diff --git a/src/include/ZMap/zmapStyle.h b/src/include/ZMap/zmapStyle.h
index 09d09a13efe77d7ac9e54dd247bd23fdf78c7726..c2dc3cd88507c963a44c121fac61a0f19a2e0d38 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: Mar 5 11:24 2008 (edgrif)
+ * Last edited: Mar 31 14:26 2008 (edgrif)
* Created: Mon Feb 26 09:28:26 2007 (edgrif)
- * CVS info: $Id: zmapStyle.h,v 1.18 2008-03-05 11:33:23 edgrif Exp $
+ * CVS info: $Id: zmapStyle.h,v 1.19 2008-04-01 13:04:58 edgrif Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_STYLE_H
@@ -203,12 +203,7 @@ void zMapStyleSetGFF(ZMapFeatureTypeStyle style, char *gff_source, char *gff_fea
char *zMapStyleGetGFFSource(ZMapFeatureTypeStyle style) ;
char *zMapStyleGetGFFFeature(ZMapFeatureTypeStyle style) ;
-unsigned int zmapStyleGetWithinAlignError(ZMapFeatureTypeStyle style) ;
-gboolean zMapStyleIsParseGaps(ZMapFeatureTypeStyle style) ;
gboolean zMapStyleIsDirectionalEnd(ZMapFeatureTypeStyle style) ;
-gboolean zMapStyleIsAlignGaps(ZMapFeatureTypeStyle style) ;
-void zMapStyleSetAlignGaps(ZMapFeatureTypeStyle style, gboolean show_gaps) ;
-
void zMapStyleSetDisplayable(ZMapFeatureTypeStyle style, gboolean displayable) ;
gboolean zMapStyleIsDisplayable(ZMapFeatureTypeStyle style) ;
@@ -266,12 +261,19 @@ void zMapStyleGetStrandAttrs(ZMapFeatureTypeStyle type,
gboolean *strand_specific, gboolean *frame_specific,
gboolean *show_rev_strand, gboolean *show_as_3_frame) ;
void zMapStyleSetEndStyle(ZMapFeatureTypeStyle style, gboolean directional) ;
-void zMapStyleSetGappedAligns(ZMapFeatureTypeStyle style, gboolean show_gaps, gboolean parse_gaps,
- unsigned int within_align_error) ;
+
+void zMapStyleSetGappedAligns(ZMapFeatureTypeStyle style, gboolean parse_gaps, unsigned int within_align_error) ;
gboolean zMapStyleGetGappedAligns(ZMapFeatureTypeStyle style, unsigned int *within_align_error) ;
-void zMapStyleSetJoinAligns(ZMapFeatureTypeStyle style, gboolean join_aligns, unsigned int between_align_error) ;
+void zMapStyleSetJoinAligns(ZMapFeatureTypeStyle style, unsigned int between_align_error) ;
gboolean zMapStyleGetJoinAligns(ZMapFeatureTypeStyle style, unsigned int *between_align_error) ;
gboolean zMapStyleGetParseGaps(ZMapFeatureTypeStyle style) ;
+unsigned int zmapStyleGetWithinAlignError(ZMapFeatureTypeStyle style) ;
+gboolean zMapStyleIsParseGaps(ZMapFeatureTypeStyle style) ;
+gboolean zMapStyleIsAlignGaps(ZMapFeatureTypeStyle style) ;
+void zMapStyleSetAlignGaps(ZMapFeatureTypeStyle style, gboolean show_gaps) ;
+
+
+
void zMapStyleSetGlyphMode(ZMapFeatureTypeStyle style, ZMapStyleGlyphMode glyph_mode) ;
diff --git a/src/zmapFeature/zmapFeatureTypes.c b/src/zmapFeature/zmapFeatureTypes.c
index e0c03bcd2b21000f72e1ac5ccbd9879ff302bc96..f7ab6713e6f1a6c2d898d3d2c6a1fa1485716cb1 100755
--- a/src/zmapFeature/zmapFeatureTypes.c
+++ b/src/zmapFeature/zmapFeatureTypes.c
@@ -27,9 +27,9 @@
*
* Exported functions: See ZMap/zmapFeature.h
* HISTORY:
- * Last edited: Mar 5 10:30 2008 (edgrif)
+ * Last edited: Apr 1 14:02 2008 (edgrif)
* Created: Tue Dec 14 13:15:11 2004 (edgrif)
- * CVS info: $Id: zmapFeatureTypes.c,v 1.60 2008-03-05 10:30:51 edgrif Exp $
+ * CVS info: $Id: zmapFeatureTypes.c,v 1.61 2008-04-01 13:04:58 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -569,7 +569,6 @@ void zMapStylePrint(ZMapFeatureTypeStyle style, char *prefix)
ZMAPSTYLEPRINTOPT(style->opts.showText, showText) ;
ZMAPSTYLEPRINTOPT(style->opts.parse_gaps, parse_gaps) ;
ZMAPSTYLEPRINTOPT(style->opts.align_gaps, align_gaps) ;
- ZMAPSTYLEPRINTOPT(style->opts.join_aligns, join_aligns) ;
ZMAPSTYLEPRINTOPT(style->opts.strand_specific, strand_specific) ;
ZMAPSTYLEPRINTOPT(style->opts.show_rev_strand, show_rev_strand) ;
ZMAPSTYLEPRINTOPT(style->opts.frame_specific, frame_specific) ;
@@ -1379,7 +1378,6 @@ GData *zMapFeatureTypeGetFromFile(char *styles_file_name)
/* Not good to hard code the TRUE here, but I guess blixem requires the gaps array. */
zMapStyleSetGappedAligns(new_type,
zMapConfigGetElementBool(next_styles, "gapped_align"),
- TRUE,
zMapConfigGetElementBool(next_styles, "gapped_error")) ;
if (zMapConfigGetElementBool(next_styles, "hidden_init"))
