new files for separate style stuff.

src/zmapFeature/zmapStyle.c

+/*  File: zmapStyle.c
+ *  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: Contains functions for handling styles and sets of
+ *              styles.
+ *
+ * Exported functions: See ZMap/zmapStyle.h
+ * HISTORY:
+ * Last edited: Feb 26 15:49 2007 (edgrif)
+ * Created: Mon Feb 26 09:12:18 2007 (edgrif)
+ * CVS info:   $Id: zmapStyle.c,v 1.1 2007-02-28 18:15:51 edgrif Exp $
+ *-------------------------------------------------------------------
+ */
+
+
+#include <ZMap/zmapUtils.h>
+#include <zmapStyle_P.h>
+
+
+
+
+ZMapStyleMode zMapStyleGetMode(ZMapFeatureTypeStyle style)
+{
+  zMapAssert(style) ;
+
+  return style->mode ;
+}
+
+
+
+/* First attempt at using the macro trick to have enums/string equivalents defined in one place
+ * and then define an enum type and strings from that. */
+#define ZMAP_MODE_STR(Name) #Name,
+
+const char *zMapStyleMode2Str(ZMapStyleMode mode)
+{
+  static const char *names_array[] =
+    {
+      ZMAP_MODE_METADEFS(ZMAP_MODE_STR)
+    };
+  const char *mode_str = NULL ;
+
+  zMapAssert(mode > 0 && mode < sizeof(names_array)/sizeof(names_array[0])) ;
+
+  mode_str = names_array[mode] ;
+
+  return mode_str ;
+}
+
+
+
+GQuark zMapStyleGetID(ZMapFeatureTypeStyle style)
+{
+  zMapAssert(style) ;
+
+  return style->original_id ;
+}
+
+GQuark zMapStyleGetUniqueID(ZMapFeatureTypeStyle style)
+{
+  zMapAssert(style) ;
+
+  return style->unique_id ;
+}
+
+
+char *zMapStyleGetDescription(ZMapFeatureTypeStyle style)
+{
+  char *description = NULL ;
+
+  zMapAssert(style) ;
+
+  if (style->fields_set.description)
+    description = style->description ;
+
+  return description ;
+}
+
+
+gboolean zMapStyleIsColour(ZMapFeatureTypeStyle style, ZMapStyleDrawContext colour_context)
+{
+  gboolean is_colour = FALSE ;
+
+  zMapAssert(style) ;
+
+  switch(colour_context)
+    {
+    case ZMAPSTYLE_DRAW_BACKGROUND:
+      is_colour = style->fields_set.background_set ;
+      break ;
+    case ZMAPSTYLE_DRAW_FOREGROUND:
+      is_colour = style->fields_set.foreground_set ;
+      break ;
+    case ZMAPSTYLE_DRAW_OUTLINE:
+      is_colour = style->fields_set.outline_set ;
+      break ;
+    default:
+      zMapAssertNotReached() ;
+    }
+
+  return is_colour ;
+}
+
+GdkColor *zMapStyleGetColour(ZMapFeatureTypeStyle style, ZMapStyleDrawContext colour_context)
+{
+  GdkColor *colour = NULL ;
+
+  zMapAssert(style) ;
+
+  if (zMapStyleIsColour(style, colour_context))
+    {
+      switch(colour_context)
+	{
+	case ZMAPSTYLE_DRAW_BACKGROUND:
+	  colour = &(style->normal_colours.background) ;
+	  break ;
+	case ZMAPSTYLE_DRAW_FOREGROUND:
+	  colour = &(style->normal_colours.foreground) ;
+	  break ;
+	case ZMAPSTYLE_DRAW_OUTLINE:
+	  colour = &(style->normal_colours.outline) ;
+	  break ;
+	default:
+	  zMapAssertNotReached() ;
+	}
+    }
+
+  return colour ;
+}
+
+
+char *zMapStyleGetGFFSource(ZMapFeatureTypeStyle style)
+{
+  char *gff_source = NULL ;
+
+  zMapAssert(style) ;
+
+  if (style->fields_set.gff_source)
