X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=c4c2c5bf13fe9d20e6a92efb6e9c2817405d031d;hb=56e5bdc625697d50d7d3f422616f0f1b40ca2828;hp=1ecf25453756a18794214d8b7281749fd5ed6a13;hpb=b67b5e0fb0aa385f944431a402efcc05051a0127;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 1ecf254..c4c2c5b 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -172,18 +172,26 @@ public class AlignFrame extends Frame implements ActionListener,
       StringTokenizer st;
       SequenceFeature sf;
       FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
-      int lineNo = 0;
-      String featureGroup = null;
+      String featureGroup = null, groupLink = null;
+      Hashtable typeLink = new Hashtable();
+
       while ( (line = in.readLine()) != null)
       {
-        lineNo++;
         st = new StringTokenizer(line, "\t");
-        if (st.countTokens() == 2)
+        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"))
           {
@@ -191,11 +199,19 @@ public class AlignFrame extends Frame implements ActionListener,
             //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;
         }
@@ -203,6 +219,7 @@ public class AlignFrame extends Frame implements ActionListener,
         while (st.hasMoreElements())
         {
           desc = st.nextToken();
+
           token = st.nextToken();
           if (!token.equals("ID_NOT_SPECIFIED"))
           {
@@ -229,9 +246,21 @@ public class AlignFrame extends Frame implements ActionListener,
             fr.setColour(type, ucs.findColour("A"));
           }
 
-          sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
-
+          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);
         }
       }
 
@@ -248,6 +277,33 @@ public class AlignFrame extends Frame implements ActionListener,
     }
   }
 
+  void parseDescriptionHTML(SequenceFeature sf)
+  {
+    StringBuffer sb = new StringBuffer();
+    StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");
+    String token,  link;
+    while(st.hasMoreElements())
+    {
+      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);
+    }
+
+    sf.description = sb.toString();
+  }
+
   public void keyPressed(KeyEvent evt)
   {
     if (viewport.cursorMode
@@ -1733,7 +1789,7 @@ public void itemStateChanged(ItemEvent evt)
         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);
         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",
                      x, y += fh);
-        g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);
+        g.drawString("Bioinformatics,  2004 20;426-7.", x, y += fh);
       }
     }