X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=03c0db9d20c8814eaa106c75ce7c4fb57bc987ef;hb=4944c2f33bb34b4f262fd2f3ae40dcdc2a825557;hp=fbe21b58de07ce093470a56454e5cfa6093c2bde;hpb=1d37661bae76ec6d499ff50a88ea249b8b33430e;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index fbe21b5..03c0db9 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -140,19 +140,30 @@ public class AlignFrame extends Frame implements ActionListener,
 
   public void parseFeaturesFile(String file)
   {
+    String line = null;
     try
     {
-      URL url = new URL(file);
+      BufferedReader in = null;
+      java.io.InputStream is = getClass().getResourceAsStream("/" + file);
+      if (is != null)
+      {
+        in = new BufferedReader(new java.io.InputStreamReader(is));
+      }
+      else
+      {
+        URL url = new URL(file);
+        in = new BufferedReader(new InputStreamReader(url.openStream()));
+      }
 
-      BufferedReader in =  new BufferedReader(new InputStreamReader(url.openStream()));
       SequenceI seq = null;
-      String line, type, desc, token;
+      String type, desc, token;
 
       int index, start, end;
       StringTokenizer st;
       SequenceFeature sf;
       FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
       int lineNo = 0;
+      String featureGroup = null;
       while ( (line = in.readLine()) != null)
       {
         lineNo++;
@@ -160,8 +171,22 @@ public class AlignFrame extends Frame implements ActionListener,
         if (st.countTokens() == 2)
         {
           type = st.nextToken();
-          UserColourScheme ucs = new UserColourScheme(st.nextToken());
-          fr.setColour(type, ucs.findColour("A"));
+          if(type.equalsIgnoreCase("startgroup"))
+          {
+            featureGroup = st.nextToken();
+          }
+          else if(type.equalsIgnoreCase("endgroup"))
+          {
+            //We should check whether this is the current group,
+            //but at present theres no way of showing more than 1 group
+            st.nextToken();
+            featureGroup = null;
+          }
+          else
+          {
+            UserColourScheme ucs = new UserColourScheme(st.nextToken());
+            fr.setColour(type, ucs.findColour("A"));
+          }
           continue;
         }
 
@@ -184,8 +209,6 @@ public class AlignFrame extends Frame implements ActionListener,
           end = Integer.parseInt(st.nextToken());
 
           seq = viewport.alignment.getSequenceAt(index);
-          start = seq.findIndex(start) - 1;
-          end = seq.findIndex(end) - 1;
 
           type = st.nextToken();
 
@@ -197,6 +220,7 @@ public class AlignFrame extends Frame implements ActionListener,
           }
 
           sf = new SequenceFeature(type, desc, "", start, end);
+          sf.setFeatureGroup(featureGroup);
 
           seq.addSequenceFeature(sf);
         }
@@ -213,7 +237,8 @@ public class AlignFrame extends Frame implements ActionListener,
     }
     catch (Exception ex)
     {
-      System.out.println("Error parsing groups file: " + ex);
+      ex.printStackTrace();
+      System.out.println("Error parsing groups file: " + ex +"\n"+line);
     }
   }