From 6ce8b88ca3d675b5ce00a8ca54416f970c2632d8 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 23 Jun 2006 13:45:06 +0000
Subject: [PATCH] Uses FeaturesFile parser, GFF and Jalview

---
 src/jalview/appletgui/AlignFrame.java |  157 +++------------------------------
 1 file changed, 12 insertions(+), 145 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index c4c2c5b..d7bf91a 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -148,162 +148,29 @@ public class AlignFrame extends Frame implements ActionListener,
    * @param String DOCUMENT ME!
    */
 
-  public void parseFeaturesFile(String file)
+  public void parseFeaturesFile(String file, String type)
   {
-    String line = null;
-    try
-    {
-      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()));
-      }
-
-      SequenceI seq = null;
-      String type, desc, token;
-
-      int index, start, end;
-      StringTokenizer st;
-      SequenceFeature sf;
-      FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
-      String featureGroup = null, groupLink = null;
-      Hashtable typeLink = new Hashtable();
-
-      while ( (line = in.readLine()) != null)
-      {
-        st = new StringTokenizer(line, "\t");
-        if(!st.hasMoreTokens())
-          continue;
-
-        if (st.countTokens() < 4)
-        {
-          type = st.nextToken();
-          if(type.equalsIgnoreCase("startgroup"))
-          {
-            featureGroup = st.nextToken();
-            if (st.hasMoreElements())
-            {
-              groupLink = st.nextToken();
-              fr.addFeatureLink(featureGroup, groupLink);
-            }
-          }
-          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;
-            groupLink = null;
-          }
-          else
-          {
-            UserColourScheme ucs = new UserColourScheme(st.nextToken());
-            fr.setColour(type, ucs.findColour("A"));
-            if (st.hasMoreElements())
-            {
-                String link = st.nextToken();
-                typeLink.put(type, link);
-                fr.addFeatureLink(type, link);
-            }
-
-          }
-          continue;
-        }
-
-        while (st.hasMoreElements())
-        {
-          desc = st.nextToken();
-
-          token = st.nextToken();
-          if (!token.equals("ID_NOT_SPECIFIED"))
-          {
-            index = viewport.alignment.findIndex(viewport.alignment.findName(
-                token));
-            st.nextToken();
-          }
-          else
-          {
-            index = Integer.parseInt(st.nextToken());
-          }
-
-          start = Integer.parseInt(st.nextToken());
-          end = Integer.parseInt(st.nextToken());
-
-          seq = viewport.alignment.getSequenceAt(index);
-
-          type = st.nextToken();
-
-          if(fr.getColour(type)==null)
-          {
-            // Probably the old style groups file
-            UserColourScheme ucs = new UserColourScheme(type);
-            fr.setColour(type, ucs.findColour("A"));
-          }
-
-          sf = new SequenceFeature(type, desc, start, end, 0f, featureGroup);
-          seq.addSequenceFeature(sf);
-
-          if(groupLink!=null)
-          {
-            sf.addLink(groupLink);
-            sf.description += "%LINK%";
-          }
-          if(typeLink.containsKey(type))
-          {
-            sf.addLink(typeLink.get(type).toString());
-            sf.description += "%LINK%";
-          }
-
-          parseDescriptionHTML(sf);
-        }
-      }
-
-      viewport.showSequenceFeatures = true;
-      sequenceFeatures.setState(true);
-
-      alignPanel.repaint();
-
+    boolean featuresFile = false;
+    try{
+      featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,
+                                         alignPanel.seqPanel.seqCanvas.
+                                         getFeatureRenderer().featureColours);
     }
-    catch (Exception ex)
+    catch(Exception ex)
     {
       ex.printStackTrace();
-      System.out.println("Error parsing groups file: " + ex +"\n"+line);
     }
-  }
 
-  void parseDescriptionHTML(SequenceFeature sf)
-  {
-    StringBuffer sb = new StringBuffer();
-    StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");
-    String token,  link;
-    while(st.hasMoreElements())
+    if(featuresFile)
     {
-      token = st.nextToken("<>");
-      if(token.equalsIgnoreCase("html") || token.startsWith("/"))
-        continue;
-
-      if(token.startsWith("a href="))
-      {
-        link = token.substring(token.indexOf("\"")+1, token.length()-1);
-        String label = st.nextToken("<>");
-        sf.addLink(label+"|"+link);
-        sb.append(label+"%LINK%");
-      }
-      else if(token.equalsIgnoreCase("br"))
-        sb.append("\n");
-      else
-        sb.append(token);
+      viewport.showSequenceFeatures = true;
+      sequenceFeatures.setState(true);
+      alignPanel.repaint();
     }
 
-    sf.description = sb.toString();
   }
 
+
   public void keyPressed(KeyEvent evt)
   {
     if (viewport.cursorMode
-- 
1.7.10.2