diff --git a/src/zmapFeature/zmapFeatureTypes.c b/src/zmapFeature/zmapFeatureTypes.c
index bcb57dd03bf7f633436493d8794cbb750187b195..f9b1cb2d6fc12688c7f82f52143cf61da83c6497 100755
--- a/src/zmapFeature/zmapFeatureTypes.c
+++ b/src/zmapFeature/zmapFeatureTypes.c
@@ -27,9 +27,9 @@
*
* Exported functions: See ZMap/zmapFeature.h
* HISTORY:
- * Last edited: Jun 25 08:56 2008 (rds)
+ * Last edited: Sep 24 15:35 2008 (edgrif)
* Created: Tue Dec 14 13:15:11 2004 (edgrif)
- * CVS info: $Id: zmapFeatureTypes.c,v 1.67 2008-06-25 14:00:13 rds Exp $
+ * CVS info: $Id: zmapFeatureTypes.c,v 1.68 2008-09-24 14:42:00 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -82,29 +82,22 @@ typedef struct
static void doTypeSets(GQuark key_id, gpointer data, gpointer user_data) ;
static void typePrintFunc(GQuark key_id, gpointer data, gpointer user_data) ;
-
static void stylePrintFunc(gpointer data, gpointer user_data) ;
static void checkListName(gpointer data, gpointer user_data) ;
static gint compareNameToStyle(gconstpointer glist_data, gconstpointer user_data) ;
static void mergeStyle(GQuark style_id, gpointer data, gpointer user_data_unused) ;
-
static void destroyStyle(GQuark style_id, gpointer data, gpointer user_data_unused) ;
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-static ZMapFeatureTypeStyle createInheritedStyle(GData *style_set, char *parent_style) ;
-static void inheritStyleCB(gpointer data, gpointer user_data) ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
-
static void inheritCB(GQuark key_id, gpointer data, gpointer user_data) ;
static gboolean doStyleInheritance(GData **style_set, GData **inherited_styles, ZMapFeatureTypeStyle curr_style) ;
static void inheritAllFunc(gpointer data, gpointer user_data) ;
+static void setStrandFrameAttrs(ZMapFeatureTypeStyle type,
+ gboolean *strand_specific_in,
+ gboolean *show_rev_strand_in,
+ ZMapStyle3FrameMode *frame_mode_in) ;
@@ -177,49 +170,6 @@ gboolean zMapStyleInheritAllStyles(GData **style_set)
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-/* Creates a new style which has inherited properties from existing styles, the styles
- * are tied together in parent/child tree relationship by the parent_id tag in the style. */
-ZMapFeatureTypeStyle zMapStyleCreateFull(GData *style_set, char *parent_style,
- char *name, char *description, ZMapStyleMode mode,
- char *outline, char *foreground, char *background,
- double width)
-{
- ZMapFeatureTypeStyle new_style = NULL ;
- ZMapFeatureTypeStyle inherited_style ;
-
- /* If we can create an inherited style then overload it with the supplied style params. */
- if ((inherited_style = createInheritedStyle(style_set, parent_style)))
- {
- ZMapFeatureTypeStyle tmp_style ;
-
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- tmp_style = zMapFeatureTypeCreate(name, description, mode,
- outline, foreground, background,
- width) ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
- tmp_style = zMapFeatureTypeCreate(name, description) ;
- zMapStyleSetMode(tmp_style, mode) ;
- zMapStyleSetColours(tmp_style, outline, foreground, background) ;
- zMapStyleSetWidth(tmp_style, width) ;
-
-
- /* This will leave the fully merged style in inherited_style, so we throw new_style
- * away. */
- if (zMapStyleMerge(inherited_style, tmp_style))
- new_style = inherited_style ;
-
- zMapFeatureTypeDestroy(tmp_style) ;
- }
-
- return new_style ;
-}
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
/*!
* Overload one style with another. Values in curr_style are overwritten with those
* in the new_style. new_style is not altered.
