedef enum
#define ZMAPSTYLE_PROPERTY_ALIGNMENT_PERFECT_COLOURS "alignment-perfect-colours"
#define ZMAPSTYLE_PROPERTY_ALIGNMENT_COLINEAR_COLOURS "alignment-colinear-colours"
#define ZMAPSTYLE_PROPERTY_ALIGNMENT_NONCOLINEAR_COLOURS "alignment-noncolinear-colours"
-#define ZMAPSTYLE_PROPERTY_ALIGNMENT_SHOW_UNMARKED_COLINEAR "alignment-unmarked-colinear"
+#define ZMAPSTYLE_PROPERTY_ALIGNMENT_UNMARKED_COLINEAR "alignment-unmarked-colinear"
/* transcript properties */
#define ZMAPSTYLE_PROPERTY_TRANSCRIPT_CDS_COLOURS "transcript-cds-colours"
@@ -485,6 +486,7 @@ ZMAP_ENUM_FROM_STRING_DEC(zMapStyleStr2BumpMode, ZMapStyleBumpMode) ;
ZMAP_ENUM_FROM_STRING_DEC(zMapStyleStr2GlyphStrand, ZMapStyleGlyphStrand) ;
ZMAP_ENUM_FROM_STRING_DEC(zMapStyleStr2SubFeature, ZMapStyleSubFeature) ;
ZMAP_ENUM_FROM_STRING_DEC(zMapStyleStr2GlyphAlign, ZMapStyleGlyphAlign) ;
+ZMAP_ENUM_FROM_STRING_DEC(zMapStyleStr2BlixemType, ZMapStyleBlixemType) ;
/* Enum -> String function decs: const char *zMapStyleXXXXMode2ExactStr(ZMapStyleXXXXXMode mode); */
ZMAP_ENUM_AS_EXACT_STRING_DEC(zMapStyleMode2ExactStr, ZMapStyleMode) ;
@@ -499,6 +501,7 @@ ZMAP_ENUM_AS_EXACT_STRING_DEC(zmapStyleBumpMode2ExactStr, ZMapStyleBumpMode)
ZMAP_ENUM_AS_EXACT_STRING_DEC(zmapStyleGlyphStrand2ExactStr, ZMapStyleGlyphStrand) ;
ZMAP_ENUM_AS_EXACT_STRING_DEC(zmapStyleSubFeature2ExactStr, ZMapStyleSubFeature) ;
ZMAP_ENUM_AS_EXACT_STRING_DEC(zmapStyleGlyphAlign2ExactStr, ZMapStyleGlyphAlign) ;
+ZMAP_ENUM_AS_EXACT_STRING_DEC(zmapStyleBlixemType2ExactStr, ZMapStyleBlixemType) ;
ZMAP_ENUM_TO_SHORT_TEXT_DEC(zmapStyleBumpMode2ShortText, ZMapStyleBumpMode) ;
diff --git a/src/zmapConfig/zmapConfigLoader.c b/src/zmapConfig/zmapConfigLoader.c
index 1dc6fc356..4578bccc6 100644
--- a/src/zmapConfig/zmapConfigLoader.c
+++ b/src/zmapConfig/zmapConfigLoader.c
@@ -31,7 +31,7 @@
* HISTORY:
* Last edited: Mar 2 14:47 2010 (edgrif)
* Created: Thu Sep 25 14:12:05 2008 (rds)
- * CVS info: $Id: zmapConfigLoader.c,v 1.14 2010-04-19 11:00:39 mh17 Exp $
+ * CVS info: $Id: zmapConfigLoader.c,v 1.15 2010-04-20 12:00:37 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -910,6 +910,7 @@ static gpointer create_config_style()
{ ZMAPSTYLE_PROPERTY_FRAME2_COLOURS, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2COLOUR, {NULL} },
{ ZMAPSTYLE_PROPERTY_REV_COLOURS, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2COLOUR, {NULL} },
+ { ZMAPSTYLE_PROPERTY_DISPLAY_MODE, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2ENUM, {(ZMapConfStr2EnumFunc)zMapStyleStr2ColDisplayState} },
{ ZMAPSTYLE_PROPERTY_BUMP_MODE, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2ENUM, {(ZMapConfStr2EnumFunc)zMapStyleStr2BumpMode} },
{ ZMAPSTYLE_PROPERTY_DEFAULT_BUMP_MODE, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2ENUM, {(ZMapConfStr2EnumFunc)zMapStyleStr2BumpMode} },
{ ZMAPSTYLE_PROPERTY_BUMP_SPACING, FALSE, ZMAPCONF_DOUBLE, {FALSE}, ZMAPCONV_NONE, {NULL} },
