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Commit 0a4b9de4 authored by edgrif's avatar edgrif
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change 'overlap' to 'bump' for bumping, add short/long text to bump enums.

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src/include/ZMap/zmapStyle.h
+ 85
− 90
View file @ 0a4b9de4
......@@ -26,9 +26,9 @@
* Description: Style and Style set handling functions.
*
* HISTORY:
* Last edited: Apr 6 12:36 2009 (edgrif)
* Last edited: Apr 28 14:19 2009 (edgrif)
* Created: Mon Feb 26 09:28:26 2007 (edgrif)
* CVS info: $Id: zmapStyle.h,v 1.35 2009-04-06 13:52:44 edgrif Exp $
* CVS info: $Id: zmapStyle.h,v 1.36 2009-04-28 14:28:02 edgrif Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_STYLE_H
......@@ -61,8 +61,9 @@
#define ZMAPSTYLE_PROPERTY_FRAME2_COLOURS "frame2-colours"
#define ZMAPSTYLE_PROPERTY_REV_COLOURS "rev-colours"
#define ZMAPSTYLE_PROPERTY_DISPLAY_MODE "display-mode"
#define ZMAPSTYLE_PROPERTY_OVERLAP_MODE "overlap-mode"
#define ZMAPSTYLE_PROPERTY_DEFAULT_OVERLAP_MODE "default-overlap-mode"
#define ZMAPSTYLE_PROPERTY_BUMP_MODE "bump-mode"
#define ZMAPSTYLE_PROPERTY_DEFAULT_BUMP_MODE "default-bump-mode"
#define ZMAPSTYLE_PROPERTY_BUMP_FIXED "bump-fixed"
#define ZMAPSTYLE_PROPERTY_BUMP_SPACING "bump-spacing"
#define ZMAPSTYLE_PROPERTY_FRAME_MODE "frame-mode"
#define ZMAPSTYLE_PROPERTY_MIN_MAG "min-mag"
......@@ -118,146 +119,136 @@
* */
#define ZMAP_STYLE_MODE_LIST(_) \
_(ZMAPSTYLE_MODE_INVALID, , "invalid") /**< invalid mode */ \
_(ZMAPSTYLE_MODE_BASIC, , "basic") /**< Basic box features */ \
_(ZMAPSTYLE_MODE_ALIGNMENT, , "alignment") /**< Usual homology structure */ \
_(ZMAPSTYLE_MODE_TRANSCRIPT, , "transcript") /**< Usual transcript like structure */ \
_(ZMAPSTYLE_MODE_RAW_SEQUENCE, , "raw-sequence") /**< DNA Sequence */ \
_(ZMAPSTYLE_MODE_PEP_SEQUENCE, , "pep-sequence") /**< Peptide Sequence */ \
_(ZMAPSTYLE_MODE_TEXT, , "text") /**< Text only display */ \
_(ZMAPSTYLE_MODE_GRAPH, , "graph") /**< Graphs of various types */ \
_(ZMAPSTYLE_MODE_GLYPH, , "glyph") /**< Meta object controlling other features */ \
_(ZMAPSTYLE_MODE_META, , "meta")
_(ZMAPSTYLE_MODE_INVALID, , "invalid", "invalid mode ", "") \
_(ZMAPSTYLE_MODE_BASIC, , "basic", "Basic box features ", "") \
_(ZMAPSTYLE_MODE_ALIGNMENT, , "alignment", "Usual homology structure ", "") \
_(ZMAPSTYLE_MODE_TRANSCRIPT, , "transcript", "Usual transcript like structure ", "") \
_(ZMAPSTYLE_MODE_RAW_SEQUENCE, , "raw-sequence", "DNA Sequence ", "") \
_(ZMAPSTYLE_MODE_PEP_SEQUENCE, , "pep-sequence", "Peptide Sequence ", "") \
_(ZMAPSTYLE_MODE_TEXT, , "text", "Text only display ", "") \