@@ -237,7 +187,6 @@ gboolean zMapStyleMerge(ZMapFeatureTypeStyle curr_style, ZMapFeatureTypeStyle ne
{
gboolean result = TRUE ; /* There is nothing to fail currently. */
-
zMapAssert(curr_style && new_style) ;
curr_style->original_id = new_style->original_id ;
@@ -334,6 +283,25 @@ gboolean zMapStyleMerge(ZMapFeatureTypeStyle curr_style, ZMapFeatureTypeStyle ne
curr_style->fields_set.max_score = TRUE ;
}
+ if (new_style->fields_set.strand_specific)
+ {
+ curr_style->opts.strand_specific = new_style->opts.strand_specific ;
+ curr_style->fields_set.strand_specific = TRUE ;
+ }
+
+ if (new_style->fields_set.show_rev_strand)
+ {
+ curr_style->opts.show_rev_strand = new_style->opts.show_rev_strand ;
+ curr_style->fields_set.show_rev_strand = TRUE ;
+ }
+
+ if (new_style->fields_set.frame_specific)
+ {
+ curr_style->opts.frame_specific = new_style->opts.frame_specific ;
+ curr_style->frame_mode = new_style->frame_mode ;
+ curr_style->fields_set.frame_specific = TRUE ;
+ }
+
if (new_style->fields_set.gff_source)
{
curr_style->gff_source = new_style->gff_source ;
@@ -347,11 +315,15 @@ gboolean zMapStyleMerge(ZMapFeatureTypeStyle curr_style, ZMapFeatureTypeStyle ne
}
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
/* AGH THIS IS NOT GOOD....WE CAN TURN OFF/ON OPTIONS IN A WAY WE DON'T WANT TO...
*
* need to revisit this for sure....
* */
curr_style->opts = new_style->opts ; /* struct copy of all opts. */
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
/* Now do mode specific stuff... */
if (curr_style->mode == ZMAPSTYLE_MODE_TRANSCRIPT)
@@ -371,12 +343,6 @@ gboolean zMapStyleMerge(ZMapFeatureTypeStyle curr_style, ZMapFeatureTypeStyle ne
curr_style->mode_data.transcript.CDS_colours.normal.border = new_style->mode_data.transcript.CDS_colours.normal.border ;
curr_style->mode_data.transcript.CDS_colours.normal.fields_set.border = TRUE ;
}
-
-
-
-
-
-
}
@@ -401,6 +367,7 @@ void zMapStylePrint(ZMapFeatureTypeStyle style, char *prefix)
{
zMapAssert(style) ;
+
printf("%s Style: %s (%s)\n", (prefix ? prefix : ""),
g_quark_to_string(style->original_id), g_quark_to_string(style->unique_id)) ;
@@ -411,7 +378,7 @@ void zMapStylePrint(ZMapFeatureTypeStyle style, char *prefix)
printf("\tDescription: %s\n", style->description) ;
if (style->fields_set.mode)
- printf("Feature mode: %s\n", zmapStyleMode2Str(style->mode)) ;
+ printf("\tFeature mode: %s\n", zmapStyleMode2Str(style->mode)) ;
if (style->colours.normal.fields_set.fill)
ZMAPSTYLEPRINTCOLOUR(style->colours.normal.fill, background) ;
@@ -441,6 +408,11 @@ void zMapStylePrint(ZMapFeatureTypeStyle style, char *prefix)
if (style->fields_set.bump_spacing)
printf("\tBump width: %g\n", style->bump_spacing) ;
+ if (style->fields_set.frame_specific)
+ {
+ printf("\tCurrent 3 frame mode: %s\n", zmapStyle3FrameMode2Str(style->frame_mode));
+ }
+
if (style->fields_set.width)
printf("\tWidth: %g\n", style->width) ;
@@ -459,17 +431,22 @@ void zMapStylePrint(ZMapFeatureTypeStyle style, char *prefix)
if (style->fields_set.gff_feature)
printf("\tGFF feature: %s\n", g_quark_to_string(style->gff_feature)) ;
- printf("Column display state: %s\n", zmapStyleColDisplayState2Str(style->col_display_state));
-
+ printf("\tColumn display state: %s\n", zmapStyleColDisplayState2Str(style->col_display_state));