@@ -962,10 +963,13 @@ static gpointer create_config_style()
{ ZMAPSTYLE_PROPERTY_ALIGNMENT_PARSE_GAPS, FALSE, ZMAPCONF_BOOLEAN, {FALSE}, ZMAPCONV_NONE, {NULL} },
{ ZMAPSTYLE_PROPERTY_ALIGNMENT_SHOW_GAPS, FALSE, ZMAPCONF_BOOLEAN, {FALSE}, ZMAPCONV_NONE, {NULL} },
{ ZMAPSTYLE_PROPERTY_ALIGNMENT_PFETCHABLE, FALSE, ZMAPCONF_BOOLEAN, {FALSE}, ZMAPCONV_NONE, {NULL} },
+ { ZMAPSTYLE_PROPERTY_ALIGNMENT_BLIXEM, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2ENUM, {(ZMapConfStr2EnumFunc) zMapStyleStr2BlixemType } },
{ ZMAPSTYLE_PROPERTY_ALIGNMENT_JOIN_ALIGN, FALSE, ZMAPCONF_INT, {FALSE}, ZMAPCONV_NONE, {NULL} },
+ { ZMAPSTYLE_PROPERTY_ALIGNMENT_ALLOW_MISALIGN, FALSE, ZMAPCONF_BOOLEAN, {FALSE}, ZMAPCONV_NONE, {NULL} },
{ ZMAPSTYLE_PROPERTY_ALIGNMENT_PERFECT_COLOURS, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2COLOUR, {NULL} },
{ ZMAPSTYLE_PROPERTY_ALIGNMENT_COLINEAR_COLOURS, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2COLOUR, {NULL} },
{ ZMAPSTYLE_PROPERTY_ALIGNMENT_NONCOLINEAR_COLOURS, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2COLOUR, {NULL} },
+ { ZMAPSTYLE_PROPERTY_ALIGNMENT_UNMARKED_COLINEAR, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2ENUM, {(ZMapConfStr2EnumFunc)zMapStyleStr2ColDisplayState} },
{ ZMAPSTYLE_PROPERTY_TRANSCRIPT_CDS_COLOURS, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2COLOUR, {NULL} },
@@ -1032,6 +1036,8 @@ static ZMapConfigIniContextKeyEntry get_style_group_data(char **stanza_name, cha
{ ZMAPSTYLE_PROPERTY_FRAME2_COLOURS, G_TYPE_STRING, style_set_property, FALSE },
{ ZMAPSTYLE_PROPERTY_REV_COLOURS, G_TYPE_STRING, style_set_property, FALSE },
+ { ZMAPSTYLE_PROPERTY_DISPLAY_MODE, G_TYPE_STRING, style_set_property, FALSE },
+
{ ZMAPSTYLE_PROPERTY_BUMP_MODE, G_TYPE_STRING, style_set_property, FALSE },
{ ZMAPSTYLE_PROPERTY_DEFAULT_BUMP_MODE, G_TYPE_STRING, style_set_property, FALSE },
{ ZMAPSTYLE_PROPERTY_BUMP_SPACING, G_TYPE_DOUBLE, style_set_property, FALSE },
@@ -1070,7 +1076,7 @@ static ZMapConfigIniContextKeyEntry get_style_group_data(char **stanza_name, cha
{ ZMAPSTYLE_PROPERTY_GLYPH_ALT_COLOURS, G_TYPE_STRING, style_set_property, FALSE },
{ ZMAPSTYLE_PROPERTY_GLYPH_THRESHOLD, G_TYPE_INT, style_set_property, FALSE },
{ ZMAPSTYLE_PROPERTY_GLYPH_STRAND, G_TYPE_BOOLEAN, style_set_property, FALSE },
- { ZMAPSTYLE_PROPERTY_GLYPH_ALIGN, G_TYPE_INT, style_set_property, FALSE },
+ { ZMAPSTYLE_PROPERTY_GLYPH_ALIGN, G_TYPE_STRING, style_set_property, FALSE },
{ ZMAPSTYLE_PROPERTY_GRAPH_MODE, G_TYPE_STRING, style_set_property, FALSE },
@@ -1080,10 +1086,13 @@ static ZMapConfigIniContextKeyEntry get_style_group_data(char **stanza_name, cha
{ ZMAPSTYLE_PROPERTY_ALIGNMENT_PARSE_GAPS, G_TYPE_BOOLEAN, style_set_property, FALSE },
{ ZMAPSTYLE_PROPERTY_ALIGNMENT_SHOW_GAPS, G_TYPE_BOOLEAN, style_set_property, FALSE },
{ ZMAPSTYLE_PROPERTY_ALIGNMENT_PFETCHABLE, G_TYPE_BOOLEAN, style_set_property, FALSE },
+ { ZMAPSTYLE_PROPERTY_ALIGNMENT_BLIXEM, G_TYPE_STRING, style_set_property, FALSE },
