From f7a16a0d9831acca81cf530389820b17f8ca7b84 Mon Sep 17 00:00:00 2001
From: mh17 <mh17>
Date: Mon, 19 Apr 2010 11:00:39 +0000
Subject: [PATCH] more glyph tweaks and pipe stuff
---
src/include/ZMap/zmapStyle.h | 29 +++++++++++----
src/zmapConfig/zmapConfigLoader.c | 12 +++---
src/zmapFeature/zmapFeatureTypes.c | 11 +++++-
src/zmapFeature/zmapStyle.c | 38 +++++++++++++------
src/zmapFeature/zmapStyleUtils.c | 4 +-
src/zmapFeature/zmapStyle_I.h | 4 +-
src/zmapView/zmapView.c | 43 ++++++++++++++++------
src/zmapView/zmapViewRemoteReceive.c | 11 +++++-
src/zmapWindow/items/zmapWindowGlyphItem.c | 26 ++++++++-----
9 files changed, 127 insertions(+), 51 deletions(-)
diff --git a/src/include/ZMap/zmapStyle.h b/src/include/ZMap/zmapStyle.h
index 372316fc0..c55d3e1da 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 1.53 2010-04-15 11:19:03 mh17 Exp $
+ * CVS info: $Id: zmapStyle.h,v 1.54 2010-04-19 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_STYLE_H
@@ -155,6 +155,7 @@ typedef enum
STYLE_PROP_GLYPH_ALT_COLOURS,
STYLE_PROP_GLYPH_THRESHOLD,
STYLE_PROP_GLYPH_STRAND,
+ STYLE_PROP_GLYPH_ALIGN,
STYLE_PROP_GRAPH_MODE,
STYLE_PROP_GRAPH_BASELINE,
@@ -246,6 +247,7 @@ typedef enum
#define ZMAPSTYLE_PROPERTY_GLYPH_ALT_COLOURS "glyph-alt-colours"
#define ZMAPSTYLE_PROPERTY_GLYPH_THRESHOLD "glyph-threshold"
#define ZMAPSTYLE_PROPERTY_GLYPH_STRAND "glyph-strand"
+#define ZMAPSTYLE_PROPERTY_GLYPH_ALIGN "glyph-align"
/* graph properties. */
@@ -263,6 +265,7 @@ 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"
/* transcript properties */
#define ZMAPSTYLE_PROPERTY_TRANSCRIPT_CDS_COLOURS "transcript-cds-colours"
@@ -367,7 +370,7 @@ ZMAP_DEFINE_ENUM(ZMapStyleGraphMode, ZMAP_STYLE_GRAPH_MODE_LIST);
_(ZMAPSTYLE_SUB_FEATURE_INVALID, , "invalid", "Not used. ", "") \
_(ZMAPSTYLE_SUB_FEATURE_HOMOLOGY, , "homology" , "Incomplete-homology-marker" , "") \
_(ZMAPSTYLE_SUB_FEATURE_NON_CONCENCUS_SPLICE, , "non-concensus-splice" , "Non concensus splice marker" , "") \
-_(ZMAPSTYLE_SUBFEATURE_TRUNCATED, , "truncated" , "Truncated transcript" , "")\
+_(ZMAPSTYLE_SUB_FEATURE_TRUNCATED, , "truncated" , "Truncated transcript" , "")\
_(ZMAPSTYLE_SUB_FEATURE_POLYA, , "polyA" , "Poly A tail on RNA seq" , "") \
_(ZMAPSTYLE_SUB_FEATURE_MAX , ,"do-not-use" ,"" , "")
@@ -385,6 +388,16 @@ _(ZMAPSTYLE_GLYPH_STRAND_FLIP_Y, , "flip-y" , "" , "")
ZMAP_DEFINE_ENUM(ZMapStyleGlyphStrand, ZMAP_STYLE_GLYPH_STRAND_LIST);
+/*
+ * specifies glyph alignment: NB glyph shape should be chosen appropriately!