ZMAPSTYLEPRINTOPT(style->opts.displayable, displayable) ;
+
ZMAPSTYLEPRINTOPT(style->opts.show_when_empty, show_when_empty) ;
+
ZMAPSTYLEPRINTOPT(style->opts.showText, showText) ;
+
ZMAPSTYLEPRINTOPT(style->opts.parse_gaps, parse_gaps) ;
ZMAPSTYLEPRINTOPT(style->opts.align_gaps, align_gaps) ;
+
ZMAPSTYLEPRINTOPT(style->opts.strand_specific, strand_specific) ;
ZMAPSTYLEPRINTOPT(style->opts.show_rev_strand, show_rev_strand) ;
ZMAPSTYLEPRINTOPT(style->opts.frame_specific, frame_specific) ;
- ZMAPSTYLEPRINTOPT(style->opts.show_only_as_3_frame, show_only_as_3_frame) ;
+ printf("\tFrame display state: %s\n", zmapStyle3FrameMode2Str(style->col_display_state));
+
+
ZMAPSTYLEPRINTOPT(style->opts.directional_end, directional_end) ;
return ;
@@ -703,57 +680,95 @@ void zMapStyleSetScore(ZMapFeatureTypeStyle style, char *score_str,
+void zMapStyleSetStrandSpecific(ZMapFeatureTypeStyle type, gboolean strand_specific)
+{
+ setStrandFrameAttrs(type, &strand_specific, NULL, NULL) ;
+ return ;
+}
-
-
-
-/* These attributes are not needed for many features and are not independent,
- * hence we set them in a special routine, none of this is very good as we don't have
- * a good way of enforcing stuff...so its all a bit heuristic. */
-void zMapStyleSetStrandAttrs(ZMapFeatureTypeStyle type,
- gboolean strand_specific, gboolean frame_specific,
- gboolean show_rev_strand, gboolean show_only_as_3_frame)
+void zMapStyleSetStrandShowReverse(ZMapFeatureTypeStyle type, gboolean show_reverse)
{
- zMapAssert(type) ;
-
- if (frame_specific && !strand_specific)
- strand_specific = TRUE ;
+ setStrandFrameAttrs(type, NULL, &show_reverse, NULL) ;
- if (show_rev_strand && !strand_specific)
- strand_specific = TRUE ;
+ return ;
+}
- type->opts.strand_specific = strand_specific ;
- type->opts.frame_specific = frame_specific ;
- type->opts.show_rev_strand = show_rev_strand ;
- type->opts.show_only_as_3_frame = show_only_as_3_frame ;
+void zMapStyleSetFrameSpecific(ZMapFeatureTypeStyle type, ZMapStyle3FrameMode frame_mode)
+{
+ setStrandFrameAttrs(type, NULL, NULL, &frame_mode) ;
return ;
}
-/* These attributes are not needed for many features and are not independent,
- * hence we set them in a special routine, none of this is very good as we don't have
- * a good way of enforcing stuff...so its all a bit heuristic. */
void zMapStyleGetStrandAttrs(ZMapFeatureTypeStyle type,
- gboolean *strand_specific, gboolean *frame_specific,
- gboolean *show_rev_strand, gboolean *show_only_as_3_frame)
+ gboolean *strand_specific, gboolean *show_rev_strand, ZMapStyle3FrameMode *frame_mode)
{
zMapAssert(type) ;
-
- if (strand_specific)
+
+ if (type->fields_set.strand_specific && strand_specific)
*strand_specific = type->opts.strand_specific ;
- if (frame_specific)
- *frame_specific = type->opts.frame_specific ;
- if (show_rev_strand )
+ if (type->fields_set.show_rev_strand && show_rev_strand )
*show_rev_strand = type->opts.show_rev_strand ;
- if (show_only_as_3_frame)
- *show_only_as_3_frame = type->opts.show_only_as_3_frame ;
+ if (type->fields_set.frame_specific && frame_mode)
+ *frame_mode = type->frame_mode ;
return ;
}
+gboolean zMapStyleIsFrameSpecific(ZMapFeatureTypeStyle style)
+{