_(ZMAPSTYLE_MODE_GRAPH, , "graph", "Graphs of various types ", "") \
_(ZMAPSTYLE_MODE_GLYPH, , "glyph", "Meta object controlling other features ", "") \
_(ZMAPSTYLE_MODE_META, , "meta", "", "")
ZMAP_DEFINE_ENUM(ZMapStyleMode, ZMAP_STYLE_MODE_LIST);
#define ZMAP_STYLE_COLUMN_DISPLAY_LIST(_) \
_(ZMAPSTYLE_COLDISPLAY_INVALID, , "invalid") /**< invalid mode */ \
_(ZMAPSTYLE_COLDISPLAY_HIDE, , "hide") /**< Never show. */ \
_(ZMAPSTYLE_COLDISPLAY_SHOW_HIDE, , "show-hide") /**< Show according to zoom/mag, mark etc. */ \
_(ZMAPSTYLE_COLDISPLAY_SHOW, , "show") /**< Always show. */
_(ZMAPSTYLE_COLDISPLAY_INVALID, , "invalid", "invalid mode ", "") \
_(ZMAPSTYLE_COLDISPLAY_HIDE, , "hide", "Never show. ", "") \
_(ZMAPSTYLE_COLDISPLAY_SHOW_HIDE, , "show-hide", "Show according to zoom/mag, mark etc. ", "") \
_(ZMAPSTYLE_COLDISPLAY_SHOW, , "show", "Always show. ", "")
ZMAP_DEFINE_ENUM(ZMapStyleColumnDisplayState, ZMAP_STYLE_COLUMN_DISPLAY_LIST);
#define ZMAP_STYLE_BLIXEM_LIST(_) \
_(ZMAPSTYLE_BLIXEM_INVALID, , "invalid") /**< invalid */ \
_(ZMAPSTYLE_BLIXEM_N, , "blixem-n") /**< Blixem nucleotide sequence. */ \
_(ZMAPSTYLE_BLIXEM_X, , "blixem-x") /**< Blixem peptide sequence. */
_(ZMAPSTYLE_BLIXEM_INVALID, , "invalid", "invalid ", "") \
_(ZMAPSTYLE_BLIXEM_N, , "blixem-n", "Blixem nucleotide sequence. ", "") \
_(ZMAPSTYLE_BLIXEM_X, , "blixem-x", "Blixem peptide sequence. ", "")
ZMAP_DEFINE_ENUM(ZMapStyleBlixemType, ZMAP_STYLE_BLIXEM_LIST) ;
/* Specifies how features in columns should be overlapped for compact display. */
#define ZMAP_STYLE_OVERLAP_MODE_LIST(_) \
_(ZMAPOVERLAP_INVALID, , "invalid") \
_(ZMAPOVERLAP_COMPLETE, , "complete") /* draw on top - default */ \
_(ZMAPOVERLAP_OVERLAP, , "overlap") /* bump if feature coords overlap. */ \
_(ZMAPOVERLAP_POSITION, , "position") /* bump if features start at same coord. */ \
_(ZMAPOVERLAP_NAME, , "name") /* one column per homol target */ \
_(ZMAPOVERLAP_OSCILLATE, , "oscillate") /* Oscillate between one column and another... \
Useful for displaying tile paths. */ \
_(ZMAPOVERLAP_ITEM_OVERLAP, , "item-overlap") /* bump if item coords overlap in canvas space... */ \
_(ZMAPOVERLAP_SIMPLE, , "simple") /* one column per feature, for testing... */ \
_(ZMAPOVERLAP_ENDS_RANGE, , "ends-range") /* Sort by 5' and 3' best/biggest \
matches, one match per column, very \
fmap like but better... */ \
_(ZMAPOVERLAP_COMPLEX_INTERLEAVE, , "complex-interleave")/* all features with same name in a \
single sub-column, several names in one \
column but no 2 features overlap. */ \
_(ZMAPOVERLAP_COMPLEX_NO_INTERLEAVE, , "complex-interleave") /* as ZMAPOVERLAP_COMPLEX but no interleaving of \