diff --git a/src/zmapFeature/zmapStyle.c b/src/zmapFeature/zmapStyle.c
index 4d2b5ecc8d8e37fd4cd59ffdc977280373fdd645..8c93edf46e2eb8093bdaecdbb6c00048939b31c5 100755
--- a/src/zmapFeature/zmapStyle.c
+++ b/src/zmapFeature/zmapStyle.c
@@ -28,9 +28,9 @@
*
* Exported functions: See ZMap/zmapStyle.h
* HISTORY:
- * Last edited: Mar 5 10:33 2008 (edgrif)
+ * Last edited: Mar 31 14:28 2008 (edgrif)
* Created: Mon Feb 26 09:12:18 2007 (edgrif)
- * CVS info: $Id: zmapStyle.c,v 1.9 2008-03-05 10:34:23 edgrif Exp $
+ * CVS info: $Id: zmapStyle.c,v 1.10 2008-04-01 13:04:58 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -932,7 +932,6 @@ gboolean zMapStyleIsAlignGaps(ZMapFeatureTypeStyle style)
return style->opts.align_gaps ;
}
-
void zMapStyleSetAlignGaps(ZMapFeatureTypeStyle style, gboolean show_gaps)
{
zMapAssert(style) ;
@@ -943,12 +942,13 @@ void zMapStyleSetAlignGaps(ZMapFeatureTypeStyle style, gboolean show_gaps)
}
-void zMapStyleSetGappedAligns(ZMapFeatureTypeStyle style, gboolean show_gaps, gboolean parse_gaps,
+
+
+void zMapStyleSetGappedAligns(ZMapFeatureTypeStyle style, gboolean parse_gaps,
unsigned int within_align_error)
{
zMapAssert(style);
- style->opts.align_gaps = show_gaps ;
style->opts.parse_gaps = parse_gaps ;
style->mode_data.alignment.within_align_error = within_align_error ;
style->mode_data.alignment.fields_set.within_align_error = TRUE ;
@@ -959,23 +959,27 @@ void zMapStyleSetGappedAligns(ZMapFeatureTypeStyle style, gboolean show_gaps, gb
gboolean zMapStyleGetGappedAligns(ZMapFeatureTypeStyle style, unsigned int *within_align_error)
{
- zMapAssert(style);
+ gboolean result = FALSE ;
- if (style->opts.align_gaps && within_align_error)
- *within_align_error = style->mode_data.alignment.within_align_error ;
+ zMapAssert(style && within_align_error) ;
- return style->opts.align_gaps ;
+ if (style->mode_data.alignment.fields_set.within_align_error && within_align_error)
+ {
+ *within_align_error = style->mode_data.alignment.within_align_error ;
+ result = TRUE ;
+ }
+
+ return result ;
}
-void zMapStyleSetJoinAligns(ZMapFeatureTypeStyle style, gboolean join_aligns, unsigned int between_align_error)
+void zMapStyleSetJoinAligns(ZMapFeatureTypeStyle style, unsigned int between_align_error)
{
zMapAssert(style);
- style->opts.join_aligns = join_aligns ;
style->mode_data.alignment.between_align_error = between_align_error ;
style->mode_data.alignment.fields_set.between_align_error = TRUE ;
@@ -987,12 +991,17 @@ void zMapStyleSetJoinAligns(ZMapFeatureTypeStyle style, gboolean join_aligns, un
* otherwise returns FALSE. */
gboolean zMapStyleGetJoinAligns(ZMapFeatureTypeStyle style, unsigned int *between_align_error)
{
+ gboolean result = FALSE ;
+
zMapAssert(style);
- if (style->opts.join_aligns)
- *between_align_error = style->mode_data.alignment.between_align_error ;
+ if (style->mode_data.alignment.fields_set.between_align_error)
+ {
+ *between_align_error = style->mode_data.alignment.between_align_error ;
+ result = TRUE ;
+ }
- return style->opts.join_aligns ;
+ return result ;
}
diff --git a/src/zmapFeature/zmapStyle_P.h b/src/zmapFeature/zmapStyle_P.h
index c8f3d5f74c9a159504129b5f5be828e701b46217..8a5d8c1adf70b640786fdf652be969c0b1cea1ce 100755
--- a/src/zmapFeature/zmapStyle_P.h
+++ b/src/zmapFeature/zmapStyle_P.h
@@ -26,9 +26,9 @@
* Description: Private header for style.
*
* HISTORY:
- * Last edited: Mar 5 10:31 2008 (edgrif)
+ * Last edited: Apr 1 14:03 2008 (edgrif)
* Created: Mon Feb 26 09:13:30 2007 (edgrif)
- * CVS info: $Id: zmapStyle_P.h,v 1.8 2008-03-05 10:32:06 edgrif Exp $
+ * CVS info: $Id: zmapStyle_P.h,v 1.9 2008-04-01 13:04:58 edgrif Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_STYLE_P_H
@@ -299,10 +299,6 @@ typedef struct ZMapFeatureTypeStyleStruct_
unsigned int parse_gaps : 1 ;
unsigned int align_gaps : 1 ; /*!< TRUE: gaps within alignment are displayed,
FALSE: alignment is displayed as a single block. */
- unsigned int join_aligns : 1 ; /*!< TRUE: joins aligns if between_align_error not exceeded,
- FALSE: does not joing aligns. */
-
-
/*! These are all linked, if strand_specific is FALSE, then so are
* frame_specific and show_rev_strand. */