X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=fee5dd4bcf0c1ca0d214e29fb100242d5f8eddea;hb=4f1f764c09427cd63c3e355fa729da86735a8194;hp=f66f445094e5c9726eb43c079b896a5a823b4f2d;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index f66f445..fee5dd4 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -50,7 +50,7 @@ public class IdPanel
     idCanvas.addMouseMotionListener(this);
 
     String label, url;
-    if(av.applet!=null)
+    if (av.applet != null)
     {
       for (int i = 1; i < 10; i++)
       {
@@ -58,7 +58,9 @@ public class IdPanel
         url = av.applet.getParameter("linkURL_" + i);
 
         if (label != null && url != null)
+        {
           links.addElement(label + "|" + url);
+        }
 
       }
     }
@@ -76,24 +78,27 @@ public class IdPanel
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
-    if(sequence.getDescription()==null)
+    if (sequence.getDescription() == null)
     {
-      if(tooltip!=null)
+      if (tooltip != null)
+      {
         tooltip.setVisible(false);
+      }
       tooltip = null;
       return;
     }
 
     if (tooltip == null)
+    {
       tooltip = new Tooltip(
           sequence.getDisplayId(true)
           + "\n" + sequence.getDescription(), idCanvas);
+    }
     else
+    {
       tooltip.setTip(sequence.getDisplayId(true)
                      + "\n" + sequence.getDescription());
-
-    tooltip.repaint();
-
+    }
   }
 
   public void mouseDragged(MouseEvent e)
@@ -112,28 +117,31 @@ public class IdPanel
     }
 
     lastid = seq;
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
   public void mouseClicked(MouseEvent e)
   {
     if (e.getClickCount() < 2)
-        return;
-
+    {
+      return;
+    }
 
     //DEFAULT LINK IS FIRST IN THE LINK LIST
     int seq = alignPanel.seqPanel.findSeq(e);
     String id = av.getAlignment().getSequenceAt(seq).getName();
     if (id.indexOf("|") > -1)
-        id = id.substring(id.lastIndexOf("|") + 1);
+    {
+      id = id.substring(id.lastIndexOf("|") + 1);
+    }
 
     String target = links.elementAt(0).toString();
     target = target.substring(0, target.indexOf("|"));
     String url = links.elementAt(0).toString();
-    url = url.substring(url.indexOf("|")+1);
+    url = url.substring(url.indexOf("|") + 1);
 
     int index = url.indexOf("$SEQUENCE_ID$");
-    url = url.substring(0, index)+ id + url.substring(index+13);
+    url = url.substring(0, index) + id + url.substring(index + 13);
 
     try
     {
@@ -175,7 +183,7 @@ public class IdPanel
 
   public void mousePressed(MouseEvent e)
   {
-    if (e.getClickCount() >1 )
+    if (e.getClickCount() > 1)
     {
       return;
     }
@@ -191,22 +199,22 @@ public class IdPanel
     if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) ==
         InputEvent.BUTTON3_MASK)
     {
-      APopupMenu popup = new APopupMenu(alignPanel, (Sequence) av.getAlignment().getSequenceAt(seq), links);
+      APopupMenu popup = new APopupMenu(alignPanel,
+                                        (Sequence) av.getAlignment().
+                                        getSequenceAt(seq), links);
       this.add(popup);
       popup.show(this, e.getX(), e.getY());
       return;
     }
 
-
-    if ((av.getSelectionGroup() == null) ||
-            ((!e.isControlDown() && !e.isShiftDown()) && 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);
     }
 
-
     if (e.isShiftDown() && lastid != -1)
     {
       selectSeqs(lastid, seq);
@@ -216,7 +224,7 @@ public class IdPanel
       selectSeq(seq);
     }
 
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
   void selectSeq(int seq)
@@ -230,6 +238,12 @@ public class IdPanel
   {
 
     lastid = start;
+
+    if (end >= av.getAlignment().getHeight())
+    {
+      end = av.getAlignment().getHeight() - 1;
+    }
+
     if (end < start)
     {
       int tmp = start;
@@ -252,11 +266,13 @@ public class IdPanel
       scrollThread.running = false;
     }
 
-    if(av.getSelectionGroup()!=null)
+    if (av.getSelectionGroup() != null)
+    {
       av.getSelectionGroup().recalcConservation();
+    }
 
     mouseDragging = false;
-    PaintRefresher.Refresh(this, av.alignment);
+    PaintRefresher.Refresh(this, av.getSequenceSetId());
   }
 
   public void highlightSearchResults(java.util.Vector found)
@@ -312,12 +328,11 @@ public class IdPanel
           {
             selectSeqs(lastid - 1, seq);
           }
-          else if (seq > lastid && seq<av.alignment.getHeight())
+          else if (seq > lastid && seq < av.alignment.getHeight())
           {
             selectSeqs(lastid + 1, seq);
           }
 
-
           lastid = seq;
         }
         else
@@ -325,7 +340,7 @@ public class IdPanel
           running = false;
         }
 
-        alignPanel.repaint();
+        alignPanel.paintAlignment(true);
         try
         {
           Thread.sleep(100);