features with different names. */ \
_(ZMAPOVERLAP_COMPLEX_RANGE, , "complex-range") /* All features with same name in a \
single column if they overlap the \
'mark' range, all other features in \
a single column. */ \
_(ZMAPOVERLAP_COMPLEX_LIMIT, , "complex-limit") /* As ZMAPOVERLAP_COMPLEX_RANGE but constrain matches \
to be colinear within range or are truncated. */
/* Specifies how features in columns should be bumpped for compact display. */
#define ZMAP_STYLE_BUMP_MODE_LIST(_) \
_(ZMAPBUMP_INVALID, , "invalid", "invalid", "invalid") \
_(ZMAPBUMP_UNBUMP, , "unbump", "Unbump", "No bumping (default)") \
_(ZMAPBUMP_OVERLAP, , "overlap", "Overlap", "Bump any features overlapping each other.") \
_(ZMAPBUMP_NAVIGATOR, , "navigator", "Navigator Overlap", "Navigator bump: special for zmap navigator bumping.") \
_(ZMAPBUMP_START_POSITION, , "start-position", "Start Position", "Bump if features have same start coord.") \
_(ZMAPBUMP_ALTERNATING, , "alternating", "Alternating", "Alternate features between two sub_columns, e.g. to display assemblies.") \
_(ZMAPBUMP_ALL, , "all", "Bump All", "A sub-column for every feature.") \
_(ZMAPBUMP_NAME, , "name", "Name", "A sub-column for features with the same name.") \
_(ZMAPBUMP_NAME_INTERLEAVE, , "name-interleave", "Name Interleave", "All features with same name in a single sub-column but several names interleaved in each sub-column, the most compact display.") \
_(ZMAPBUMP_NAME_NO_INTERLEAVE, , "name-no-interleave", "Name No Interleave", "Display as for Interleave but no interleaving of different names.") \
_(ZMAPBUMP_NAME_COLINEAR, , "name-colinear", "Name No Interleave & Colinear", "As for No Interleave but for alignments only colinear shown.") \
_(ZMAPBUMP_NAME_BEST_ENDS, , "name-best-ends", "Name and Best 5'& 3' Matches", "As for No Interleave but for alignments sorted by 5' and 3' best/biggest matches, one sub_column per match.")
/* We should do this automatically or not at all..... */
#define ZMAPOVERLAP_START ZMAPOVERLAP_COMPLETE
#define ZMAPOVERLAP_END ZMAPOVERLAP_COMPLEX_LIMIT
#define ZMAPBUMP_START ZMAPBUMP_UNBUMP
#define ZMAPBUMP_END ZMAPBUMP_NAME_COLINEAR
ZMAP_DEFINE_ENUM(ZMapStyleOverlapMode, ZMAP_STYLE_OVERLAP_MODE_LIST) ;
ZMAP_DEFINE_ENUM(ZMapStyleBumpMode, ZMAP_STYLE_BUMP_MODE_LIST) ;
#define ZMAP_STYLE_3_FRAME_LIST(_) \
_(ZMAPSTYLE_3_FRAME_INVALID, , "invalid") /**< invalid mode */ \
_(ZMAPSTYLE_3_FRAME_NEVER, , "never") /**< Not frame sensitive. */ \
_(ZMAPSTYLE_3_FRAME_ALWAYS, , "always") /**< Display normally and as 3 cols in 3 frame mode. */ \
_(ZMAPSTYLE_3_FRAME_ONLY_3, , "only-3") /**< Only dislay in 3 frame mode as 3 cols. */ \
