X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=e82356c9d115a94f8212ed6e7da858018472f80d;hb=2ffe2deedb1527c067060646055bddd18d41d367;hp=efe8e639010b869c5773bcd1abffa0e48a040fa5;hpb=7bf593f3593a0392fb01d78644f7bfd75762a87e;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index efe8e63..e82356c 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.
@@ -76,21 +87,27 @@ public class AlignFrame
         getPreferredSize());
     alignPanel.setAnnotationVisible(viewport.getShowAnnotation());
 
+    String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
+
+    if(sortby.equals("Id"))
+      sortIDMenuItem_actionPerformed(null);
+    else if(sortby.equals("Pairwise Identity"))
+      sortPairwiseMenuItem_actionPerformed(null);
+
     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
 
-    addInternalFrameListener(new InternalFrameAdapter()
+    viewport.addPropertyChangeListener(new PropertyChangeListener()
     {
-      public void internalFrameActivated(InternalFrameEvent evt)
-      {
-        javax.swing.SwingUtilities.invokeLater(new Runnable()
-        {
-          public void run()
-          {
-            alignPanel.requestFocus();
-          }
-        });
-      }
-    });
+     public void propertyChange(PropertyChangeEvent evt)
+     {
+       if (evt.getPropertyName().equals("alignment"))
+       {
+         alignmentChanged();
+       }
+     }
+   });
+
+
     addServiceListeners();
   }
 
@@ -410,7 +427,7 @@ public class AlignFrame
     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
                                   HistoryItem.HIDE));
     restoreHistoryItem(hi);
-    resetAllColourSchemes();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   /**
@@ -423,9 +440,7 @@ public class AlignFrame
     HistoryItem hi = (HistoryItem) redoList.pop();
     restoreHistoryItem(hi);
     updateEditMenuBar();
-    viewport.updateConsensus();
-    resetAllColourSchemes();
-    alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   // used by undo and redo
@@ -470,9 +485,6 @@ public class AlignFrame
 
     updateEditMenuBar();
 
-    viewport.updateConsensus();
-    viewport.updateConservation();
-    alignPanel.repaint();
     viewport.firePropertyChange("alignment", null,
                                 viewport.getAlignment().getSequences());
   }
@@ -701,20 +713,17 @@ public class AlignFrame
       }
       else
       {
-        viewport.firePropertyChange("alignment", null,
-                                    viewport.getAlignment().getSequences());
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
-        viewport.updateConservation();
-        viewport.updateConsensus();
-        alignPanel.repaint();
+        viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
       }
     }
     catch (Exception ex)
     {
+        // could be anything being pasted in here
     }
 
-    // could be anything being pasted in here
+
   }
 
   /**
@@ -735,7 +744,6 @@ public class AlignFrame
    */
   protected void delete_actionPerformed(ActionEvent e)
   {
-    boolean seqsdeleted = false;
 
     if (viewport.getSelectionGroup() == null)
     {
@@ -767,7 +775,6 @@ public class AlignFrame
 
       if (seq.getSequence().length() < 1)
       {
-        seqsdeleted = true;
         viewport.getAlignment().deleteSequence(seq);
       }
       else
@@ -779,13 +786,10 @@ public class AlignFrame
     viewport.setSelectionGroup(null);
     viewport.alignment.deleteGroup(sg);
 
-    if (seqsdeleted)
-    {
-      viewport.firePropertyChange("alignment", null,
+    viewport.firePropertyChange("alignment", null,
                                   viewport.getAlignment().getSequences());
-    }
 
-    viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
+
 
     if (viewport.getAlignment().getHeight() < 1)
     {
@@ -797,10 +801,6 @@ public class AlignFrame
       {
       }
     }
-
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
   }
 
   /**
@@ -909,7 +909,7 @@ public class AlignFrame
         }
       }
 
-      alignPanel.repaint();
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     }
   }
 
@@ -947,7 +947,7 @@ public class AlignFrame
         }
       }
 
-      alignPanel.repaint();
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     }
   }
 
@@ -970,10 +970,7 @@ public class AlignFrame
 
     viewport.setStartRes(seq.findIndex(startRes)-1);
 
-    resetAllColourSchemes();
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
+   viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   /**
@@ -1006,7 +1003,7 @@ public class AlignFrame
     {
       seqs = viewport.getSelectionGroup().sequences;
       start = viewport.getSelectionGroup().getStartRes();
-      end = viewport.getSelectionGroup().getEndRes();
+      end = viewport.getSelectionGroup().getEndRes()+1;
     }
     else
     {
@@ -1018,57 +1015,91 @@ 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.updateConservation();
-    viewport.updateConsensus();
-    resetAllColourSchemes();
-    alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
+ public void alignmentChanged()
+ {
+   if(viewport.vconsensus!=null)
+   {
+     viewport.updateConsensus();
+     viewport.updateConservation();
+   }
+   resetAllColourSchemes();
+   if(alignPanel.overviewPanel!=null)
+     alignPanel.overviewPanel.updateOverviewImage();
+
+   alignPanel.repaint();
+ }
 
   void resetAllColourSchemes()
   {
     ColourSchemeI cs = viewport.globalColourScheme;
     if(cs!=null)
     {
-        cs.setConsensus(viewport.vconsensus);
-        if(cs.conservationApplied())
-        {
-          Alignment al = (Alignment) viewport.alignment;
-          Conservation c = new Conservation("All",
-                                            ResidueProperties.propHash, 3,
-                                            al.getSequences(), 0,
-                                            al.getWidth() - 1);
-          c.calculate();
-          c.verdict(false, viewport.ConsPercGaps);
+      if (cs instanceof ClustalxColourScheme)
+      {
+        ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
+            resetClustalX(viewport.alignment.getSequences(),
+                          viewport.alignment.getWidth());
+      }
 
-          cs.setConservation(c);
-        }
-    }
+      cs.setConsensus(viewport.vconsensus);
+      if (cs.conservationApplied())
+      {
+        Alignment al = (Alignment) viewport.alignment;
+        Conservation c = new Conservation("All",
+                                          ResidueProperties.propHash, 3,
+                                          al.getSequences(), 0,
+                                          al.getWidth() - 1);
+        c.calculate();
+        c.verdict(false, viewport.ConsPercGaps);
 
-    if(viewport.getGlobalColourScheme()!=null
-       && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)
-    {
-      ((ClustalxColourScheme)viewport.getGlobalColourScheme()).
-          resetClustalX(viewport.alignment.getSequences(),
-                        viewport.alignment.getWidth());
+        cs.setConservation(c);
+      }
     }
 
     int s, sSize = viewport.alignment.getGroups().size();
@@ -1079,9 +1110,7 @@ public class AlignFrame
       {
         ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
       }
-
       sg.recalcConservation();
-
     }
   }
 
@@ -1109,9 +1138,7 @@ public class AlignFrame
       }
     }
 
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
+    alignmentChanged();
   }
 
   /**
@@ -2018,17 +2045,6 @@ 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();
-        }
-      }
-    });
   }
 
   /**