+ gboolean frame_specific = FALSE ;
+
+ zMapAssert(ZMAP_IS_FEATURE_STYLE(style)) ;
+
+ if (style->fields_set.frame_specific && style->opts.frame_specific)
+ frame_specific = TRUE ;
+
+ return frame_specific ;
+}
+
+gboolean zMapStyleIsFrameOneColumn(ZMapFeatureTypeStyle style)
+{
+ gboolean one_column = FALSE ;
+
+ zMapAssert(ZMAP_IS_FEATURE_STYLE(style)) ;
+
+ if (style->fields_set.frame_specific && style->opts.frame_specific
+ && style->frame_mode == ZMAPSTYLE_3_FRAME_ONLY_1)
+ one_column = TRUE ;
+
+ return one_column ;
+}
+
+
+gboolean zMapStyleIsStrandSpecific(ZMapFeatureTypeStyle style)
+{
+ gboolean strand_specific = FALSE ;
+
+ zMapAssert(ZMAP_IS_FEATURE_STYLE(style)) ;
+
+ if (style->fields_set.strand_specific)
+ strand_specific = style->opts.strand_specific ;
+
+ return strand_specific ;
+}
+
+gboolean zMapStyleIsShowReverseStrand(ZMapFeatureTypeStyle style)
+{
+ gboolean show_rev_strand = FALSE ;
+
+ zMapAssert(ZMAP_IS_FEATURE_STYLE(style)) ;
+
+ if (style->fields_set.show_rev_strand)
+ show_rev_strand = style->opts.show_rev_strand ;
+
+ return show_rev_strand ;
+}
+
+
void zMapStyleSetGFF(ZMapFeatureTypeStyle style, char *gff_source, char *gff_feature)
{
zMapAssert(style) ;
@@ -784,20 +799,28 @@ void zMapStyleSetBump(ZMapFeatureTypeStyle style, char *bump_str)
{
if (g_ascii_strcasecmp(bump_str, "complete") == 0)
bump = ZMAPOVERLAP_COMPLETE ;
- else if (g_ascii_strcasecmp(bump_str, "smartest") == 0)
- bump = ZMAPOVERLAP_ENDS_RANGE ;
- else if (g_ascii_strcasecmp(bump_str, "smart") == 0)
- bump = ZMAPOVERLAP_NO_INTERLEAVE ;
- else if (g_ascii_strcasecmp(bump_str, "interleave") == 0)
- bump = ZMAPOVERLAP_COMPLEX ;
else if (g_ascii_strcasecmp(bump_str, "overlap") == 0)
bump = ZMAPOVERLAP_OVERLAP ;
- else if (g_ascii_strcasecmp(bump_str, "position") == 0)
+ else if (g_ascii_strcasecmp(bump_str, "item_overlap") == 0)
+ bump = ZMAPOVERLAP_ITEM_OVERLAP ;
+ else if (g_ascii_strcasecmp(bump_str, "start") == 0)
bump = ZMAPOVERLAP_POSITION ;
else if (g_ascii_strcasecmp(bump_str, "name") == 0)
bump = ZMAPOVERLAP_NAME ;
+ else if (g_ascii_strcasecmp(bump_str, "oscillate") == 0)
+ bump = ZMAPOVERLAP_OSCILLATE ;
else if (g_ascii_strcasecmp(bump_str, "simple") == 0)
bump = ZMAPOVERLAP_SIMPLE ;
+ else if (g_ascii_strcasecmp(bump_str, "ends_range") == 0)
+ bump = ZMAPOVERLAP_ENDS_RANGE ;
+ else if (g_ascii_strcasecmp(bump_str, "compact") == 0)
+ bump = ZMAPOVERLAP_COMPLEX_INTERLEAVE ;
+ else if (g_ascii_strcasecmp(bump_str, "Compact_no_interleave") == 0)
+ bump = ZMAPOVERLAP_COMPLEX_NO_INTERLEAVE ;
+ else if (g_ascii_strcasecmp(bump_str, "range") == 0)
+ bump = ZMAPOVERLAP_COMPLEX_RANGE ;
+ else if (g_ascii_strcasecmp(bump_str, "range_colinear") == 0)
+ bump = ZMAPOVERLAP_COMPLEX_LIMIT ;
}
zMapStyleSetOverlapMode(style, bump) ;
@@ -808,7 +831,7 @@ void zMapStyleSetBump(ZMapFeatureTypeStyle style, char *bump_str)
void zMapStyleSetOverlapMode(ZMapFeatureTypeStyle style, ZMapStyleOverlapMode overlap_mode)
{
- zMapAssert(style && (overlap_mode > ZMAPOVERLAP_START && overlap_mode < ZMAPOVERLAP_END)) ;
+ zMapAssert(style && (overlap_mode >= ZMAPOVERLAP_START && overlap_mode <= ZMAPOVERLAP_END)) ;
if (!style->fields_set.overlap_mode)
{
@@ -822,6 +845,30 @@ void zMapStyleSetOverlapMode(ZMapFeatureTypeStyle style, ZMapStyleOverlapMode ov
