X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=289e7611bf83c9e565ba4d07ae052fbe52c5e775;hb=a6cd54c46366acd8bc3350a79374b18f9eb0b240;hp=7289fc44b0c9fd1dec87c7d6404e717a07b798b3;hpb=d7c94f1d531ef43bbabb7d1951c8e34c1366eeb2;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 7289fc4..289e761 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -48,40 +48,43 @@ public class AlignFrame
     add(alignPanel);
     alignPanel.validate();
 
-    String treeFile = applet.getParameter("treeFile");
-    if (treeFile != null)
+    if(applet!=null)
     {
-      try
+      String treeFile = applet.getParameter("treeFile");
+      if (treeFile != null)
       {
-        treeFile = treeFile;
-        jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
-            getCodeBase() + treeFile, "URL");
-        fin.parse();
+        try
+        {
+          treeFile = treeFile;
+          jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
+              getCodeBase() + treeFile, "URL");
+          fin.parse();
 
-        if (fin.getTree() != null)
+          if (fin.getTree() != null)
+          {
+            TreePanel tp = null;
+            tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
+                               fin, "FromFile", applet.getCodeBase() + treeFile);
+            jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
+            addTreeMenuItem(tp, treeFile);
+          }
+        }
+        catch (Exception ex)
         {
-          TreePanel tp = null;
-          tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                             fin, "FromFile", applet.getCodeBase() + treeFile);
-          jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
-          addTreeMenuItem(tp, treeFile);
+          ex.printStackTrace();
         }
       }
-      catch (Exception ex)
+
+      String param = applet.getParameter("sortBy");
+      if (param != null)
       {
-        ex.printStackTrace();
+        if (param.equalsIgnoreCase("Id"))
+          sortIDMenuItem_actionPerformed(null);
+        else if (param.equalsIgnoreCase("Pairwise Identity"))
+          sortPairwiseMenuItem_actionPerformed(null);
       }
     }
 
-    String param = applet.getParameter("sortBy");
-    if(param!=null)
-    {
-      if (param.equalsIgnoreCase("Id"))
-        sortIDMenuItem_actionPerformed(null);
-      else if (param.equalsIgnoreCase("Pairwise Identity"))
-        sortPairwiseMenuItem_actionPerformed(null);
-    }
-
     this.addWindowListener(new WindowAdapter()
     {
       public void windowClosing(WindowEvent e)
@@ -127,6 +130,8 @@ public class AlignFrame
   {
     PaintRefresher.components.remove(viewport.alignment);
     dispose();
+    if(PaintRefresher.components.size()==0 && applet==null)
+      System.exit(0);
   }
 
   Stack historyList = new Stack();
@@ -623,30 +628,56 @@ public class AlignFrame
     {
       seqs = viewport.getSelectionGroup().sequences;
       start = viewport.getSelectionGroup().getStartRes();
-      end = viewport.getSelectionGroup().getEndRes();
+      end = viewport.getSelectionGroup().getEndRes()+1;
     }
     else
       seqs = viewport.alignment.getSequences();
 
-    for (int i = 0; i <seqs.size(); i++)
+    for (int i = 0; i < seqs.size(); i++)
     {
-      current = (SequenceI)seqs.elementAt(i);
+      current = (SequenceI) seqs.elementAt(i);
       jSize = current.getLength();
 
+      // Removing a range is much quicker than removing gaps
+      // one by one for long sequences
       int j = start;
+      int rangeStart=-1, rangeEnd=-1;
+
       do
       {
         if (jalview.util.Comparison.isGap(current.getCharAt(j)))
         {
-          current.deleteCharAt(j);
-          j--;
-          jSize--;
+          if(rangeStart==-1)
+           {
+             rangeStart = j;
+             rangeEnd = j+1;
+           }
+           else
+           {
+             rangeEnd++;
+           }
+           j++;
+        }
+        else
+        {
+          if(rangeStart>-1)
+          {
+            current.deleteChars(rangeStart, rangeEnd);
+            j-=rangeEnd-rangeStart;
+            jSize-=rangeEnd-rangeStart;
+            rangeStart = -1;
+            rangeEnd = -1;
+          }
+          else
+            j++;
         }
-        j++;
       }
-      while(j < end && j < jSize) ;
+      while (j < end && j < jSize);
+      if(rangeStart>-1)
+      {
+       current.deleteChars(rangeStart, rangeEnd);
+      }
     }
-
     viewport.setStartRes(seq.findIndex(startRes)-1);
     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
@@ -656,6 +687,8 @@ public class AlignFrame
     viewport.updateConsensus();
     viewport.updateConservation ();
     resetAllColourSchemes();
+    if(alignPanel.overviewPanel!=null)
+      alignPanel.overviewPanel.updateOverviewImage();
     alignPanel.repaint();
   }
 
@@ -1161,13 +1194,13 @@ public class AlignFrame
     if (viewport.getSelectionGroup() != null &&
         viewport.getSelectionGroup().getSize() > 3)
     {
-      tp = new TreePanel(alignPanel, viewport.getSelectionGroup().sequences, type,
+      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
                          pwType,
                          0, viewport.alignment.getWidth());
     }
     else
     {
-      tp = new TreePanel(alignPanel, viewport.getAlignment().getSequences(),
+      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
                          type, pwType, 0, viewport.alignment.getWidth());
     }