{ ZMAPSTYLE_PROPERTY_ALIGNMENT_JOIN_ALIGN, G_TYPE_INT, style_set_property, FALSE },
+ { ZMAPSTYLE_PROPERTY_ALIGNMENT_ALLOW_MISALIGN, G_TYPE_BOOLEAN, style_set_property, FALSE },
{ ZMAPSTYLE_PROPERTY_ALIGNMENT_PERFECT_COLOURS, G_TYPE_STRING, style_set_property, FALSE },
{ ZMAPSTYLE_PROPERTY_ALIGNMENT_COLINEAR_COLOURS, G_TYPE_STRING, style_set_property, FALSE },
{ ZMAPSTYLE_PROPERTY_ALIGNMENT_NONCOLINEAR_COLOURS, G_TYPE_STRING, style_set_property, FALSE },
+ { ZMAPSTYLE_PROPERTY_ALIGNMENT_UNMARKED_COLINEAR, G_TYPE_STRING, style_set_property, FALSE },
{ ZMAPSTYLE_PROPERTY_TRANSCRIPT_CDS_COLOURS, G_TYPE_STRING, style_set_property, FALSE },
diff --git a/src/zmapFeature/zmapFeatureTypes.c b/src/zmapFeature/zmapFeatureTypes.c
index 7efbb61ca..a82e15581 100755
--- a/src/zmapFeature/zmapFeatureTypes.c
+++ b/src/zmapFeature/zmapFeatureTypes.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Jan 26 12:02 2010 (edgrif)
* Created: Tue Dec 14 13:15:11 2004 (edgrif)
- * CVS info: $Id: zmapFeatureTypes.c,v 1.94 2010-04-19 11:00:39 mh17 Exp $
+ * CVS info: $Id: zmapFeatureTypes.c,v 1.95 2010-04-20 12:00:37 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -368,6 +368,14 @@ ZMapStyleBumpMode zMapStyleGetDefaultBumpMode(ZMapFeatureTypeStyle style)
}
+gboolean zMapStyleGetUnmarked(ZMapFeatureTypeStyle style)
+{
+ gboolean x = TRUE; // spec says default to true
+
+ if(zMapStyleIsPropertySetId(style,STYLE_PROP_ALIGNMENT_UNMARKED_COLINEAR))
+ x = style->mode_data.alignment.unmarked_colinear;
+ return(x);
+}
void zMapStyleSetParent(ZMapFeatureTypeStyle style, char *parent_name)
diff --git a/src/zmapFeature/zmapStyle.c b/src/zmapFeature/zmapStyle.c
index b88eac2e1..761a3e62a 100755
--- a/src/zmapFeature/zmapStyle.c
+++ b/src/zmapFeature/zmapStyle.c
@@ -28,7 +28,7 @@
*
* Exported functions: See ZMap/zmapStyle.h
*
- * CVS info: $Id: zmapStyle.c,v 1.47 2010-04-19 11:45:57 mh17 Exp $
+ * CVS info: $Id: zmapStyle.c,v 1.48 2010-04-20 12:00:37 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -271,6 +271,9 @@ ZMapStyleParamStruct zmapStyleParams_G[_STYLE_PROP_N_ITEMS] =
{ STYLE_PROP_ALIGNMENT_NONCOLINEAR_COLOURS, STYLE_PARAM_TYPE_COLOUR, ZMAPSTYLE_PROPERTY_ALIGNMENT_NONCOLINEAR_COLOURS,
"noncolinear alignment indicator colour", "Colours used to show two alignments have exactly contiguous coords.",
offsetof(zmapFeatureTypeStyleStruct, mode_data.alignment.noncolinear) ,ZMAPSTYLE_MODE_ALIGNMENT },
+ { STYLE_PROP_ALIGNMENT_UNMARKED_COLINEAR, STYLE_PARAM_TYPE_COLDISP, ZMAPSTYLE_PROPERTY_ALIGNMENT_UNMARKED_COLINEAR,
+ "paint colinear lines when unmarked", "paint colinear lines when unmarked ?",
+ offsetof(zmapFeatureTypeStyleStruct, mode_data.alignment.unmarked_colinear), ZMAPSTYLE_MODE_ALIGNMENT },
{ STYLE_PROP_TRANSCRIPT_CDS_COLOURS, STYLE_PARAM_TYPE_COLOUR, ZMAPSTYLE_PROPERTY_TRANSCRIPT_CDS_COLOURS,
diff --git a/src/zmapFeature/zmapStyleUtils.c b/src/zmapFeature/zmapStyleUtils.c
index 20ca1fd53..f52516485 100755