return ;
}
+void zMapStyleSetBumpSpace(ZMapFeatureTypeStyle style, double bump_spacing)
+{
+ zMapAssert(style) ;
+
+ style->fields_set.bump_spacing = TRUE ;
+ style->bump_spacing = bump_spacing ;
+
+ return ;
+}
+
+
+double zMapStyleGetBumpSpace(ZMapFeatureTypeStyle style)
+{
+ double spacing = 0.0 ;
+
+ zMapAssert(style) ;
+
+ if (style->fields_set.bump_spacing)
+ spacing = style->bump_spacing ;
+
+ return spacing ;
+}
+
+
/* Reset overlap mode to default and returns the default mode. */
ZMapStyleOverlapMode zMapStyleResetOverlapMode(ZMapFeatureTypeStyle style)
@@ -839,16 +886,18 @@ void zMapStyleInitOverlapMode(ZMapFeatureTypeStyle style,
ZMapStyleOverlapMode default_overlap_mode, ZMapStyleOverlapMode curr_overlap_mode)
{
zMapAssert(style
- && (default_overlap_mode >= ZMAPOVERLAP_START && default_overlap_mode < ZMAPOVERLAP_END)
- && (curr_overlap_mode >= ZMAPOVERLAP_START && curr_overlap_mode < ZMAPOVERLAP_END)) ;
+ && (default_overlap_mode == ZMAPOVERLAP_INVALID
+ || (default_overlap_mode >= ZMAPOVERLAP_START && default_overlap_mode <= ZMAPOVERLAP_END))
+ && (curr_overlap_mode == ZMAPOVERLAP_INVALID
+ || (curr_overlap_mode >= ZMAPOVERLAP_START && curr_overlap_mode <= ZMAPOVERLAP_END))) ;
- if (curr_overlap_mode > ZMAPOVERLAP_START)
+ if (curr_overlap_mode != ZMAPOVERLAP_INVALID)
{
style->fields_set.overlap_mode = TRUE ;
style->curr_overlap_mode = curr_overlap_mode ;
}
- if (default_overlap_mode > ZMAPOVERLAP_START)
+ if (default_overlap_mode != ZMAPOVERLAP_INVALID)
{
style->fields_set.overlap_default = TRUE ;
style->default_overlap_mode = default_overlap_mode ;
@@ -1014,6 +1063,7 @@ GData *zMapStyleGetAllPredefined(void)
GData *style_list = NULL ;
ZMapFeatureTypeStyle curr = NULL ;
+
/* 3 Frame */
curr = zMapFeatureTypeCreate(ZMAP_FIXED_STYLE_3FRAME,
ZMAP_FIXED_STYLE_3FRAME_TEXT);
@@ -1024,6 +1074,7 @@ GData *zMapStyleGetAllPredefined(void)
"displayable", FALSE,
NULL);
g_datalist_id_set_data(&style_list, curr->unique_id, curr) ;
+
/* 3 Frame Translation */
curr = zMapFeatureTypeCreate(ZMAP_FIXED_STYLE_3FT_NAME,
@@ -1040,6 +1091,7 @@ GData *zMapStyleGetAllPredefined(void)
* same column at the moment so it's not frame specific! */
{
ZMapStyleColourStringsStruct normal_normal = {"white", "black", NULL};
+ /* we need draw colour here as well.... */
g_object_set(G_OBJECT(curr),
"mode", ZMAPSTYLE_MODE_PEP_SEQUENCE,
"displayable", TRUE,
@@ -1049,14 +1101,14 @@ GData *zMapStyleGetAllPredefined(void)
"default-overlap-mode", ZMAPOVERLAP_COMPLETE,
"bump-spacing", 10.0,
"strand-specific", TRUE,
- "frame-specific", TRUE,
"show-rev-strand", FALSE,
- "show-only-as-3-frame", TRUE,
+ "frame-mode", ZMAPSTYLE_3_FRAME_ONLY_3,
"main-colour-normal", &normal_normal,
NULL);
}
g_datalist_id_set_data(&style_list, curr->unique_id, curr);
+
/* DNA */
curr = zMapFeatureTypeCreate(ZMAP_FIXED_STYLE_DNA_NAME,
ZMAP_FIXED_STYLE_DNA_NAME_TEXT);
@@ -1071,15 +1123,13 @@ GData *zMapStyleGetAllPredefined(void)
"overlap-mode", ZMAPOVERLAP_COMPLETE,
"default-overlap-mode", ZMAPOVERLAP_COMPLETE,
"strand-specific", TRUE,
- "frame-specific", FALSE,
- "show-rev-strand", FALSE,
- "show-only-as-3-frame", FALSE,
"main-colour-normal", &normal_normal,
"main-colour-selected", &normal_selected,
NULL);
