functions for feature context

src/zmapFeature/zmapFeatureContextUtils.c

+/*  File: zmapFeatureContextUtils.c
+ *  Author: Roy Storey (rds@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: 
+ *
+ * Exported functions: See XXXXXXXXXXXXX.h
+ * HISTORY:
+ * Last edited: May 24 11:24 2007 (rds)
+ * Created: Thu May 24 10:34:47 2007 (rds)
+ * CVS info:   $Id: zmapFeatureContextUtils.c,v 1.1 2007-05-24 10:34:30 rds Exp $
+ *-------------------------------------------------------------------
+ */
+
+#include <ZMap/zmapFeature.h>
+#include <ZMap/zmapUtils.h>
+
+static ZMapFeatureContextExecuteStatus addModeCB(GQuark key_id, 
+						 gpointer data, 
+						 gpointer user_data,
+						 char **error_out) ;
+static void addFeatureModeCB(GQuark key_id, gpointer data, gpointer user_data) ;
+
+
+
+gboolean zMapFeatureAnyAddModesToStyles(ZMapFeatureAny feature_any)
+{
+  gboolean result = TRUE;
+
+  zMapFeatureContextExecuteSubset(feature_any, 
+                                  ZMAPFEATURE_STRUCT_FEATURESET,
+                                  addModeCB,
+                                  &result);
+
+  return result;
+}
+
+
+/* go through all the feature sets in a context and find out what type of features are in the
+ * set and set the style mode from that...a bit hacky really...think about this.... */
+gboolean zMapFeatureContextAddModesToStyles(ZMapFeatureContext context)
+{
+  gboolean result = TRUE ;
+
+
+  zMapFeatureContextExecute((ZMapFeatureAny)context,
+			    ZMAPFEATURE_STRUCT_FEATURESET,
+			    addModeCB,
+			    &result) ;
+
+  return result ;
+}
+
+
+static ZMapFeatureContextExecuteStatus addModeCB(GQuark key_id, 
+						 gpointer data, 
+						 gpointer user_data,
+						 char **error_out)
+{
+  ZMapFeatureAny feature_any = (ZMapFeatureAny)data ;
+  gboolean *error_ptr = (gboolean *)user_data ;
+  ZMapFeatureStructType feature_type ;
+  ZMapFeatureContextExecuteStatus status = ZMAP_CONTEXT_EXEC_STATUS_OK;
+
+  feature_type = feature_any->struct_type ;
+
+  switch(feature_type)
+    {
+    case ZMAPFEATURE_STRUCT_CONTEXT:
+    case ZMAPFEATURE_STRUCT_ALIGN:
+    case ZMAPFEATURE_STRUCT_BLOCK:
+      {
+	break ;
+      }
+    case ZMAPFEATURE_STRUCT_FEATURESET:
+      {
+	ZMapFeatureSet feature_set ;
+
+        feature_set = (ZMapFeatureSet)feature_any ;
+
+	g_datalist_foreach(&(feature_set->features), addFeatureModeCB, feature_set) ;
+
+	break;
+      }
+    case ZMAPFEATURE_STRUCT_FEATURE:
+    case ZMAPFEATURE_STRUCT_INVALID:
+    default:
+      {
+	status = ZMAP_CONTEXT_EXEC_STATUS_ERROR;
+	zMapAssertNotReached();
+	break;
+      }
+    }
+
+  return status ;
+}
+
+
+
+/* A GDataForeachFunc() to add a mode to the styles for all features in a set, note that
+ * this is not efficient as we go through all features but we would need more information
+ * stored in the feature set to avoid this. */
+static void addFeatureModeCB(GQuark key_id, gpointer data, gpointer user_data)
+{
+  ZMapFeature feature = (ZMapFeature)data ;
+  ZMapFeatureSet feature_set = (ZMapFeatureSet)user_data ;
+
+  if (!zMapStyleHasMode(feature->style))
+    {
+      ZMapStyleMode mode ;
+
+      switch (feature->type)
+	{
+	case ZMAPFEATURE_BASIC:
+	  mode = ZMAPSTYLE_MODE_BASIC ;
+
+	  if (g_ascii_strcasecmp(g_quark_to_string(zMapStyleGetID(feature->style)), "GF_splice") == 0)
+	    {
+	      mode = ZMAPSTYLE_MODE_GLYPH ;
+	      zMapStyleSetGlyphMode(feature->style, ZMAPSTYLE_GLYPH_SPLICE) ;
+
+	      zMapStyleSetColours(feature->style, ZMAPSTYLE_COLOURTARGET_FRAME0, ZMAPSTYLE_COLOURTYPE_NORMAL,
+				  "red", NULL, NULL) ;
+	      zMapStyleSetColours(feature->style, ZMAPSTYLE_COLOURTARGET_FRAME1, ZMAPSTYLE_COLOURTYPE_NORMAL,
+				  "blue", NULL, NULL) ;
+	      zMapStyleSetColours(feature->style, ZMAPSTYLE_COLOURTARGET_FRAME2, ZMAPSTYLE_COLOURTYPE_NORMAL,
+				  "green", NULL, NULL) ;
+	    }
+	  break ;
+	case ZMAPFEATURE_ALIGNMENT:
+	  mode = ZMAPSTYLE_MODE_ALIGNMENT ;
+	  break ;
+	case ZMAPFEATURE_TRANSCRIPT:
+	  mode = ZMAPSTYLE_MODE_TRANSCRIPT ;
+	  break ;
+	case ZMAPFEATURE_RAW_SEQUENCE:
+	  mode = ZMAPSTYLE_MODE_TEXT ;
+	  break ;
+	case ZMAPFEATURE_PEP_SEQUENCE:
+	  mode = ZMAPSTYLE_MODE_TEXT ;
+	  break ;
+	  /* What about glyph and graph..... */
+
+	default:
+	  zMapAssertNotReached() ;
+	  break ;
+	}
+
+      /* Tricky....we can have features within a single feature set that have _different_
+       * styles, if this is the case we must be sure to set the mode in feature_set style
+       * (where in fact its kind of useless as this is a style for the whole column) _and_
+       * we must set it in the features own style. */
+      zMapStyleSetMode(feature_set->style, mode) ;
+
+      if (feature_set->style != feature->style)
+	zMapStyleSetMode(feature->style, mode) ;
+    }
+
+
+  return ;
+}