+ */
+#define ZMAP_STYLE_GLYPH_ALIGN_LIST(_) \
+_(ZMAPSTYLE_GLYPH_ALIGN_INVALID, , "invalid", "Initial setting. ", "") \
+_(ZMAPSTYLE_GLYPH_ALIGN_LEFT, , "left" , "" , "") \
+_(ZMAPSTYLE_GLYPH_ALIGN_CENTRE,, "centre" , "" , "") \
+_(ZMAPSTYLE_GLYPH_ALIGN_RIGHT, , "right" , "" , "")
+
+ZMAP_DEFINE_ENUM(ZMapStyleGlyphAlign, ZMAP_STYLE_GLYPH_ALIGN_LIST);
/* Specifies type of colour, e.g. normal or selected. */
@@ -410,12 +423,12 @@ ZMAP_DEFINE_ENUM(ZMapStyleDrawContext, ZMAP_STYLE_DRAW_CONTEXT_LIST) ;
#define ZMAP_STYLE_SCORE_MODE_LIST(_) \
_(ZMAPSCORE_INVALID, , "invalid" , "Use column width only - default. ", "") \
_(ZMAPSCORE_WIDTH, , "width" , "Use column width only - default. ", "") \
+_(ZMAPSCORE_HEIGHT, , "height" , "scale height of glyph. ", "") \
+_(ZMAPSCORE_SIZE, , "size" , "scale size of glyph. ", "") \
_(ZMAPSCORE_OFFSET, , "offset" , "" , "") \
_(ZMAPSCORE_HISTOGRAM, , "histogram", "" , "") \
_(ZMAPSCORE_PERCENT, , "percent" , "" , "")\
-_(ZMAPSTYLE_SCORE_GLYPH_HEIGHT, , "glyph-height" , "variable height for glyph" , "") \
-_(ZMAPSTYLE_SCORE_GLYPH_WIDTH , , "glyph-width" , "variable width for glyph" , "") \
-_(ZMAPSTYLE_SCORE_ALT, , "alt" , "alternate colour for glyph" , "")
+_(ZMAPSTYLE_SCORE_ALT, , "alt" , "alternate colour for glyph" , "")
ZMAP_DEFINE_ENUM(ZMapStyleScoreMode, ZMAP_STYLE_SCORE_MODE_LIST) ;
@@ -470,7 +483,7 @@ ZMAP_ENUM_FROM_STRING_DEC(zMapStyleStr2ScoreMode, ZMapStyleScoreMode) ;
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) ;
/* Enum -> String function decs: const char *zMapStyleXXXXMode2ExactStr(ZMapStyleXXXXXMode mode); */
ZMAP_ENUM_AS_EXACT_STRING_DEC(zMapStyleMode2ExactStr, ZMapStyleMode) ;
@@ -484,7 +497,7 @@ ZMAP_ENUM_AS_EXACT_STRING_DEC(zmapStyleScoreMode2ExactStr, ZMapStyleScoreM
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_TO_SHORT_TEXT_DEC(zmapStyleBumpMode2ShortText, ZMapStyleBumpMode) ;
@@ -558,8 +571,8 @@ double zMapStyleGetWidth(ZMapFeatureTypeStyle style) ;
int zMapStyleGlyphThreshold(ZMapFeatureTypeStyle style);
-
ZMapStyleGlyphStrand zMapStyleGlyphStrand(ZMapFeatureTypeStyle style);
+ZMapStyleGlyphAlign zMapStyleGetAlign(ZMapFeatureTypeStyle style);
void zMapStyleGetGappedAligns(ZMapFeatureTypeStyle style, gboolean *parse_gaps, gboolean *show_gaps) ;
diff --git a/src/zmapConfig/zmapConfigLoader.c b/src/zmapConfig/zmapConfigLoader.c
index eb01d1003..1dc6fc356 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 1.13 2010-04-15 11:19:03 mh17 Exp $
+ * CVS info: $Id: zmapConfigLoader.c,v 1.14 2010-04-19 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -948,13 +948,12 @@ static gpointer create_config_style()
{ ZMAPSTYLE_PROPERTY_GLYPH_NAME_3, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2ENUM, {(ZMapConfStr2EnumFunc)zMapStyleQuark} },
{ ZMAPSTYLE_PROPERTY_GLYPH_SHAPE_3, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_NONE, {NULL} },
-// { ZMAPSTYLE_PROPERTY_GLYPH_COLOURS, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2COLOUR, {NULL} },
{ ZMAPSTYLE_PROPERTY_GLYPH_ALT_COLOURS, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2COLOUR, {NULL} },
-// { ZMAPSTYLE_PROPERTY_GLYPH_MODE, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2ENUM, {(ZMapConfStr2EnumFunc)zMapStyleStr2GlyphMode} },