}
g_datalist_id_set_data(&style_list, curr->unique_id, curr);
+
/* Locus */
curr = zMapFeatureTypeCreate(ZMAP_FIXED_STYLE_LOCUS_NAME,
ZMAP_FIXED_STYLE_LOCUS_NAME_TEXT);
@@ -1092,14 +1142,12 @@ GData *zMapStyleGetAllPredefined(void)
"overlap-mode", ZMAPOVERLAP_COMPLETE,
"default-overlap-mode", ZMAPOVERLAP_COMPLETE,
"strand-specific", TRUE,
- "frame-specific", FALSE,
- "show-rev-strand", FALSE,
- "show-only-as-3-frame", FALSE,
"main-colour-normal", &normal_normal,
NULL);
g_datalist_id_set_data(&style_list, curr->unique_id, curr);
}
+
/* GeneFinderFeatures */
curr = zMapFeatureTypeCreate(ZMAP_FIXED_STYLE_GFF_NAME,
ZMAP_FIXED_STYLE_GFF_NAME_TEXT);
@@ -1112,6 +1160,7 @@ GData *zMapStyleGetAllPredefined(void)
NULL);
g_datalist_id_set_data(&style_list, curr->unique_id, curr);
+
/* Scale Bar */
curr = zMapFeatureTypeCreate(ZMAP_FIXED_STYLE_SCALE_NAME,
ZMAP_FIXED_STYLE_SCALE_TEXT);
@@ -1124,6 +1173,7 @@ GData *zMapStyleGetAllPredefined(void)
NULL);
g_datalist_id_set_data(&style_list, curr->unique_id, curr);
+
/* show translation in zmap */
curr = zMapFeatureTypeCreate(ZMAP_FIXED_STYLE_SHOWTRANSLATION_NAME,
ZMAP_FIXED_STYLE_SHOWTRANSLATION_TEXT);
@@ -1138,15 +1188,13 @@ GData *zMapStyleGetAllPredefined(void)
"default-overlap-mode", ZMAPOVERLAP_COMPLETE,
"width", 300.0,
"strand-specific", TRUE,
- "frame-specific", FALSE,
- "show-rev-strand", FALSE,
- "show-only-as-3-frame", FALSE,
"main-colour-normal", &normal_normal,
"main-colour-selected", &normal_selected,
NULL);
}
g_datalist_id_set_data(&style_list, curr->unique_id, curr);
+
/* strand separator */
curr = zMapFeatureTypeCreate(ZMAP_FIXED_STYLE_STRAND_SEPARATOR,
ZMAP_FIXED_STYLE_STRAND_SEPARATOR_TEXT);
@@ -1159,6 +1207,7 @@ GData *zMapStyleGetAllPredefined(void)
NULL);
g_datalist_id_set_data(&style_list, curr->unique_id, curr);
+
/* Search results hits */
curr = zMapFeatureTypeCreate(ZMAP_FIXED_STYLE_SEARCH_MARKERS_NAME,
ZMAP_FIXED_STYLE_SEARCH_MARKERS_TEXT);
@@ -1173,9 +1222,6 @@ GData *zMapStyleGetAllPredefined(void)
"default-overlap-mode", ZMAPOVERLAP_COMPLETE,
"width", 15.0,
"strand-specific", FALSE,
- "frame-specific", FALSE,
- "show-rev-strand", FALSE,
- "show-only-as-3-frame", FALSE,
"show-only-in-separator", TRUE,
"main-colour-normal", &normal_normal,
"rev-colour-normal", &strand_normal,
@@ -1188,31 +1234,6 @@ GData *zMapStyleGetAllPredefined(void)
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-/* NOT SURE WE NEED THIS AT THE MOMENT.....if will need to take a list of predefined ones as a param. */
-ZMapFeatureTypeStyle zMapStyleGetPredefined(char *style_name)
-{
- ZMapFeatureTypeStyle style = NULL, curr = NULL ;
-
- style_id = zMapStyleCreateID(style_name) ;
- curr = &(predefined_styles[0]) ;
- while ((curr->original_id))
- {
- if (style_id == curr->unique_id)
- {
- style = curr ;
- break ;
- }
- else
- curr++ ;
- }
-
- return style ;
-}
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
/* need a func to free a styles list here..... */
void zMapStyleDestroyStyles(GData **styles)
{
@@ -1227,7 +1248,7 @@ void zMapStyleDestroyStyles(GData **styles)
-
+/* I THINK THIS IS BADLY OUT OF DATE NOW AS WE HAVEN'T BEEN DOING STYLES FROM A FILE SO NEEDS REDOING.... */
/* Read the type/method/source (call it what you will) information from the given file