+    gff_source = (char *)g_quark_to_string(style->gff_source) ;
+
+  return gff_source ;
+}
+
+char *zMapStyleGetGFFFeature(ZMapFeatureTypeStyle style)
+{
+  char *gff_feature = NULL ;
+
+  zMapAssert(style) ;
+
+  if (style->fields_set.gff_feature)
+    gff_feature = (char *)g_quark_to_string(style->gff_feature) ;
+
+  return gff_feature ;
+}
+
+
+unsigned int zmapStyleGetWithinAlignError(ZMapFeatureTypeStyle style)
+{
+  zMapAssert(style) ;
+
+  return style->within_align_error ;
+}
+
+
+gboolean zMapStyleIsParseGaps(ZMapFeatureTypeStyle style)
+{
+  zMapAssert(style) ;
+
+  return style->opts.parse_gaps ;
+}
+
+gboolean zMapStyleIsDirectionalEnd(ZMapFeatureTypeStyle style)
+{
+  zMapAssert(style) ;
+
+  return style->opts.directional_end ;
+}
+
+
+gboolean zMapStyleIsAlignGaps(ZMapFeatureTypeStyle style)
+{
+  zMapAssert(style) ;
+
+  return style->opts.align_gaps ;
+}
+
+
+gboolean zMapStyleIsFrameSpecific(ZMapFeatureTypeStyle style)
+{
+  zMapAssert(style) ;
+
+  return style->opts.frame_specific ;
+}
+
+gboolean zMapStyleIsHiddenAlways(ZMapFeatureTypeStyle style)
+{
+  zMapAssert(style) ;
+
+  return style->opts.hidden_always ;
+}
+
+gboolean zMapStyleIsHiddenNow(ZMapFeatureTypeStyle style)
+{
+  zMapAssert(style) ;
+
+  return style->opts.hidden_now ;
+}
+
+gboolean zMapStyleIsStrandSpecific(ZMapFeatureTypeStyle style)
+{
+  zMapAssert(style) ;
+
+  return style->opts.strand_specific ;
+}
+
+gboolean zMapStyleIsShowReverseStrand(ZMapFeatureTypeStyle style)
+{
+  zMapAssert(style) ;
+
+  return style->opts.show_rev_strand ;
+}
+
+
+/* this function illustrates a problem, if we don't return the type directly it makes the
+ * interface awkward for the user, and really we shouldn't as we have a "set" field to test for this field. */
+double zMapStyleGetWidth(ZMapFeatureTypeStyle style)
+{
+  zMapAssert(style) ;
+
+  return style->width ;
+}
+
+double zMapStyleGetMaxScore(ZMapFeatureTypeStyle style)
+{
+  zMapAssert(style) ;
+
+  return style->max_score ;
+}
+
+double zMapStyleGetMinScore(ZMapFeatureTypeStyle style)
+{
+  zMapAssert(style) ;
+
+  return style->min_score ;
+}
+
+
+double zMapStyleGetMinMag(ZMapFeatureTypeStyle style)
+{
+  zMapAssert(style) ;
+
+  return style->min_mag ;
+}
+
+double zMapStyleGetMaxMag(ZMapFeatureTypeStyle style)
+{
+  zMapAssert(style) ;
+
+  return style->max_mag ;
+}
+
+
+
+double zMapStyleBaseline(ZMapFeatureTypeStyle style)
+{
+  zMapAssert(style) ;
+
+  return style->baseline ;
+}
+
+

src/zmapFeature/zmapStyle_P.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: Feb 26 09:27 2007 (edgrif)
+ * Created: Mon Feb 26 09:13:30 2007 (edgrif)
+ * CVS info:   $Id: zmapStyle_P.h,v 1.1 2007-02-28 18:15:51 edgrif Exp $
+ *-------------------------------------------------------------------
+ */
+#ifndef ZMAP_STYLE_P_H
+#define ZMAP_STYLE_P_H
+
+
+
+/* TEMP....WHILE I MOVE STYLE STUFF IN HERE.... */
+#include <ZMap/zmapFeature.h>
+
+
+#include <ZMap/zmapStyle.h>
+
+
+
+
+
+typedef struct ZMapFeatureTypeStyleStruct_
+{
+  /* _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.