-// { ZMAPSTYLE_PROPERTY_GLYPH_SCORE_MODE, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2ENUM, {(ZMapConfStr2EnumFunc)zMapStyleStr2GlyphScoreMode} },
{ ZMAPSTYLE_PROPERTY_GLYPH_THRESHOLD, FALSE, ZMAPCONF_INT, {FALSE}, ZMAPCONV_NONE, {NULL} },
+ { ZMAPSTYLE_PROPERTY_GLYPH_STRAND, FALSE, ZMAPCONF_BOOLEAN, {FALSE}, ZMAPCONV_NONE, {NULL} },
+ { ZMAPSTYLE_PROPERTY_GLYPH_ALIGN, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2ENUM, {(ZMapConfStr2EnumFunc)zMapStyleStr2GlyphAlign} },
{ ZMAPSTYLE_PROPERTY_GRAPH_MODE, FALSE, ZMAPCONF_STR, {FALSE}, ZMAPCONV_STR2ENUM, {(ZMapConfStr2EnumFunc)zMapStyleStr2GraphMode} },
{ ZMAPSTYLE_PROPERTY_GRAPH_BASELINE, FALSE, ZMAPCONF_DOUBLE, {FALSE}, ZMAPCONV_NONE, {NULL} },
@@ -1068,11 +1067,10 @@ static ZMapConfigIniContextKeyEntry get_style_group_data(char **stanza_name, cha
{ ZMAPSTYLE_PROPERTY_GLYPH_NAME, G_TYPE_STRING, style_set_property, FALSE },
{ ZMAPSTYLE_PROPERTY_GLYPH_NAME_5, G_TYPE_STRING, style_set_property, FALSE },
{ ZMAPSTYLE_PROPERTY_GLYPH_NAME_3, G_TYPE_STRING, style_set_property, FALSE },
-// { ZMAPSTYLE_PROPERTY_GLYPH_COLOURS, G_TYPE_STRING, style_set_property, FALSE },
{ ZMAPSTYLE_PROPERTY_GLYPH_ALT_COLOURS, G_TYPE_STRING, style_set_property, FALSE },
-// { ZMAPSTYLE_PROPERTY_GLYPH_MODE, G_TYPE_STRING, style_set_property, FALSE },
-// { ZMAPSTYLE_PROPERTY_GLYPH_SCORE_MODE, 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_GRAPH_MODE, G_TYPE_STRING, style_set_property, FALSE },
diff --git a/src/zmapFeature/zmapFeatureTypes.c b/src/zmapFeature/zmapFeatureTypes.c
index d55b858d5..7efbb61ca 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 1.93 2010-04-15 11:19:03 mh17 Exp $
+ * CVS info: $Id: zmapFeatureTypes.c,v 1.94 2010-04-19 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -785,6 +785,15 @@ double zMapStyleGetMinScore(ZMapFeatureTypeStyle style)
return min_score ;
}
+ZMapStyleGlyphAlign zMapStyleGetAlign(ZMapFeatureTypeStyle style)
+{
+ ZMapStyleGlyphAlign z = ZMAPSTYLE_GLYPH_ALIGN_INVALID;
+
+ if(zMapStyleIsPropertySetId(style,STYLE_PROP_GLYPH_ALIGN))
+ z = style->mode_data.glyph.glyph_align;
+ return(z);
+}
+
ZMapStyleScoreMode zMapStyleGetScoreMode(ZMapFeatureTypeStyle style)
{
ZMapStyleScoreMode z = ZMAPSCORE_INVALID;
diff --git a/src/zmapFeature/zmapStyle.c b/src/zmapFeature/zmapStyle.c
index 684329ac8..a0813f361 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 1.45 2010-04-15 11:19:03 mh17 Exp $
+ * CVS info: $Id: zmapStyle.c,v 1.46 2010-04-19 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -194,33 +194,43 @@ ZMapStyleParamStruct zmapStyleParams_G[_STYLE_PROP_N_ITEMS] =
{ STYLE_PROP_GLYPH_NAME, STYLE_PARAM_TYPE_QUARK, ZMAPSTYLE_PROPERTY_GLYPH_NAME,
"glyph-name", "Glyph name used to reference glyphs config stanza",
- offsetof(zmapFeatureTypeStyleStruct, mode_data.glyph.glyph_name),0 },
+ offsetof(zmapFeatureTypeStyleStruct, mode_data.glyph.glyph_name),ZMAPSTYLE_MODE_GLYPH },
+
{ STYLE_PROP_GLYPH_SHAPE, STYLE_PARAM_TYPE_GLYPH_SHAPE, ZMAPSTYLE_PROPERTY_GLYPH_SHAPE,
"glyph-type", "Type of glyph to show.",
- offsetof(zmapFeatureTypeStyleStruct, mode_data.glyph.glyph), 0 },
- { STYLE_PROP_GLYPH_NAME, STYLE_PARAM_TYPE_QUARK, ZMAPSTYLE_PROPERTY_GLYPH_NAME_5,
