X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=71acfa2565b13ad94e0b14a7ac03fa27974eec0a;hb=7d451923bf2ad5a358109eed435f354fc935f6ab;hp=f3db9be7a1b8d9215b6d2d815f5d6583226fac4f;hpb=29f89f52f3fc99e904a55e426c53a830290408cc;p=jalview.git

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index f3db9be..71acfa2 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -50,14 +50,17 @@ public class IdPanel
     idCanvas.addMouseMotionListener(this);
 
     String label, url;
-    for(int i=1; i<10; i++)
+    if(parent.alignFrame.applet!=null)
     {
-      label = parent.alignFrame.applet.getParameter("linkLabel_"+i);
-      url = parent.alignFrame.applet.getParameter("linkURL_"+i);
+      for (int i = 1; i < 10; i++)
+      {
+        label = parent.alignFrame.applet.getParameter("linkLabel_" + i);
+        url = parent.alignFrame.applet.getParameter("linkURL_" + i);
 
-      if(label!=null && url!=null)
-        links.addElement(label+"|"+url);
+        if (label != null && url != null)
+          links.addElement(label + "|" + url);
 
+      }
     }
     if (links.size() < 1)
     {
@@ -113,6 +116,8 @@ public class IdPanel
     //DEFAULT LINK IS FIRST IN THE LINK LIST
     int seq = av.getIndex(y);
     String id = av.getAlignment().getSequenceAt(seq).getName();
+    if (id.indexOf("|") > -1)
+        id = id.substring(id.lastIndexOf("|") + 1);
 
     String target = links.elementAt(0).toString();
     target = target.substring(0, target.indexOf("|"));
@@ -124,7 +129,8 @@ public class IdPanel
 
     try
     {
-      jalview.bin.JalviewLite.showURL(url, target);
+
+      alignPanel.alignFrame.showURL(url, target);
     }
     catch (Exception ex)
     {
@@ -187,31 +193,15 @@ public class IdPanel
       return;
     }
 
-    if (!e.isControlDown() && !e.isShiftDown() &&
-        av.alignment.findGroup(av.alignment.getSequenceAt(seq)) != null)
-    {
-
-      SequenceGroup selection = new SequenceGroup();
-      SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(seq));
-      selection.setStartRes(0);
-      selection.setEndRes(av.alignment.getWidth() - 1);
-      for (int i = 0; i < sg.getSize(); i++)
-      {
-        selection.addSequence(sg.getSequenceAt(i), true);
-      }
-
-      av.setSelectionGroup(selection);
-      return;
-    }
 
-    if (av.getSelectionGroup() == null ||
-        (!e.isControlDown() && av.getSelectionGroup() != null))
+    if ((av.getSelectionGroup() == null) ||
+            ((!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null))
     {
       av.setSelectionGroup(new SequenceGroup());
+      av.getSelectionGroup().setStartRes(0);
+      av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
     }
 
-    av.getSelectionGroup().setStartRes(0);
-    av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
 
     if (e.isShiftDown() && lastid != -1)
     {