+   * 
+   * IN FACT THIS MAY NOT BE TRUE AS SOME OF THESE FLAGS ARE NOT INDEPENDENT...WE'LL SEE....
+   *  */
+  struct
+  {
+    unsigned int parent_style : 1 ;
+
+    unsigned int description : 1 ;
+
+    unsigned int mode : 1 ;
+
+    unsigned int graph_mode : 1 ;
+    unsigned int baseline : 1 ;
+    unsigned int min_score : 1 ;
+    unsigned int max_score : 1 ;
+
+    unsigned int foreground_set : 1 ;
+    unsigned int background_set : 1 ;
+    unsigned int outline_set    : 1 ;
+
+    unsigned int overlap_mode : 1 ;
+
+    unsigned int min_mag : 1 ;
+    unsigned int max_mag : 1 ;
+
+    unsigned int width : 1 ;
+    unsigned int bump_width : 1 ;
+
+    unsigned int score_mode : 1 ;
+
+    unsigned int within_align_error : 1 ;
+    unsigned int between_align_error : 1 ;
+
+    unsigned int gff_source : 1 ;
+    unsigned int gff_feature : 1 ;
+
+  } fields_set ;
+
+
+
+  /*
+   * Data fields for the style.
+   */
+
+  /* Styles can inherit from other styles, the parent style _must_ be identified by its unique id. */
+  GQuark parent_id ;
+
+  char *description ;					    /* Description of what this style
+							       represents. */
+
+  ZMapStyleMode mode ;					    /* Specifies how features that
+							       reference this style will be processed. */
+
+  /* graph parameters. */
+  ZMapStyleGraphMode graph_mode ;			    /* Says how to draw a graph. */
+
+  double baseline ;
+
+
+  struct
+  {
+    GdkColor  foreground ;      /* Overlaid on background. */
+    GdkColor  background ;      /* Fill colour. */
+    GdkColor  outline ;         /* Surround/line colour. */
+  } normal_colours ;
+
+
+  ZMapStyleOverlapMode overlap_mode ;			    /* Controls how features are grouped
+							       into sub columns within a column. */
+
+  double min_mag ;					    /* Don't display if fewer bases/line */
+  double max_mag ;					    /* Don't display if more bases/line */
+
+  double   width ;					    /* column width */
+  double bump_width;					    /* gap between bumped columns. */
+
+  ZMapStyleScoreMode   score_mode ;			    /* Controls width of features that
+							       have scores. */
+  double    min_score, max_score ;			    /* Min/max for score width calc. */
+
+
+  /* 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 ;
+
+  /* GFF feature dumping, allows specifying of source/feature types independently of feature
+   * attributes. */
+  GQuark gff_source ;
+  GQuark gff_feature ;
+
+
+  /* State information for the style. */
+  struct
+  {
+    /* I don't want a general show/hide flag here because we should
+     * get that dynamically from the state of the column canvas
+     * item.                     ummm, doesn't fit with the hidden_now flag ??????  */
+    unsigned int hidden_always   : 1 ;			    /* Column always hidden. */
+
+    unsigned int hidden_now      : 1 ;			    /* Column hidden now ? */
+
+    unsigned int show_when_empty : 1 ;			    /* If TRUE, 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. */
+
+    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. */
+    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 directional_end : 1 ;			    /* Display pointy ends on exons etc. */
+
+  } opts ;
+
+} ZMapFeatureTypeStyleStruct ;
+
+
+
+
+
+
+
+#endif /* !ZMAP_STYLE_P_H */