+ offsetof(zmapFeatureTypeStyleStruct, mode_data.glyph.glyph), ZMAPSTYLE_MODE_GLYPH },
+
+ { STYLE_PROP_GLYPH_NAME_5, STYLE_PARAM_TYPE_QUARK, ZMAPSTYLE_PROPERTY_GLYPH_NAME_5,
"glyph-name for 5' end", "Glyph name used to reference glyphs config stanza",
- offsetof(zmapFeatureTypeStyleStruct, mode_data.glyph.glyph_name_5),0 },
+ offsetof(zmapFeatureTypeStyleStruct, mode_data.glyph.glyph_name_5),ZMAPSTYLE_MODE_GLYPH },
+
{ STYLE_PROP_GLYPH_SHAPE_5, STYLE_PARAM_TYPE_GLYPH_SHAPE, ZMAPSTYLE_PROPERTY_GLYPH_SHAPE_5,
"glyph-type-5", "Type of glyph to show at 5' end.",
- offsetof(zmapFeatureTypeStyleStruct, mode_data.glyph.glyph5), 0 },
+ offsetof(zmapFeatureTypeStyleStruct, mode_data.glyph.glyph5), ZMAPSTYLE_MODE_GLYPH },
+
{ STYLE_PROP_GLYPH_NAME_3, STYLE_PARAM_TYPE_QUARK, ZMAPSTYLE_PROPERTY_GLYPH_NAME_3,
"glyph-name for 3' end", "Glyph name used to reference glyphs config stanza",
- offsetof(zmapFeatureTypeStyleStruct, mode_data.glyph.glyph_name_3),0 },
+ offsetof(zmapFeatureTypeStyleStruct, mode_data.glyph.glyph_name_3),ZMAPSTYLE_MODE_GLYPH },
+
{ STYLE_PROP_GLYPH_SHAPE_3, STYLE_PARAM_TYPE_GLYPH_SHAPE, ZMAPSTYLE_PROPERTY_GLYPH_SHAPE_3,
"glyph-type-3", "Type of glyph to show at 3' end.",
- offsetof(zmapFeatureTypeStyleStruct, mode_data.glyph.glyph3), 0 },
+ offsetof(zmapFeatureTypeStyleStruct, mode_data.glyph.glyph3), ZMAPSTYLE_MODE_GLYPH },
{ STYLE_PROP_GLYPH_ALT_COLOURS, STYLE_PARAM_TYPE_COLOUR,ZMAPSTYLE_PROPERTY_GLYPH_ALT_COLOURS,
"alternate glyph colour", "Colours used to show glyphs when below thrashold.",
- offsetof(zmapFeatureTypeStyleStruct, mode_data.glyph.glyph_alt_colours) ,0 },
+ offsetof(zmapFeatureTypeStyleStruct, mode_data.glyph.glyph_alt_colours) ,ZMAPSTYLE_MODE_GLYPH },
{ STYLE_PROP_GLYPH_THRESHOLD, STYLE_PARAM_TYPE_UINT, ZMAPSTYLE_PROPERTY_GLYPH_THRESHOLD,
"glyph-threshold", "Glyph threshold for alternate coloura",
- offsetof(zmapFeatureTypeStyleStruct, mode_data.glyph.glyph_threshold) ,0},
+ offsetof(zmapFeatureTypeStyleStruct, mode_data.glyph.glyph_threshold) ,ZMAPSTYLE_MODE_GLYPH },
+
{ STYLE_PROP_GLYPH_STRAND, STYLE_PARAM_TYPE_GLYPH_STRAND, ZMAPSTYLE_PROPERTY_GLYPH_STRAND,
"glyph-strand", "What to do for the reverse strand",
- offsetof(zmapFeatureTypeStyleStruct, mode_data.glyph.glyph_strand) ,0},
+ offsetof(zmapFeatureTypeStyleStruct, mode_data.glyph.glyph_strand) ,ZMAPSTYLE_MODE_GLYPH },
+
+ { STYLE_PROP_GLYPH_ALIGN, STYLE_PARAM_TYPE_GLYPH_ALIGN, ZMAPSTYLE_PROPERTY_GLYPH_ALIGN,
+ "glyph-align", "where to centre the glyph",
+ offsetof(zmapFeatureTypeStyleStruct, mode_data.glyph.glyph_align) ,ZMAPSTYLE_MODE_GLYPH },
@@ -1459,7 +1469,7 @@ ZMapFeatureTypeStyle zMapStyleLegacyStyle(char *name)
ZMAPSTYLE_PROPERTY_GLYPH_SHAPE_3, zMapStyleGetGlyphShape("<0,0; 15,0; 15,-10>"),
ZMAPSTYLE_PROPERTY_FRAME_MODE, ZMAPSTYLE_3_FRAME_ONLY_1,
- ZMAPSTYLE_PROPERTY_SCORE_MODE, ZMAPSTYLE_SCORE_GLYPH_WIDTH,
+ ZMAPSTYLE_PROPERTY_SCORE_MODE, ZMAPSCORE_WIDTH,
ZMAPSTYLE_PROPERTY_GLYPH_STRAND,ZMAPSTYLE_GLYPH_STRAND_FLIP_X,
ZMAPSTYLE_PROPERTY_SHOW_REVERSE_STRAND,TRUE,
@@ -1537,6 +1547,7 @@ guint zmapStyleParamSize(ZMapStyleParamType type)
case STYLE_PARAM_TYPE_GRAPH_MODE: return(sizeof(ZMapStyleGraphMode)); break;
case STYLE_PARAM_TYPE_BLIXEM: return(sizeof(ZMapStyleBlixemType)); break;
