Use new zmapEnum.h

previous contents of zmapStyle_P.h plus #ifdef'd out gobject stuff

src/zmapFeature/zmapStyle_I.h

+/*  File: zmapStyle_P.h
+ *  Author: Ed Griffiths (edgrif@sanger.ac.uk)
+ *  Copyright (c) 2007: Genome Research Ltd.
+ *-------------------------------------------------------------------
+ * ZMap is free software; you can redistribute it and/or
+ * 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.
+ * or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
+ *-------------------------------------------------------------------
+ * This file is part of the ZMap genome database package
+ * originally written by:
+ *
+ * 	Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
+ *      Roy Storey (Sanger Institute, UK) rds@sanger.ac.uk
+ *
+ * Description: Private header for style.
+ *
+ * HISTORY:
+ * Last edited: Jun 10 10:46 2008 (rds)
+ * Created: Mon Feb 26 09:13:30 2007 (edgrif)
+ * CVS info:   $Id: zmapStyle_I.h,v 1.1 2008-06-12 21:03:58 rds Exp $
+ *-------------------------------------------------------------------
+ */
+
+#ifndef __ZMAP_STYLE_I_H__
+#define __ZMAP_STYLE_I_H__
+
+
+/* TEMP....WHILE I MOVE STYLE STUFF IN HERE.... */
+#include <ZMap/zmapFeature.h>
+
+#include <ZMap/zmapStyle.h>
+
+#ifdef STYLES_ARE_G_OBJECTS
+
+#include <ZMap/zmapStyle.h>
+
+#define ZMAP_PARAM_STATIC (G_PARAM_STATIC_NAME | G_PARAM_STATIC_NICK | G_PARAM_STATIC_BLURB)
+#define ZMAP_PARAM_STATIC_RW (ZMAP_PARAM_STATIC | G_PARAM_READWRITE)
+#define ZMAP_PARAM_STATIC_RO (ZMAP_PARAM_STATIC | G_PARAM_READABLE)
+
+typedef struct _zmapFeatureTypeStyleClassStruct
+{
+  GObjectClass __parent__;
+
+} zmapFeatureTypeStyleClassStruct;
+
+#endif /* STYLES_ARE_G_OBJECTS */
+
+/*! @addtogroup zmapstyles
+ * @{
+ *  */
+
+
+/*! @struct ZMapStyleColour zmapStyle_P.h
+ *  @brief ZMap object colours
+ *
+ * All ZMap objects can potentially have a border colour, a fill colour and a draw colour
+ * which can be used to "draw" over the fill colour. */
+
+typedef struct
+{
+  struct
+  {
+    unsigned int draw : 1 ;
+    unsigned int fill : 1 ;
+    unsigned int border : 1 ;
+  } fields_set ;
+
+  GdkColor  draw ;					    /* Overlaid on fill colour. */
+  GdkColor  fill ;					    /* Fill/background colour. */
+  GdkColor  border ;					    /* Surround/line colour. */
+} ZMapStyleColourStruct, *ZMapStyleColour ;
+
+
+/*! @struct ZMapStyleFullColour zmapStyle_P.h
+ *  @brief ZMap feature colours
+ *
+ * All features in ZMap can be selected and hence must have both "normal" and "selected"
+ * colours. */
+typedef struct
+{
+  ZMapStyleColourStruct normal ;
+  ZMapStyleColourStruct selected ;
+} ZMapStyleFullColourStruct, *ZMapStyleFullColour ;
+
+
+/*! Styles have different modes, e.g. graph, alignment etc, information specific to a particular
+ * style is held in its own struct. */
+
+
+/*! @struct ZMapBasicGraph zmapStyle_P.h
+ *  @brief Basic feature
+ *
+ * < currently this is empty > */
+typedef struct
+{
+  char *dummy ;
+
+} ZMapStyleBasicStruct, *ZMapBasicGraph ;
+
+/*! @struct ZMapSequenceGraph zmapStyle_P.h
+ *  @brief Sequence feature
+ *
+ * (currently this is empty) */
+typedef struct
+{
+  char *dummy ;
+
+} ZMapStyleSequenceStruct, *ZMapSequenceGraph ;
+
+/*! @struct ZMapTextGraph zmapStyle_P.h
+ *  @brief Text feature
+ *
+ * (currently this is empty) */
+typedef struct
+{
+  char *dummy ;
+
+} ZMapStyleTextStruct, *ZMapTextGraph ;
+
+
+
+/*! @struct ZMapStyleGraph zmapStyle_P.h
+ *  @brief Graph feature
+ *
+ * Draws a feature as a graph, the feature must contain graph points. */
+typedef struct
+{
+  struct
+  {
+    unsigned int mode : 1 ;
+    unsigned int baseline : 1 ;
+  } fields_set ;					    /*!< Fields set.  */