_(ZMAPSTYLE_3_FRAME_ONLY_1, , "only-1") /**< Only display in 3 frame mode as 1 col. */
_(ZMAPSTYLE_3_FRAME_INVALID, , "invalid", "invalid mode ", "") \
_(ZMAPSTYLE_3_FRAME_NEVER, , "never", "Not frame sensitive. ", "") \
_(ZMAPSTYLE_3_FRAME_ALWAYS, , "always", "Display normally and as 3 cols in 3 frame mode. ", "") \
_(ZMAPSTYLE_3_FRAME_ONLY_3, , "only-3", "Only dislay in 3 frame mode as 3 cols. ", "") \
_(ZMAPSTYLE_3_FRAME_ONLY_1, , "only-1", "Only display in 3 frame mode as 1 col. ", "")
ZMAP_DEFINE_ENUM(ZMapStyle3FrameMode, ZMAP_STYLE_3_FRAME_LIST);
/* Specifies the style of graph. */
#define ZMAP_STYLE_GRAPH_MODE_LIST(_) \
_(ZMAPSTYLE_GRAPH_INVALID, , "invalid") /**< Initial setting. */ \
_(ZMAPSTYLE_GRAPH_LINE, , "line") /**< Just points joining a line. */ \
_(ZMAPSTYLE_GRAPH_HISTOGRAM, , "histogram") /**< Usual blocky like graph. */
_(ZMAPSTYLE_GRAPH_INVALID, , "invalid", "Initial setting. ", "") \
_(ZMAPSTYLE_GRAPH_LINE, , "line", "Just points joining a line. ", "") \
_(ZMAPSTYLE_GRAPH_HISTOGRAM, , "histogram", "Usual blocky like graph.", "")
ZMAP_DEFINE_ENUM(ZMapStyleGraphMode, ZMAP_STYLE_GRAPH_MODE_LIST);
/* Specifies the style of glyph. */
#define ZMAP_STYLE_GLYPH_MODE_LIST(_) \
_(ZMAPSTYLE_GLYPH_INVALID, , "invalid") /**< Initial setting. */ \
_(ZMAPSTYLE_GLYPH_SPLICE, , "splice")
_(ZMAPSTYLE_GLYPH_INVALID, , "invalid", "Initial setting. ", "") \
_(ZMAPSTYLE_GLYPH_SPLICE, , "splice", "", "")
ZMAP_DEFINE_ENUM(ZMapStyleGlyphMode, ZMAP_STYLE_GLYPH_MODE_LIST);
/* Specifies type of colour, e.g. normal or selected. */
#define ZMAP_STYLE_COLOUR_TYPE_LIST(_) \
_(ZMAPSTYLE_COLOURTYPE_INVALID, , "invalid") /**< */ \
_(ZMAPSTYLE_COLOURTYPE_NORMAL, , "normal") /**< */ \
_(ZMAPSTYLE_COLOURTYPE_SELECTED, , "selected") /**< */
_(ZMAPSTYLE_COLOURTYPE_INVALID, , "invalid", " ", "") \
_(ZMAPSTYLE_COLOURTYPE_NORMAL, , "normal", " ", "") \
_(ZMAPSTYLE_COLOURTYPE_SELECTED, , "selected", " ", "")
ZMAP_DEFINE_ENUM(ZMapStyleColourType, ZMAP_STYLE_COLOUR_TYPE_LIST) ;
/* For drawing/colouring the various parts of a feature. */
#define ZMAP_STYLE_DRAW_CONTEXT_LIST(_) \
_(ZMAPSTYLE_DRAW_INVALID, , "invalid") /**< invalid, initial setting */ \
_(ZMAPSTYLE_DRAW_FILL, , "fill") /**< */ \
_(ZMAPSTYLE_DRAW_DRAW, , "draw") /**< */ \
_(ZMAPSTYLE_DRAW_BORDER, , "border")
_(ZMAPSTYLE_DRAW_INVALID, , "invalid", "invalid, initial setting ", "") \
_(ZMAPSTYLE_DRAW_FILL, , "fill", " ", "") \
_(ZMAPSTYLE_DRAW_DRAW, , "draw", " ", "") \
_(ZMAPSTYLE_DRAW_BORDER, , "border", "", "")
ZMAP_DEFINE_ENUM(ZMapStyleDrawContext, ZMAP_STYLE_DRAW_CONTEXT_LIST) ;
/* Specifies the target type of the colour. */