case STYLE_PARAM_TYPE_GLYPH_STRAND:return(sizeof(ZMapStyleGlyphStrand)); break;
+ case STYLE_PARAM_TYPE_GLYPH_ALIGN: return(sizeof(ZMapStyleGlyphAlign)); break;
case STYLE_PARAM_TYPE_GLYPH_SHAPE: return(sizeof(ZMapStyleGlyphShapeStruct)); break;
case STYLE_PARAM_TYPE_SUB_FEATURES:return(sizeof(GQuark) * ZMAPSTYLE_SUB_FEATURE_MAX); break;
@@ -1610,6 +1621,7 @@ void zmap_param_spec_init(ZMapStyleParam param)
case STYLE_PARAM_TYPE_GRAPH_MODE: // ZMapStyleGraphMode
case STYLE_PARAM_TYPE_BLIXEM: // ZMapStyleBlixemType
case STYLE_PARAM_TYPE_GLYPH_STRAND: // ZMapStyleGlyphStrand
+ case STYLE_PARAM_TYPE_GLYPH_ALIGN: // ZMapStyleGlyphAlign
case STYLE_PARAM_TYPE_UINT:
@@ -1872,6 +1884,7 @@ static void zmap_feature_type_style_set_property_full(ZMapFeatureTypeStyle style
STYLE_SET_PROP (STYLE_PARAM_TYPE_GRAPH_MODE, ZMapStyleGraphMode);
STYLE_SET_PROP (STYLE_PARAM_TYPE_BLIXEM, ZMapStyleBlixemType);
STYLE_SET_PROP (STYLE_PARAM_TYPE_GLYPH_STRAND, ZMapStyleGlyphStrand);
+ STYLE_SET_PROP (STYLE_PARAM_TYPE_GLYPH_ALIGN, ZMapStyleGlyphAlign);
case STYLE_PARAM_TYPE_UINT:
* (guint *) (((void *) style) + param->offset) = g_value_get_uint(value);
@@ -2051,6 +2064,7 @@ static void zmap_feature_type_style_get_property(GObject *gobject,
STYLE_GET_PROP (STYLE_PARAM_TYPE_GRAPH_MODE , ZMapStyleGraphMode);
STYLE_GET_PROP (STYLE_PARAM_TYPE_BLIXEM , ZMapStyleBlixemType);
STYLE_GET_PROP (STYLE_PARAM_TYPE_GLYPH_STRAND , ZMapStyleGlyphStrand);
+ STYLE_GET_PROP (STYLE_PARAM_TYPE_GLYPH_ALIGN , ZMapStyleGlyphAlign);
case STYLE_PARAM_TYPE_UINT:
g_value_set_uint(value, * (guint *) (((void *) style) + param->offset));
diff --git a/src/zmapFeature/zmapStyleUtils.c b/src/zmapFeature/zmapStyleUtils.c
index 8bc123ea0..20ca1fd53 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 1.15 2010-04-15 11:19:03 mh17 Exp $
+ * CVS info: $Id: zmapStyleUtils.c,v 1.16 2010-04-19 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -124,6 +124,7 @@ ZMAP_ENUM_FROM_STRING_FUNC(zMapStyleStr2ScoreMode, ZMapStyleScoreMode,
ZMAP_ENUM_FROM_STRING_FUNC(zMapStyleStr2BumpMode, ZMapStyleBumpMode, ZMAPBUMP_INVALID, ZMAP_STYLE_BUMP_MODE_LIST, , );
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, , );
@@ -147,6 +148,7 @@ ZMAP_ENUM_AS_EXACT_STRING_FUNC(zmapStyleScoreMode2ExactStr, ZMapStyleScore
ZMAP_ENUM_AS_EXACT_STRING_FUNC(zmapStyleBumpMode2ExactStr, ZMapStyleBumpMode, ZMAP_STYLE_BUMP_MODE_LIST);
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);
/* 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 1b50ad6c2..2d2346e9c 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 1.20 2010-04-15 11:19:03 mh17 Exp $
+ * CVS info: $Id: zmapStyle_I.h,v 1.21 2010-04-19 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -67,6 +67,7 @@ typedef enum
STYLE_PARAM_TYPE_GRAPH_MODE, // ZMapStyleGraphMode
STYLE_PARAM_TYPE_BLIXEM, // ZMapStyleBlixemType
STYLE_PARAM_TYPE_GLYPH_STRAND, // ZMapStyleGlyphStrand
+ STYLE_PARAM_TYPE_GLYPH_ALIGN, // ZMapStyleGlyphAlign
STYLE_PARAM_TYPE_GLYPH_SHAPE, // ZMapStyleGlyphShapeStruct, external = string
STYLE_PARAM_TYPE_SUB_FEATURES // GQuark[ZMAPSTYLE_SUB_FEATURE_MAX], external = string
@@ -243,6 +244,7 @@ typedef struct
ZMapStyleGlyphShapeStruct glyph3; // shape for 3' end
ZMapStyleFullColourStruct glyph_alt_colours;