* which currently must reside in the users $HOME/.ZMap directory. */
@@ -1254,6 +1275,7 @@ GData *zMapFeatureTypeGetFromFile(char *styles_file_name)
{"frame_specific", ZMAPCONFIG_BOOL, {NULL}},
{"show_reverse", ZMAPCONFIG_BOOL , {NULL}},
{"show_only_as_3_frame", ZMAPCONFIG_BOOL , {NULL}},
+ {"show_only_as_1_column", ZMAPCONFIG_BOOL , {NULL}},
{"minmag" , ZMAPCONFIG_INT, {NULL}},
{"maxmag" , ZMAPCONFIG_INT, {NULL}},
{"bump" , ZMAPCONFIG_STRING, {NULL}},
@@ -1325,11 +1347,18 @@ GData *zMapFeatureTypeGetFromFile(char *styles_file_name)
zMapConfigGetElementInt(next_styles, "minmag"),
zMapConfigGetElementInt(next_styles, "maxmag")) ;
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+ /* Needs redoing for new strand/frame flags. */
+
zMapStyleSetStrandAttrs(new_type,
zMapConfigGetElementBool(next_styles, "strand_specific"),
zMapConfigGetElementBool(next_styles, "frame_specific"),
zMapConfigGetElementBool(next_styles, "show_reverse"),
- zMapConfigGetElementBool(next_styles, "show_only_as_3_frame")) ;
+ zMapConfigGetElementBool(next_styles, "show_only_as_3_frame"),
+ zMapConfigGetElementBool(next_styles, "show_only_as_1_column")) ;
+#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
zMapStyleSetBump(new_type, zMapConfigGetElementString(next_styles, "bump")) ;
zMapStyleSetBumpWidth(new_type, zMapConfigGetElementFloat(next_styles, "bump_spacing")) ;
@@ -1500,10 +1529,9 @@ static void mergeStyle(GQuark style_id, gpointer data, gpointer user_data)
ZMapFeatureTypeStyle curr_style = NULL ;
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- if (zMapStyleNameCompare(new_style, "genomic_canonical") || zMapStyleNameCompare(new_style, "orfeome"))
+ if (zMapStyleNameCompare(new_style, "atg"))
printf("found it\n") ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
+
/* If we find the style then merge it, if not then add a copy to the curr_styles. */
if ((curr_style = zMapFindStyle(curr_styles, new_style->unique_id)))
@@ -1540,95 +1568,6 @@ static void destroyStyle(GQuark style_id, gpointer data, gpointer user_data_unus
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
-static ZMapFeatureTypeStyle createInheritedStyle(GData *style_set, char *parent_style)
-
-{
- ZMapFeatureTypeStyle inherited_style = NULL ;
- GQuark parent_id ;
-
- if ((parent_id = zMapStyleCreateID(parent_style)))
- {
- GQueue *style_queue ;
- gboolean parent, error ;
- ZMapFeatureTypeStyle curr_style ;
- GQuark curr_id ;
-
- style_queue = g_queue_new() ;
-
- curr_id = parent_id ;
- parent = TRUE ;
- error = FALSE ;
- do
- {
- if ((curr_style = zMapFindStyle(style_set, curr_id)))
- {
- g_queue_push_head(style_queue, curr_style) ;
-
- if (!curr_style->fields_set.parent_style)
- parent = FALSE ;
- else
- curr_id = curr_style->parent_id ;
- }
- else
- {
- error = TRUE ;
- }
- } while (parent && !error) ;
-
- if (!error && !g_queue_is_empty(style_queue))
- {
- InheritStyleCBStruct new_style = {FALSE, NULL} ;
-
- g_queue_foreach(style_queue, inheritStyleCB, &new_style) ;
-
- if (!(new_style.error))
- inherited_style = new_style.inherited_style ;
- }
-
- g_queue_free(style_queue) ; /* We only hold pointers here so no
- data to free. */
- }
-
- return inherited_style ;
-}
-
-
-/* A GFunc to merge styles.