+  
+  ZMapStyleGraphMode mode ;				    /*!< Graph style. */
+
+  double baseline ;					    /*!< zero level for graph.  */
+
+} ZMapStyleGraphStruct, *ZMapStyleGraph ;
+
+
+/*! @struct ZMapStyleGlyph zmapStyle_P.h
+ *  @brief Glyph feature
+ *
+ * Draws shapes of various kinds, e.g. splice site indicators etc. */
+typedef struct
+{
+  struct
+  {
+    unsigned int unused : 1 ;
+  } fields_set ;					    /*!< Fields set.  */
+
+  ZMapStyleGlyphMode mode ;				    /*!< Glyph style. */
+
+} ZMapStyleGlyphStruct, *ZMapStyleGlyph ;
+
+
+/*! @struct ZMapStyleAlignment zmapStyle_P.h
+ *  @brief Alignment feature
+ *
+ * Draws an alignment as a series of blocks joined by straight lines. The lines can be coloured
+ * to indicate colinearity between adjacent blocks. */
+typedef struct
+ {
+  struct
+  {
+    unsigned int within_align_error : 1 ;
+    unsigned int between_align_error : 1 ;
+  } fields_set ;						    /*!< Fields set.  */
+
+  /*! Allowable align errors, used to decide whether a match should be classified as "perfect".
+   *   within_align_error   is used to assess the blocks in a single gapped alignment if align_gaps = TRUE
+   *  between_align_error   is used to assess several alignments (e.g. for exon matches) if join_homols = TRUE
+   * 
+   * Number is allowable number of missing bases between blocks/alignments, default is 0. */
+  unsigned int within_align_error ;
+  unsigned int between_align_error ;
+
+  /*! Colours for bars joining up intra/inter alignment gaps. */
+  ZMapStyleFullColourStruct perfect ;
+  ZMapStyleFullColourStruct colinear ;
+  ZMapStyleFullColourStruct noncolinear ;
+
+   /* State for alignments. */
+  struct
+  {
+    unsigned int pfetchable : 1 ;			    /* TRUE => alignments have pfetch entries. */
+  } state ;
+
+} ZMapStyleAlignmentStruct, *ZMapStyleAlignment ;
+
+
+/*! @struct ZMapStyleTranscript zmapStyle_P.h
+ *  @brief Transcript feature
+ *
+ * Draws a transcript as a series of boxes joined by angled lines. */
+typedef struct
+{
+  struct
+  {
+    unsigned int unused : 1 ;
+  } fields_set ;					    /*!< Fields set.  */
+
+
+  ZMapStyleFullColourStruct CDS_colours ;		    /*!< Colour for CDS part of feature. */
+
+} ZMapStyleTranscriptStruct, *ZMapStyleTranscript ;
+
+
+/*! @struct ZMapFeatureTypeStyle zmapStyle_P.h
+ *  @brief ZMap Style
+ *
+ * ZMap Style definition, the style must have a mode which specifies what sort of
+ * of feature the style represents. */
+typedef struct _zmapFeatureTypeStyleStruct
+{
+
+#ifdef STYLES_ARE_G_OBJECTS
+  GObject __parent__;
+#endif /* STYLES_ARE_G_OBJECTS */
+
+  /*! _All_ styles must have these fields set, no other fields are compulsory. */
+  GQuark original_id ;					    /*!< Original name. */
+  GQuark unique_id ;					    /*!< Name normalised to be unique. */
+
+
+  /*! Since all these fields are optional we need flags for all of them to show whether they were
+   *  set. */
+  struct
+  {
+    unsigned int parent_style : 1 ;
+
+    unsigned int description : 1 ;
+
+    unsigned int mode : 1 ;
+
+    unsigned int min_score : 1 ;
+    unsigned int max_score : 1 ;
+
+    unsigned int overlap_mode : 1 ;
+    unsigned int overlap_default : 1 ;
+    unsigned int bump_spacing : 1 ;
+
+    unsigned int min_mag : 1 ;
+    unsigned int max_mag : 1 ;
+
+    unsigned int width : 1 ;
+
+    unsigned int score_mode : 1 ;
+
+    unsigned int gff_source : 1 ;
+    unsigned int gff_feature : 1 ;
+
+  } fields_set ;					    /*!< Fields set.  */
+
+
+
+  /*! Data fields for the style. */
+
+  
+  GQuark parent_id ;					    /*!< Styles can inherit from other
+							       styles, the parent style _must_ be