ZMapStyleGlyphStrand glyph_strand;
+ ZMapStyleGlyphAlign glyph_align;
guint glyph_threshold;
} ZMapStyleGlyphStruct, *ZMapStyleGlyph ;
diff --git a/src/zmapView/zmapView.c b/src/zmapView/zmapView.c
index 2147c69d7..507d15d78 100755
--- a/src/zmapView/zmapView.c
+++ b/src/zmapView/zmapView.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Apr 7 15:59 2010 (edgrif)
* Created: Thu May 13 15:28:26 2004 (edgrif)
- * CVS info: $Id: zmapView.c,v 1.193 2010-04-15 11:19:03 mh17 Exp $
+ * CVS info: $Id: zmapView.c,v 1.194 2010-04-19 11:00:39 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -97,7 +97,7 @@ typedef struct
} UnsetDeferredLoadStylesStruct, *UnsetDeferredLoadStyles ;
-static GList *zmapViewGetIniSources(char *config_str);
+static GList *zmapViewGetIniSources(char *config_str,char **stylesfile);
static ZMapView createZMapView(GtkWidget *xremote_widget, char *view_name,
GList *sequences, void *app_data) ;
@@ -395,7 +395,7 @@ static GHashTable *zmapViewGetIniFeaturesets(char *config_str)
gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
{
gboolean result = TRUE ;
-
+ char *stylesfile = NULL;
if (zmap_view->state != ZMAPVIEW_INIT) // && zmap_view->state != ZMAPVIEW_LOADED)
@@ -419,7 +419,7 @@ gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
* and load in one call but we will almost certainly need the extra states later... */
zmap_view->state = ZMAPVIEW_CONNECTING ;
- settings_list = zmapViewGetIniSources(config_str); // get the stanza structs from ZMap config
+ settings_list = zmapViewGetIniSources(config_str,&stylesfile); // get the stanza structs from ZMap config
/* There are a number of predefined methods that we require so add these in as well
@@ -437,7 +437,7 @@ gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
free_this_list = settings_list ;
- current_server = (ZMapConfigSource)settings_list->data ;
+// current_server = (ZMapConfigSource)settings_list->data ;
@@ -450,6 +450,7 @@ gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
ZMapViewConnection view_con ;
current_server = (ZMapConfigSource)settings_list->data ;
+// if global current_server->stylesfile = g_strdup(stylesfile);
if(current_server->delayed) // only request data when asked by otterlace
continue;
@@ -580,6 +581,8 @@ gboolean zMapViewConnect(ZMapView zmap_view, char *config_str)
*/
startStateConnectionChecking(zmap_view) ;
}
+// if(stylesfile)
+// g_free(stylesfile);
return result ;
}
@@ -1254,7 +1257,7 @@ char *zmapViewGetStatusAsStr(ZMapViewState state)
-static GList *zmapViewGetIniSources(char *config_str)
+static GList *zmapViewGetIniSources(char *config_str,char ** stylesfile)
{
ZMapConfigIniContext context ;
GList *settings_list = NULL;
@@ -1266,8 +1269,17 @@ static GList *zmapViewGetIniSources(char *config_str)
zMapConfigIniContextIncludeBuffer(context, config_str);
settings_list = zMapConfigIniContextGetSources(context);
-
+#if MH17_NOT_NEEDED
+// now specified per server
+ if(stylesfile)
+ {
+ zMapConfigIniContextGetString(context,
+ ZMAPSTANZA_APP_CONFIG,ZMAPSTANZA_APP_CONFIG,
+ ZMAPSTANZA_APP_STYLESFILE,stylesfile);
+ }
+#endif
zMapConfigIniContextDestroy(context);
+
}
return(settings_list);
@@ -1338,10 +1350,11 @@ void zmapViewLoadFeatures(ZMapView view, ZMapFeatureBlock block_orig, GList *req