- *
- * Note that if there is an error at any stage in processing the styles then we return NULL. */
-static void inheritStyleCB(gpointer data, gpointer user_data)
-{
- ZMapFeatureTypeStyle child_style = (ZMapFeatureTypeStyle)data ;
- InheritStyleCB inherited = (InheritStyleCB)user_data ;
-
- if (!(inherited->inherited_style))
- {
- inherited->inherited_style = child_style ;
- }
- else
- {
- ZMapFeatureTypeStyle curr_style = inherited->inherited_style ;
-
- if (zMapStyleMerge(curr_style, child_style))
- inherited->inherited_style = curr_style ;
- else
- {
- zMapFeatureTypeDestroy(curr_style) ;
- inherited->inherited_style = NULL ;
- inherited->error = TRUE ;
- }
- }
-
- return ;
-}
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
-
-
/* Functions to sort out the inheritance of styles by copying and overloading. */
/* A GDataForeachFunc() to ..... */
@@ -1742,24 +1681,8 @@ static void inheritAllFunc(gpointer data, gpointer user_data)
{
tmp_style = zMapFeatureStyleCopy(prev_style) ;
-
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- zMapStylePrint(tmp_style, "Parent") ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
if (zMapStyleMerge(tmp_style, curr_style))
{
-
-
-#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
- zMapStylePrint(tmp_style, "child") ;
-#endif /* ED_G_NEVER_INCLUDE_THIS_CODE */
-
-
-
inherited->prev_style = tmp_style ;
/* The g_datalist call overwrites the old style reference with the new one, we then
@@ -1784,3 +1707,58 @@ static void inheritAllFunc(gpointer data, gpointer user_data)
}
+
+
+/* These attributes are not independent hence the bundling into this call, only one input can be
+ * set at a time. */
+static void setStrandFrameAttrs(ZMapFeatureTypeStyle type,
+ gboolean *strand_specific_in,
+ gboolean *show_rev_strand_in,
+ ZMapStyle3FrameMode *frame_mode_in)
+{
+ if (strand_specific_in)
+ {
+ type->fields_set.strand_specific = TRUE ;
+
+ if (*strand_specific_in)
+ {
+ type->opts.strand_specific = TRUE ;
+ }
+ else
+ {
+ type->opts.strand_specific = FALSE ;
+
+ if (type->fields_set.show_rev_strand && type->opts.show_rev_strand)
+ type->fields_set.show_rev_strand = FALSE ;
+
+ if (type->fields_set.frame_specific)
+ {
+ type->opts.frame_specific = FALSE ;
+ type->frame_mode = ZMAPSTYLE_3_FRAME_INVALID ;
+ }
+ }
+ }
+ else if (show_rev_strand_in)
+ {
+ type->fields_set.show_rev_strand = TRUE ;
+ type->opts.show_rev_strand = *show_rev_strand_in ;
+
+ if (*show_rev_strand_in)
+ type->fields_set.strand_specific = type->opts.strand_specific = TRUE ;
+ }
+ else
+ {
+ type->fields_set.frame_specific = TRUE ;
+ type->opts.frame_specific = TRUE ;
+ type->frame_mode = *frame_mode_in ;
+
+ type->fields_set.strand_specific = type->opts.strand_specific = TRUE ;
+ }
+
+ return ;
+}
+
+
+
+
+