X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=9762258403bb4d2f6d08efd6937b499f150d52cb;hb=ceb4fd3a8909862e45ac79b242ed112a15998d84;hp=ba9237b00933ca6cb8c70cfcb9596c95ac54c166;hpb=9be70e5fd6d8a50a4989ca230dda0f7c6e7d2852;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ba9237b..9762258 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -68,6 +68,17 @@ public class AlignFrame
   {
     viewport = new AlignViewport(al);
 
+    if(viewport.vconsensus==null)
+    {
+      //Out of memory caluclating consensus.
+      BLOSUM62Colour.setEnabled(false);
+      PIDColour.setEnabled(false);
+      conservationMenuItem.setEnabled(false);
+      modifyConservation.setEnabled(false);
+      abovePIDThreshold.setEnabled(false);
+      modifyPID.setEnabled(false);
+    }
+
     alignPanel = new AlignmentPanel(this, viewport);
     alignPanel.annotationPanel.adjustPanelHeight();
     alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.
@@ -96,6 +107,7 @@ public class AlignFrame
      }
    });
 
+
     addServiceListeners();
   }
 
@@ -548,15 +560,16 @@ public class AlignFrame
   {
     if (viewport.getSelectionGroup() == null)
     {
+      System.out.println("null here");
       return;
     }
 
     SequenceGroup sg = viewport.getSelectionGroup();
 
     Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-    StringBuffer buffer = new StringBuffer();
 
     Hashtable orderedSeqs = new Hashtable();
+    SequenceI [] seqs = new SequenceI[sg.getSize()];
 
     for (int i = 0; i < sg.getSize(); i++)
     {
@@ -586,6 +599,8 @@ public class AlignFrame
           index++;
         }
       }
+
+
       //FIND START RES
       //Returns residue following index if gap
       startRes = seq.findPosition(sg.getStartRes());
@@ -608,14 +623,15 @@ public class AlignFrame
         endRes += seq.getStart() - 1;
       }
 
-      buffer.append(seq.getName() + "\t" +
-                    startRes + "\t" +
-                    endRes + "\t" +
-                    seq.getSequence(sg.getStartRes(),
-                                    sg.getEndRes() + 1) + "\n");
+      seqs[i] = new Sequence(seq.getName(),
+                             seq.getSequence(sg.getStartRes(), sg.getEndRes()+1),
+                             startRes,
+                             endRes);
     }
 
-    c.setContents(new StringSelection(buffer.toString()), null);
+    System.out.println("BLOBL"+FastaFile.print(seqs));
+
+    c.setContents(new StringSelection(FastaFile.print(seqs)), null);
   }
 
   /**
@@ -658,33 +674,14 @@ public class AlignFrame
       }
 
       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
-      StringTokenizer st = new StringTokenizer(str);
-      ArrayList seqs = new ArrayList();
 
-      while (st.hasMoreElements())
-      {
-        String name = st.nextToken();
-        int start = Integer.parseInt(st.nextToken());
-        int end = Integer.parseInt(st.nextToken());
-        Sequence sequence = new Sequence(name, st.nextToken(), start,
-                                         end);
+      String format = IdentifyFile.Identify(str, "Paste");
+      SequenceI[] sequences = FormatAdapter.readFile(str, "Paste", format);
 
-        if (!newAlignment)
-        {
-          viewport.alignment.addSequence(sequence);
-        }
-        else
-        {
-          seqs.add(sequence);
-        }
-      }
 
       if (newAlignment)
       {
-        SequenceI[] newSeqs = new SequenceI[seqs.size()];
-        seqs.toArray(newSeqs);
-
-        AlignFrame af = new AlignFrame(new Alignment(newSeqs));
+        AlignFrame af = new AlignFrame(new Alignment(sequences));
         String newtitle = new String("Copied sequences");
 
         if (title.startsWith("Copied sequences"))
@@ -701,6 +698,10 @@ public class AlignFrame
       }
       else
       {
+        //!newAlignment
+        for (int i = 0; i < sequences.length; i++)
+          viewport.alignment.addSequence(sequences[i]);
+
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
@@ -732,7 +733,6 @@ public class AlignFrame
    */
   protected void delete_actionPerformed(ActionEvent e)
   {
-    boolean seqsdeleted = false;
 
     if (viewport.getSelectionGroup() == null)
     {
@@ -764,7 +764,6 @@ public class AlignFrame
 
       if (seq.getSequence().length() < 1)
       {
-        seqsdeleted = true;
         viewport.getAlignment().deleteSequence(seq);
       }
       else
@@ -993,7 +992,7 @@ public class AlignFrame
     {
       seqs = viewport.getSelectionGroup().sequences;
       start = viewport.getSelectionGroup().getStartRes();
-      end = viewport.getSelectionGroup().getEndRes();
+      end = viewport.getSelectionGroup().getEndRes()+1;
     }
     else
     {
@@ -1005,32 +1004,63 @@ public class AlignFrame
       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);
+      if(rangeStart>-1)
+      {
+       current.deleteChars(rangeStart, rangeEnd);
+      }
     }
 
     viewport.setStartRes(seq.findIndex(startRes)-1);
 
-
     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
  public void alignmentChanged()
  {
-   viewport.updateConsensus();
-   viewport.updateConservation();
+   if(viewport.vconsensus!=null)
+   {
+     viewport.updateConsensus();
+     viewport.updateConservation();
+   }
    resetAllColourSchemes();
+   if(alignPanel.overviewPanel!=null)
+     alignPanel.overviewPanel.updateOverviewImage();
+
    alignPanel.repaint();
  }
 
@@ -1808,21 +1838,11 @@ public class AlignFrame
       return;
     }
 
-    try
-    {
       PCAPanel pcaPanel = new PCAPanel(viewport, null);
       JInternalFrame frame = new JInternalFrame();
       frame.setContentPane(pcaPanel);
       Desktop.addInternalFrame(frame, "Principal component analysis",
                                400, 400);
-    }
-    catch (java.lang.OutOfMemoryError ex)
-    {
-      JOptionPane.showInternalMessageDialog(this,
-                                            "Too many sequences selected\nfor Principal Component Analysis!!",
-                                            "Out of memory",
-                                            JOptionPane.WARNING_MESSAGE);
-    }
   }
 
   /**
@@ -2004,17 +2024,6 @@ public class AlignFrame
       }
       ;
     });
-    viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
-    {
-      public void propertyChange(PropertyChangeEvent evt)
-      {
-        if (evt.getPropertyName().equals("alignment"))
-        {
-          treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
-          treePanel.repaint();
-        }
-      }
-    });
   }
 
   /**