--- a/src/zmapFeature/zmapStyleUtils.c
+++ b/src/zmapFeature/zmapStyleUtils.c
@@ -30,7 +30,7 @@
* HISTORY:
* Last edited: Jul 29 09:53 2009 (edgrif)
* Created: Thu Oct 30 10:24:35 2008 (edgrif)
- * CVS info: $Id: zmapStyleUtils.c,v 1.16 2010-04-19 11:00:39 mh17 Exp $
+ * CVS info: $Id: zmapStyleUtils.c,v 1.17 2010-04-20 12:00:37 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -125,6 +125,7 @@ ZMAP_ENUM_FROM_STRING_FUNC(zMapStyleStr2BumpMode, ZMapStyleBumpMode,
ZMAP_ENUM_FROM_STRING_FUNC(zMapStyleStr2GlyphStrand, ZMapStyleGlyphStrand, ZMAPSTYLE_GLYPH_STRAND_INVALID, ZMAP_STYLE_GLYPH_STRAND_LIST, , );
ZMAP_ENUM_FROM_STRING_FUNC(zMapStyleStr2SubFeature, ZMapStyleSubFeature, ZMAPSTYLE_SUB_FEATURE_INVALID, ZMAP_STYLE_SUB_FEATURE_LIST, , );
ZMAP_ENUM_FROM_STRING_FUNC(zMapStyleStr2GlyphAlign, ZMapStyleGlyphAlign, ZMAPSTYLE_GLYPH_ALIGN_INVALID, ZMAP_STYLE_GLYPH_ALIGN_LIST, , );
+ZMAP_ENUM_FROM_STRING_FUNC(zMapStyleStr2BlixemType, ZMapStyleBlixemType, ZMAPSTYLE_BLIXEM_INVALID, ZMAP_STYLE_BLIXEM_LIST, , );
@@ -149,6 +150,7 @@ ZMAP_ENUM_AS_EXACT_STRING_FUNC(zmapStyleBumpMode2ExactStr, ZMapStyleBumpMode
ZMAP_ENUM_AS_EXACT_STRING_FUNC(zmapStyleGlyphStrand2ExactStr, ZMapStyleGlyphStrand, ZMAP_STYLE_GLYPH_STRAND_LIST);
ZMAP_ENUM_AS_EXACT_STRING_FUNC(zmapStyleSubFeature2ExactStr, ZMapStyleSubFeature, ZMAP_STYLE_SUB_FEATURE_LIST);
ZMAP_ENUM_AS_EXACT_STRING_FUNC(zmapStyleGlyphAlign2ExactStr, ZMapStyleGlyphAlign, ZMAP_STYLE_GLYPH_ALIGN_LIST);
+ZMAP_ENUM_AS_EXACT_STRING_FUNC(zmapStyleBlixemType2ExactStr, ZMapStyleBlixemType, ZMAP_STYLE_BLIXEM_LIST);
/* Enum -> Short Text functions, these functions convert the enums to their corresponding short
diff --git a/src/zmapFeature/zmapStyle_I.h b/src/zmapFeature/zmapStyle_I.h
index 2d2346e9c..bc9337795 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 1.21 2010-04-19 11:00:39 mh17 Exp $
+ * CVS info: $Id: zmapStyle_I.h,v 1.22 2010-04-20 12:00:37 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -272,9 +272,7 @@ typedef struct
ZMapStyleFullColourStruct colinear ;
ZMapStyleFullColourStruct noncolinear ;
- /*! glyph type and colours for markimng incomplete ends */
-// ZMapStyleFullColourStruct incomplete_glyph_colour ;
-// ZMapStyleGlyphShape incomplete_glyph_type;
+ ZMapStyleColumnDisplayState unmarked_colinear; /* paint colinear lines even if not marked */
gboolean pfetchable; /* TRUE => alignments have pfetch entries. */
gboolean parse_gaps;
diff --git a/src/zmapWindow/items/zmapWindowContainerFeatureSet.c b/src/zmapWindow/items/zmapWindowContainerFeatureSet.c
index a891f69d6..5ff7488b9 100755
--- a/src/zmapWindow/items/zmapWindowContainerFeatureSet.c
+++ b/src/zmapWindow/items/zmapWindowContainerFeatureSet.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Mar 19 13:42 2010 (edgrif)
* Created: Mon Jul 30 13:09:33 2007 (rds)
- * CVS info: $Id: zmapWindowContainerFeatureSet.c,v 1.24 2010-04-15 11:19:04 mh17 Exp $
