X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=f3db9be7a1b8d9215b6d2d815f5d6583226fac4f;hb=d72c37ab022b3a8ff6f6cda1d3f09de5c5d004ab;hp=39fab0a6aee7ad564431a4274de95c50401e69de;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 39fab0a..f3db9be 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -37,6 +37,7 @@ public class IdPanel
   int width;
   int lastid = -1;
   boolean mouseDragging = false;
+  java.util.Vector links = new java.util.Vector();
 
   public IdPanel(AlignViewport av, AlignmentPanel parent)
   {
@@ -47,6 +48,22 @@ public class IdPanel
     add(idCanvas, BorderLayout.CENTER);
     idCanvas.addMouseListener(this);
     idCanvas.addMouseMotionListener(this);
+
+    String label, url;
+    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 (links.size() < 1)
+    {
+      links = new java.util.Vector();
+      links.addElement("SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");
+    }
   }
 
   public void mouseMoved(MouseEvent e)
@@ -83,29 +100,36 @@ public class IdPanel
 
   public void mouseClicked(MouseEvent e)
   {
-    if (e.getClickCount() == 2)
-    {
-      int y = e.getY();
-      if (av.getWrapAlignment())
-      {
-        y -= 2 * av.charHeight;
-      }
+    if (e.getClickCount() < 2)
+        return;
 
-      int seq = av.getIndex(y);
-      String id = av.getAlignment().getSequenceAt(seq).getName();
+    int y = e.getY();
 
-      try
-      {
-        jalview.bin.JalviewLite.showURL(
-            "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id +
-            "]+-vn+2");
-      }
-      catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
+    if (av.getWrapAlignment())
+    {
+      y -= (2 * av.charHeight);
     }
 
+    //DEFAULT LINK IS FIRST IN THE LINK LIST
+    int seq = av.getIndex(y);
+    String id = av.getAlignment().getSequenceAt(seq).getName();
+
+    String target = links.elementAt(0).toString();
+    target = target.substring(0, target.indexOf("|"));
+    String url = links.elementAt(0).toString();
+    url = url.substring(url.indexOf("|")+1);
+
+    int index = url.indexOf("$SEQUENCE_ID$");
+    url = url.substring(0, index)+ id + url.substring(index+13);
+
+    try
+    {
+      jalview.bin.JalviewLite.showURL(url, target);
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
   }
 
   public void mouseEntered(MouseEvent e)
@@ -137,7 +161,7 @@ public class IdPanel
 
   public void mousePressed(MouseEvent e)
   {
-    if (e.getClickCount() == 2)
+    if (e.getClickCount() >1 )
     {
       return;
     }
@@ -157,7 +181,7 @@ public class IdPanel
     if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) ==
         InputEvent.BUTTON3_MASK)
     {
-      APopupMenu popup = new APopupMenu(alignPanel, null);
+      APopupMenu popup = new APopupMenu(alignPanel, (Sequence) av.getAlignment().getSequenceAt(seq), links);
       this.add(popup);
       popup.show(this, e.getX(), e.getY());
       return;
@@ -173,7 +197,7 @@ public class IdPanel
       selection.setEndRes(av.alignment.getWidth() - 1);
       for (int i = 0; i < sg.getSize(); i++)
       {
-        selection.addSequence(sg.getSequenceAt(i));
+        selection.addSequence(sg.getSequenceAt(i), true);
       }
 
       av.setSelectionGroup(selection);
@@ -205,7 +229,7 @@ public class IdPanel
   {
     lastid = seq;
     SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
-    av.getSelectionGroup().addOrRemove(pickedSeq);
+    av.getSelectionGroup().addOrRemove(pickedSeq, false);
   }
 
   void selectSeqs(int start, int end)
@@ -222,7 +246,7 @@ public class IdPanel
 
     for (int i = start; i <= end; i++)
     {
-      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i));
+      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), false);
     }
 
   }
@@ -234,8 +258,11 @@ public class IdPanel
       scrollThread.running = false;
     }
 
+    if(av.getSelectionGroup()!=null)
+      av.getSelectionGroup().recalcConservation();
+
     mouseDragging = false;
-    PaintRefresher.Refresh(this);
+    PaintRefresher.Refresh(this, av.alignment);
   }
 
   public void highlightSearchResults(java.util.Vector found)