GHashTable *hash = NULL;
GList * sources = NULL;
ZMapConfigSource server;
+ char *stylesfile = NULL;
gboolean requested = FALSE;
- sources = zmapViewGetIniSources(NULL);
+ sources = zmapViewGetIniSources(NULL,&stylesfile);
hash = zmapViewGetFeatureSourceHash(sources);
for(;req_sources;req_sources = g_list_next(req_sources))
@@ -1357,6 +1370,7 @@ void zmapViewLoadFeatures(ZMapView view, ZMapFeatureBlock block_orig, GList *req
featureset = GFFset->feature_set_id;
}
server = zmapViewGetSourceFromFeatureset(hash,featureset);
+// if global server->stylesfile = g_strdup(stylesfile);
if(server)
{
@@ -1432,6 +1446,9 @@ void zmapViewLoadFeatures(ZMapView view, ZMapFeatureBlock block_orig, GList *req
(*(view_cbs_G->state_change))(view, view->app_data, NULL) ;
}
+// if(stylesfile)
+// g_free(stylesfile);
+
if(sources)
zMapConfigSourcesFreeList(sources);
if(hash)
@@ -2238,7 +2255,11 @@ static gboolean dispatchContextRequests(ZMapViewConnection connection, ZMapServe
return result ;
}
-
+void printStyle(GQuark style_id, gpointer data, gpointer user_data)
+{
+ char *x = (char *) user_data;
+ printf("%s: style %s\n",x,g_quark_to_string(style_id));
+}
/* This is _not_ a generalised processing function, it handles a sequence of replies from
* a thread that build up a feature context from a source. The steps are interdependent
@@ -2356,7 +2377,6 @@ static gboolean processDataRequests(ZMapViewConnection view_con, ZMapServerReqAn
zmap_view->source_2_featureset = feature_sets->source_2_featureset_out ;
if (!(zmap_view->source_2_sourcedata))
-
zmap_view->source_2_sourcedata = feature_sets->source_2_sourcedata_out ;
@@ -2370,7 +2390,8 @@ static gboolean processDataRequests(ZMapViewConnection view_con, ZMapServerReqAn
/* Merge the retrieved styles into the views canonical style list. */
zmap_view->orig_styles = zMapStyleMergeStyles(zmap_view->orig_styles, get_styles->styles_out,
ZMAPSTYLE_MERGE_PRESERVE) ;
-
+//printf("merging...\n");
+//g_datalist_foreach(&(zmap_view->orig_styles), printStyle, "view") ;
/* For dynamic loading the styles need to be set to load the features.*/
if (connect_data->dynamic_loading)
{
diff --git a/src/zmapView/zmapViewRemoteReceive.c b/src/zmapView/zmapViewRemoteReceive.c
index 6b127ff00..d6f489eef 100755
--- a/src/zmapView/zmapViewRemoteReceive.c
+++ b/src/zmapView/zmapViewRemoteReceive.c
@@ -31,7 +31,7 @@
* HISTORY:
* Last edited: Mar 25 14:43 2010 (edgrif)
* Created: Tue Jul 10 21:02:42 2007 (rds)
- * CVS info: $Id: zmapViewRemoteReceive.c,v 1.43 2010-03-29 09:56:50 edgrif Exp $
+ * CVS info: $Id: zmapViewRemoteReceive.c,v 1.44 2010-04-19 11:00:40 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -1238,18 +1238,27 @@ static gboolean xml_featureset_start_cb(gpointer user_data, ZMapXMLElement set_e
{
request_data->style_id = source_data->style_id ;
}
+#if MH17_OLD_CODE
+// i think this was related to a deferred style and the need to avoid an assert later
+// it prevents delayed pipeServers from working as the styles are not there due to not having been requested yet
+// this should be safe as this eventaully calls loadFeatures() which does a complete step list of requests
+// including req styles and features will be dropped if there are no styles to match