+ * CVS info: $Id: zmapWindowContainerFeatureSet.c,v 1.25 2010-04-20 12:00:38 mh17 Exp $
*-------------------------------------------------------------------
*/
#include <string.h> /* memset */
@@ -53,6 +53,7 @@ enum
ITEM_FEATURE_SET_VISIBLE,
ITEM_FEATURE_SET_BUMP_MODE,
ITEM_FEATURE_SET_DEFAULT_BUMP_MODE,
+ ITEM_FEATURE_SET_BUMP_UNMARKED,
ITEM_FEATURE_SET_FRAME_MODE,
ITEM_FEATURE_SET_SHOW_WHEN_EMPTY,
ITEM_FEATURE_SET_DEFERRED,
@@ -811,6 +812,27 @@ ZMapStyleBumpMode zmapWindowContainerFeatureSetGetDefaultBumpMode(ZMapWindowCont
return mode;
}
+
+ZMapStyleBumpMode zmapWindowContainerFeatureSetGetBumpUnmarked(ZMapWindowContainerFeatureSet container_set)
+{
+ gboolean x = TRUE;
+
+ container_set->settings.bump_unmarked = ZMAPSTYLE_COLDISPLAY_INVALID;
+
+ // this gets the data from a lot of styles
+ // perhaps it should be assigned when the property is set??
+ g_object_get(G_OBJECT(container_set),
+ ZMAPSTYLE_PROPERTY_ALIGNMENT_UNMARKED_COLINEAR, &(container_set->settings.bump_unmarked),
+ NULL);
+
+ if(container_set->settings.bump_unmarked &&
+ container_set->settings.bump_unmarked != ZMAPSTYLE_COLDISPLAY_SHOW)
+ x = FALSE;
+
+ return x;
+}
+
+
/*!
* \brief reset the bump modes
*
@@ -1179,7 +1201,17 @@ static void zmap_window_item_feature_set_class_init(ZMapWindowContainerFeatureSe
ZMAPBUMP_END,
ZMAPBUMP_INVALID,
ZMAP_PARAM_STATIC_RO));
- /* bump default */
+ /* bump unmarked */
+ g_object_class_install_property(gobject_class,
+ ITEM_FEATURE_SET_BUMP_UNMARKED,
+ g_param_spec_uint(ZMAPSTYLE_PROPERTY_ALIGNMENT_UNMARKED_COLINEAR,
+ ZMAPSTYLE_PROPERTY_ALIGNMENT_UNMARKED_COLINEAR,
+ "[ hide | show_hide | show ]",
+ ZMAPSTYLE_COLDISPLAY_INVALID,
+ ZMAPSTYLE_COLDISPLAY_SHOW,
+ ZMAPSTYLE_COLDISPLAY_INVALID,
+ ZMAP_PARAM_STATIC_RO));
+ /* join aligns */
g_object_class_install_property(gobject_class,
ITEM_FEATURE_SET_JOIN_ALIGNS,
g_param_spec_uint(ZMAPSTYLE_PROPERTY_ALIGNMENT_JOIN_ALIGN,
@@ -1307,6 +1339,7 @@ static void zmap_window_item_feature_set_get_property(GObject *gobject,
case ITEM_FEATURE_SET_VISIBLE:
case ITEM_FEATURE_SET_BUMP_MODE:
case ITEM_FEATURE_SET_DEFAULT_BUMP_MODE:
+ case ITEM_FEATURE_SET_BUMP_UNMARKED:
case ITEM_FEATURE_SET_FRAME_MODE:
case ITEM_FEATURE_SET_SHOW_WHEN_EMPTY:
case ITEM_FEATURE_SET_DEFERRED:
@@ -1501,6 +1534,9 @@ static void extract_value_from_style_table(gpointer key, gpointer value, gpointe
break;
}
+ case ITEM_FEATURE_SET_BUMP_UNMARKED:
+ if(zMapStyleGetMode(style) != ZMAPSTYLE_MODE_ALIGNMENT)
+ break;
case ITEM_FEATURE_SET_VISIBLE:
{
guint style_version = 0, current;
diff --git a/src/zmapWindow/items/zmapWindowContainerFeatureSet_I.h b/src/zmapWindow/items/zmapWindowContainerFeatureSet_I.h
index 5be2fc933..aeb238ec8 100755
--- a/src/zmapWindow/items/zmapWindowContainerFeatureSet_I.h
+++ b/src/zmapWindow/items/zmapWindowContainerFeatureSet_I.h
@@ -6,12 +6,12 @@
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
@@ -23,13 +23,13 @@
* Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
* Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
*
- * Description:
+ * Description:
*
* Exported functions: See XXXXXXXXXXXXX.h
* HISTORY:
* Last edited: Oct 27 10:46 2009 (edgrif)
* Created: Fri Feb 6 11:49:03 2009 (rds)
- * CVS info: $Id: zmapWindowContainerFeatureSet_I.h,v 1.8 2010-03-04 15:12:10 mh17 Exp $
+ * CVS info: $Id: zmapWindowContainerFeatureSet_I.h,v 1.9 2010-04-20 12:00:38 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -53,7 +53,7 @@ typedef struct _zmapWindowContainerFeatureSetStruct
/* Empty columns are only hidden ATM and as they have no
* ZMapFeatureSet removing them from the FToI hash becomes difficult
- * without the align, block and set ids. No doubt it'l be true for
+ * without the align, block and set ids. No doubt it'l be true for
* empty block and align containers too at some point. */
GQuark align_id;
@@ -68,7 +68,7 @@ typedef struct _zmapWindowContainerFeatureSetStruct
/* These fields are used for some of the more exotic column bumping. */
gboolean hidden_bump_features ; /* Features were hidden because they
- * are out of the marked range. */
+ * are out of the marked range. */
struct
{
@@ -78,6 +78,7 @@ typedef struct _zmapWindowContainerFeatureSetStruct
gboolean frame_specific;
gboolean strand_specific;
gboolean show_reverse_strand;
+ ZMapStyleColumnDisplayState bump_unmarked;
ZMapStyle3FrameMode frame_mode;
ZMapStyleColumnDisplayState display_state;
ZMapStyleBumpMode bump_mode;
diff --git a/src/zmapWindow/zmapWindowColBump.c b/src/zmapWindow/zmapWindowColBump.c
index b44089da8..7514a109d 100755
--- a/src/zmapWindow/zmapWindowColBump.c
+++ b/src/zmapWindow/zmapWindowColBump.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Mar 4 12:11 2010 (edgrif)
* Created: Tue Sep 4 10:52:09 2007 (edgrif)
- * CVS info: $Id: zmapWindowColBump.c,v 1.69 2010-04-15 11:19:03 mh17 Exp $
+ * CVS info: $Id: zmapWindowColBump.c,v 1.70 2010-04-20 12:00:37 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -377,7 +377,8 @@ void zmapWindowColumnBumpRange(FooCanvasItem *bump_item, ZMapStyleBumpMode bump_
BumpColStruct bump_data = {NULL} ;
FooCanvasGroup *column_features ;
ZMapWindowContainerFeatureSet container = NULL;
- BumpPropertiesStruct bump_properties = {NULL};
+ ZMapWindowContainerFeatureSetClass container_class = NULL;
+ BumpPropertiesStruct bump_properties = {NULL};
ZMapStyleBumpMode historic_bump_mode;
ZMapWindow window;
gboolean column = FALSE ;
@@ -724,7 +725,7 @@ void zmapWindowColumnBumpRange(FooCanvasItem *bump_item, ZMapStyleBumpMode bump_
/* TRY JUST ADDING GAPS IF A MARK IS SET */
- if (mark_set && bump_mode != ZMAPBUMP_NAME_INTERLEAVE)
+ if ((mark_set || zmapWindowContainerFeatureSetGetBumpUnmarked(container)) && bump_mode != ZMAPBUMP_NAME_INTERLEAVE)
{
/* NOTE THERE IS AN ISSUE HERE...WE SHOULD ADD COLINEAR STUFF FOR ALIGN FEATURES
* THIS IS NOT EXPLICIT IN THE CODE WHICH IS NOT CORRECT....NEED TO THINK THIS
--
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