#define ZMAP_STYLE_COLOUR_TARGET_LIST(_) \
_(ZMAPSTYLE_COLOURTARGET_INVALID, , "invalid") /* Normal colour */ \
_(ZMAPSTYLE_COLOURTARGET_NORMAL, , "normal") /* Normal colour */ \
_(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_STRAND, , "strand") /* Colour to apply to Strand */
_(ZMAPSTYLE_COLOURTARGET_INVALID, , "invalid", "Normal colour ", "") \
_(ZMAPSTYLE_COLOURTARGET_NORMAL, , "normal", "Normal colour ", "") \
_(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_STRAND, , "strand", "Colour to apply to Strand ", "")
ZMAP_DEFINE_ENUM(ZMapStyleColourTarget, ZMAP_STYLE_COLOUR_TARGET_LIST) ;
/* Specifies how wide features should be in relation to their score. */
#define ZMAP_STYLE_SCORE_MODE_LIST(_) \
_(ZMAPSCORE_INVALID, , "invalid") /* Use column width only - default. */ \
_(ZMAPSCORE_WIDTH, , "width") /* Use column width only - default. */ \
_(ZMAPSCORE_OFFSET, , "offset") \
_(ZMAPSCORE_HISTOGRAM, , "histogram") \
_(ZMAPSCORE_PERCENT, , "percent")
_(ZMAPSCORE_INVALID, , "invalid", "Use column width only - default. ", "") \
_(ZMAPSCORE_WIDTH, , "width", "Use column width only - default. ", "") \
_(ZMAPSCORE_OFFSET, , "offset", "", "") \
_(ZMAPSCORE_HISTOGRAM, , "histogram", "", "") \
_(ZMAPSCORE_PERCENT, , "percent", "", "")
ZMAP_DEFINE_ENUM(ZMapStyleScoreMode, ZMAP_STYLE_SCORE_MODE_LIST) ;
#define ZMAP_STYLE_MERGE_MODE_LIST(_) \
_(ZMAPSTYLE_MERGE_INVALID, , "invalid") /* invalid mode */ \
_(ZMAPSTYLE_MERGE_PRESERVE, , "preserve") /* If a style already exists, do nothing. */ \
_(ZMAPSTYLE_MERGE_REPLACE, , "replace") /* Replace existing styles with the new one. */ \
_(ZMAPSTYLE_MERGE_MERGE, , "merge") /* Merge existing styles with new ones by overriding. */
_(ZMAPSTYLE_MERGE_INVALID, , "invalid", "invalid mode ", "") \
_(ZMAPSTYLE_MERGE_PRESERVE, , "preserve", "If a style already exists, do nothing. ", "") \
_(ZMAPSTYLE_MERGE_REPLACE, , "replace", "Replace existing styles with the new one. ", "") \
_(ZMAPSTYLE_MERGE_MERGE, , "merge", "Merge existing styles with new ones by overriding. ", "")
ZMAP_DEFINE_ENUM(ZMapStyleMergeMode, ZMAP_STYLE_MERGE_MODE_LIST) ;
......@@ -300,7 +291,7 @@ ZMAP_ENUM_FROM_STRING_DEC(zMapStyleStr2DrawContext, ZMapStyleDrawContext) ;
ZMAP_ENUM_FROM_STRING_DEC(zMapStyleStr2ColourType, ZMapStyleColourType) ;
ZMAP_ENUM_FROM_STRING_DEC(zMapStyleStr2ColourTarget, ZMapStyleColourTarget) ;
ZMAP_ENUM_FROM_STRING_DEC(zMapStyleStr2ScoreMode, ZMapStyleScoreMode) ;
ZMAP_ENUM_FROM_STRING_DEC(zMapStyleStr2OverlapMode, ZMapStyleOverlapMode) ;
ZMAP_ENUM_FROM_STRING_DEC(zMapStyleStr2BumpMode, ZMapStyleBumpMode) ;
/* Enum -> String function decs: const char *zMapStyleXXXXMode2ExactStr(ZMapStyleXXXXXMode mode); */