if (!(request_data->style = zMapFindStyle(request_data->view->orig_styles, request_data->style_id)))
{
char *err_msg ;
+void printStyle(GQuark style_id, gpointer data, gpointer user_data);
err_msg = g_strdup_printf("Style %s not found in view->orig_styles",
g_quark_to_string(request_data->style_id)) ;
zMapXMLParserRaiseParsingError(parser, err_msg) ;
+printf("%s\n",err_msg);
+g_datalist_foreach(&(request_data->view->orig_styles), printStyle, "remote") ;
g_free(err_msg) ;
result = FALSE ;
}
+#endif
}
diff --git a/src/zmapWindow/items/zmapWindowGlyphItem.c b/src/zmapWindow/items/zmapWindowGlyphItem.c
index 1e8f77fd2..f41ae02fa 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 1.10 2010-04-15 11:19:04 mh17 Exp $
+ * CVS info: $Id: zmapWindowGlyphItem.c,v 1.11 2010-04-19 11:00:40 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -148,6 +148,8 @@ ZMapWindowGlyphItem zMapWindowGlyphItemCreate(FooCanvasGroup *parent,
ZMapStyleScoreMode score_mode = ZMAPSCORE_INVALID;
double min = 0.0,max = 0.0;
ZMapStyleGlyphStrand strand = ZMAPSTYLE_GLYPH_STRAND_INVALID;
+ ZMapStyleGlyphAlign align;
+ double offset;
shape = (which == 5) ? zMapStyleGlyphShape5(style) :
(which == 3) ? zMapStyleGlyphShape3(style) :
@@ -188,9 +190,9 @@ ZMapWindowGlyphItem zMapWindowGlyphItemCreate(FooCanvasGroup *parent,
if(score > max)
score = max;
- if(score_mode == ZMAPSTYLE_SCORE_GLYPH_WIDTH)
+ if(score_mode == ZMAPSCORE_WIDTH || score_mode == ZMAPSCORE_SIZE)
width = width * score / max;
- else if(score_mode == ZMAPSTYLE_SCORE_GLYPH_HEIGHT)
+ else if(score_mode == ZMAPSCORE_HEIGHT || score_mode == ZMAPSCORE_SIZE)
height = height * score / max;
}
// invert H or V??
@@ -198,14 +200,20 @@ ZMapWindowGlyphItem zMapWindowGlyphItemCreate(FooCanvasGroup *parent,
strand = zMapStyleGlyphStrand(style);
if(strand == ZMAPSTYLE_GLYPH_STRAND_FLIP_X)
- {
width = -width;
- }
if(strand == ZMAPSTYLE_GLYPH_STRAND_FLIP_Y)
- {
height = -height;
- }
+
+ // if niether of thse are set we'll offset by zero and default to centred glyphs
+ // they'll look silly so no need for an error messgae
+ align = zMapStyleGetAlign(style);
+ offset = zMapStyleGetWidth(style) / 2;
+ if(align == ZMAPSTYLE_GLYPH_ALIGN_LEFT)
+ x_coord -= offset;
+ else if(align == ZMAPSTYLE_GLYPH_ALIGN_RIGHT)
+ x_coord += offset;
+
glyph = ZMAP_WINDOW_GLYPH_ITEM (foo_canvas_item_new(parent, ZMAP_TYPE_WINDOW_GLYPH_ITEM,
"x", x_coord,
@@ -750,7 +758,7 @@ static void glyph_fill_points(ZMapWindowGlyphItem glyph)
if(coord != GLYPH_COORD_INVALID)
{
coord *= glyph->width;
- glyph->coords[j] = glyph->cx + coord; // points are centred around the anchor of 0,0
+ glyph->coords[j] = glyph->cx + coord; // points are centred around the anchor of 0,0
}
else
glyph->coords[j] = GLYPH_CANVAS_COORD_INVALID; // zero, will be ignored
@@ -760,7 +768,7 @@ static void glyph_fill_points(ZMapWindowGlyphItem glyph)
if(coord != GLYPH_COORD_INVALID)
{
coord *= glyph->height;
- glyph->coords[j] = glyph->cy + coord; // points are centred around the anchor of 0,0
+ glyph->coords[j] = glyph->cy + coord; // points are centred around the anchor of 0,0
}
else
glyph->coords[j] = GLYPH_CANVAS_COORD_INVALID; // zero, will be ignored
--
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