+							       identified by its unique id. */
+
+  char *description ;					    /*!< Description of what this style
+							       represents. */
+
+  ZMapStyleMode mode ;					    /*!< Specifies how features that
+							       reference this style will be processed. */
+
+  ZMapStyleFullColourStruct colours ;			    /*!< Main feature colours. */
+
+  /*! Colours for when feature is shown in frames. */
+  ZMapStyleFullColourStruct frame0_colours ;
+  ZMapStyleFullColourStruct frame1_colours ;
+  ZMapStyleFullColourStruct frame2_colours ;
+
+  /*! Colours for when feature is shown stranded by colour  */
+  ZMapStyleFullColourStruct strand_rev_colours;
+
+  ZMapStyleOverlapMode default_overlap_mode ;		    /*!< Allows return to original bump mode. */
+  ZMapStyleOverlapMode curr_overlap_mode ;		    /*!< Controls how features are grouped
+							       into sub columns within a column. */
+  double bump_spacing ;					    /*!< gap between bumped features. */
+
+  double min_mag ;					    /*!< Don't display if fewer bases/line */
+  double max_mag ;					    /*!< Don't display if more bases/line */
+
+  double width ;					    /*!< column width */
+
+  ZMapStyleScoreMode score_mode ;			    /*!< Controls width of features that
+							       have scores. */
+  double min_score, max_score ;				    /*!< Min/max for score width calc. */
+
+
+  /*! GFF feature dumping, allows specifying of source/feature types independently of feature
+   * attributes. */
+  GQuark gff_source ;
+  GQuark gff_feature ;
+
+  ZMapStyleColumnDisplayState col_display_state ;	    /* Controls how/when col is displayed. */
+
+  /*! State information for the style. */
+  struct
+  {
+    unsigned int displayable     : 1 ;			    /* FALSE means never, ever display,
+							       for TRUE see col_display_state. */
+
+
+    unsigned int show_when_empty : 1 ;			    /*!< If FALSE, features' column is
+							       displayed even if there are no features. */
+
+
+    unsigned int showText        : 1 ;			    /*!< Should feature text be displayed. */
+
+    unsigned int parse_gaps      : 1 ;
+    unsigned int align_gaps      : 1 ;			    /*!< TRUE: gaps within alignment are displayed,
+							       FALSE: alignment is displayed as a single block. */
+
+    /*! These are all linked, if strand_specific is FALSE, then so are
+     * frame_specific and show_rev_strand. */
+    unsigned int strand_specific : 1 ;			    /*!< Feature that is on one strand of the dna. */
+    unsigned int show_rev_strand : 1 ;			    /*!< Only display the feature on the
+							       reverse strand if this is set. */
+    unsigned int frame_specific  : 1 ;			    /*!< Feature that is in some way linked
+							       to the reading frame of the dna. */
+    unsigned int show_only_as_3_frame : 1 ;		    /*!< frame specific feature that should
+							       only be displayed when all 3 frames
+							       are shown. */
+
+    unsigned int show_only_in_separator : 1;
+
+    unsigned int directional_end : 1 ;			    /*!< Display pointy ends on exons etc. */
+
+    unsigned int deferred : 1; 	/* flag for to say if this style is deferred loaded */
+
+    unsigned int loaded : 1;	/* flag to say if we're loaded */
+  } opts ;
+
+  /*! Mode specific fields, see docs for individual structs. */  
+  union
+  {
+    ZMapStyleBasicStruct basic ;
+    ZMapStyleSequenceStruct sequence ;
+    ZMapStyleTextStruct text ;
+    ZMapStyleTranscriptStruct transcript ;
+    ZMapStyleAlignmentStruct alignment ;
+    ZMapStyleGraphStruct graph ;
+    ZMapStyleGlyphStruct glyph ;
+  } mode_data ;
+
+
+} zmapFeatureTypeStyleStruct ;
+
+
+
+
+/*! @} end of zmapstyles docs. */
+
+
+
+
+#endif /* !ZMAP_STYLE_P_H */