......@@ -313,7 +304,11 @@ ZMAP_ENUM_AS_EXACT_STRING_DEC(zmapStyleDrawContext2ExactStr, ZMapStyleDrawCo
ZMAP_ENUM_AS_EXACT_STRING_DEC(zmapStyleColourType2ExactStr, ZMapStyleColourType) ;
ZMAP_ENUM_AS_EXACT_STRING_DEC(zmapStyleColourTarget2ExactStr, ZMapStyleColourTarget) ;
ZMAP_ENUM_AS_EXACT_STRING_DEC(zmapStyleScoreMode2ExactStr, ZMapStyleScoreMode) ;
ZMAP_ENUM_AS_EXACT_STRING_DEC(zmapStyleOverlapMode2ExactStr, ZMapStyleOverlapMode) ;
ZMAP_ENUM_AS_EXACT_STRING_DEC(zmapStyleBumpMode2ExactStr, ZMapStyleBumpMode) ;
ZMAP_ENUM_TO_SHORT_TEXT_DEC(zmapStyleBumpMode2ShortText, ZMapStyleBumpMode) ;
ZMapFeatureTypeStyle zMapStyleCreate(char *name, char *description) ;
......@@ -343,12 +338,12 @@ void zMapStyleSetDisplay(ZMapFeatureTypeStyle style, ZMapStyleColumnDisplayState
void zMapStyleSetMode(ZMapFeatureTypeStyle style, ZMapStyleMode mode) ;
ZMapStyleMode zMapStyleGetMode(ZMapFeatureTypeStyle style) ;
char *zMapStyleGetName(ZMapFeatureTypeStyle style) ;
ZMapStyleOverlapMode zMapStyleGetOverlapMode(ZMapFeatureTypeStyle style) ;
void zMapStyleSetOverlapMode(ZMapFeatureTypeStyle style, ZMapStyleOverlapMode overlap_mode) ;
ZMapStyleBumpMode zMapStyleGetBumpMode(ZMapFeatureTypeStyle style) ;
void zMapStyleSetBumpMode(ZMapFeatureTypeStyle style, ZMapStyleBumpMode bump_mode) ;
char *zMapStyleGetGFFSource(ZMapFeatureTypeStyle style) ;
char *zMapStyleGetGFFFeature(ZMapFeatureTypeStyle style) ;
void zMapStyleSetDescription(ZMapFeatureTypeStyle style, char *description) ;
ZMapStyleOverlapMode zMapStyleGetDefaultOverlapMode(ZMapFeatureTypeStyle style);
ZMapStyleBumpMode zMapStyleGetDefaultBumpMode(ZMapFeatureTypeStyle style);
double zMapStyleGetWidth(ZMapFeatureTypeStyle style) ;
double zMapStyleGetBumpSpace(ZMapFeatureTypeStyle style) ;
ZMapStyleColumnDisplayState zMapStyleGetDisplay(ZMapFeatureTypeStyle style) ;
......@@ -445,9 +440,9 @@ void zMapFeatureTypeDestroy(ZMapFeatureTypeStyle type) ;
ZMapFeatureTypeStyle zMapStyleGetPredefined(char *style_name) ;
gboolean zMapFeatureTypeSetAugment(GData **current, GData **new) ;
void zMapStyleInitOverlapMode(ZMapFeatureTypeStyle style,
ZMapStyleOverlapMode default_overlap_mode, ZMapStyleOverlapMode curr_overlap_mode) ;
ZMapStyleOverlapMode zMapStyleResetOverlapMode(ZMapFeatureTypeStyle style) ;
void zMapStyleInitBumpMode(ZMapFeatureTypeStyle style,
ZMapStyleBumpMode default_bump_mode, ZMapStyleBumpMode curr_bump_mode) ;
ZMapStyleBumpMode zMapStyleResetBumpMode(ZMapFeatureTypeStyle style) ;
ZMapFeatureTypeStyle zMapFeatureStyleCopy(ZMapFeatureTypeStyle style) ;
......
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