add setChadoOptions()

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@6928 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/Options.java

@@ -20,7 +20,7 @@
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
  *
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/Options.java,v 1.11 2007-09-07 14:12:08 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/Options.java,v 1.12 2008-01-16 16:07:50 tjc Exp $
  **/
 
 package uk.ac.sanger.artemis;
@@ -44,7 +44,7 @@ import java.util.*;
  *  read in new options.
  *
  *  @author Kim Rutherford
- *  @version $Id: Options.java,v 1.11 2007-09-07 14:12:08 tjc Exp $
+ *  @version $Id: Options.java,v 1.12 2008-01-16 16:07:50 tjc Exp $
  **/
 
 public class Options extends Properties 
@@ -327,8 +327,9 @@ public class Options extends Properties
     setDefaultColourMap();
 
     readOptions();
-    readSystemOptions();
+    setChadoOptions();
     
+    readSystemOptions();
     resetCachedValues();
 
 /////
@@ -344,6 +345,25 @@ public class Options extends Properties
 
   }
   
+  private void setChadoOptions()
+  {
+    final StringVector exon_models = getOptionValues("chado_exon_model");
+    if(exon_models != null)
+    {
+      DatabaseDocument.EXONMODEL = (String)exon_models.elementAt(0);
+      if(getProperty("colour_of_" + DatabaseDocument.EXONMODEL) == null)
+        put("colour_of_" + DatabaseDocument.EXONMODEL, "7");
+    }
+    
+    final StringVector chado_transcript = getOptionValues("chado_transcript");
+    if(chado_transcript != null)
+    {
+      DatabaseDocument.TRANSCRIPT = (String)chado_transcript.elementAt(0);
+      if(getProperty("colour_of_" + DatabaseDocument.TRANSCRIPT) == null)
+        put("colour_of_" + DatabaseDocument.TRANSCRIPT, "1");
+    }
+  }
+
   /**
    *  Call load() from the super class and then reset the cached values for
    *  Font and Color objects.