X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=7289fc44b0c9fd1dec87c7d6404e717a07b798b3;hb=064f2fdaa463367f8bf7e6aea5e7fc6a32170138;hp=1b5629f4a418b4944f5cef7a66237537b88e7662;hpb=4f0f6c493f753878483fb75d943e5e5f9fd73cca;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 1b5629f..7289fc4 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -39,24 +39,6 @@ public class AlignFrame
   public static final int NEW_WINDOW_HEIGHT = 500;
   jalview.bin.JalviewLite applet;
 
-  public AlignFrame(AlignmentI al)
-  {
-    this.applet = null;
-    viewport = new AlignViewport(al, null);
-    alignPanel = new AlignmentPanel(this, viewport);
-    add(alignPanel);
-    alignPanel.validate();
-
-    this.addWindowListener(new WindowAdapter()
-    {
-      public void windowClosing(WindowEvent e)
-      {
-        closeMenuItem_actionPerformed(null);
-      }
-    });
-
-  }
-
 
   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)
   {
@@ -91,6 +73,15 @@ public class AlignFrame
       }
     }
 
+    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)
@@ -99,13 +90,21 @@ public class AlignFrame
           }
     });
 
-
-
+    viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+    {
+     public void propertyChange(java.beans.PropertyChangeEvent evt)
+     {
+       if (evt.getPropertyName().equals("alignment"))
+       {
+         alignmentChanged();
+       }
+     }
+   });
   }
 
   public void inputText_actionPerformed(ActionEvent e)
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(true);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
@@ -113,7 +112,7 @@ public class AlignFrame
 
   protected void outputText_actionPerformed(ActionEvent e)
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame,
@@ -172,6 +171,7 @@ public class AlignFrame
     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
                                   HistoryItem.HIDE));
     restoreHistoryItem(hi);
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   protected void redoMenuItem_actionPerformed(ActionEvent e)
@@ -179,9 +179,7 @@ public class AlignFrame
     HistoryItem hi = (HistoryItem) redoList.pop();
     restoreHistoryItem(hi);
     updateEditMenuBar();
-    viewport.updateConsensus();
-    alignPanel.repaint();
-    alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   // used by undo and redo
@@ -225,9 +223,7 @@ public class AlignFrame
 
     updateEditMenuBar();
 
-    viewport.updateConsensus();
-    viewport.updateConservation();
-    alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   public void moveSelectedSequences(boolean up)
@@ -418,9 +414,7 @@ public class AlignFrame
       {
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
-        viewport.updateConservation();
-        viewport.updateConsensus();
-        alignPanel.repaint();
+        viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
       }
 
     }
@@ -486,9 +480,7 @@ public class AlignFrame
       catch (Exception ex)
       {}
     }
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
 
   }
 
@@ -507,7 +499,7 @@ public class AlignFrame
     {
       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
     }
-    sg.setEndRes(viewport.alignment.getWidth());
+    sg.setEndRes(viewport.alignment.getWidth()-1);
     viewport.setSelectionGroup(sg);
     alignPanel.repaint();
     PaintRefresher.Refresh(null, viewport.alignment);
@@ -518,6 +510,7 @@ public class AlignFrame
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
+    alignPanel.repaint();
     PaintRefresher.Refresh(null, viewport.alignment);
   }
 
@@ -557,8 +550,7 @@ public class AlignFrame
           viewport.alignment.deleteGroup(sg);
         }
       }
-
-      alignPanel.repaint();
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     }
   }
 
@@ -585,8 +577,7 @@ public class AlignFrame
           viewport.alignment.deleteGroup(sg);
         }
       }
-
-      alignPanel.repaint();
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     }
 
   }
@@ -596,10 +587,17 @@ public class AlignFrame
     addHistoryItem(new HistoryItem("Remove Gapped Columns",
                                    viewport.alignment,
                                    HistoryItem.HIDE));
+
+    //This is to maintain viewport position on first residue
+    //of first sequence
+    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    int startRes = seq.findPosition(viewport.startRes);
+
     viewport.getAlignment().removeGaps();
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
+
+    viewport.setStartRes(seq.findIndex(startRes)-1);
+
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
@@ -607,6 +605,11 @@ public class AlignFrame
     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
                                    HistoryItem.HIDE));
 
+    //This is to maintain viewport position on first residue
+    //of first sequence
+    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    int startRes = seq.findPosition(viewport.startRes);
+
     SequenceI current;
     int jSize;
 
@@ -644,11 +647,58 @@ public class AlignFrame
       while(j < end && j < jSize) ;
     }
 
-    viewport.updateConservation();
+    viewport.setStartRes(seq.findIndex(startRes)-1);
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+  }
+
+  public void alignmentChanged()
+  {
     viewport.updateConsensus();
+    viewport.updateConservation ();
+    resetAllColourSchemes();
     alignPanel.repaint();
   }
 
+  void resetAllColourSchemes()
+  {
+    ColourSchemeI cs = viewport.globalColourScheme;
+    if(cs!=null)
+    {
+      if (cs instanceof ClustalxColourScheme)
+      {
+        ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).
+            resetClustalX(viewport.alignment.getSequences(),
+                          viewport.alignment.getWidth());
+      }
+
+      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);
+
+        cs.setConservation(c);
+      }
+    }
+
+    int s, sSize = viewport.alignment.getGroups().size();
+    for(s=0; s<sSize; s++)
+    {
+      SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
+      if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
+      {
+        ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
+      }
+      sg.recalcConservation();
+    }
+  }
+
+
 
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
@@ -918,6 +968,7 @@ public class AlignFrame
         else
         {
           sg.cs.setConservation(null);
+          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
         }
 
       }
@@ -1034,7 +1085,7 @@ public class AlignFrame
     if (viewport.getSelectionGroup().getSize() > 1)
     {
       Frame frame = new Frame();
-      frame.add(new PairwiseAlignPanel(viewport));
+      frame.add(new PairwiseAlignPanel(alignPanel));
       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);
     }
   }
@@ -1110,13 +1161,13 @@ public class AlignFrame
     if (viewport.getSelectionGroup() != null &&
         viewport.getSelectionGroup().getSize() > 3)
     {
-      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
+      tp = new TreePanel(alignPanel, viewport.getSelectionGroup().sequences, type,
                          pwType,
                          0, viewport.alignment.getWidth());
     }
     else
     {
-      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
+      tp = new TreePanel(alignPanel, viewport.getAlignment().getSequences(),
                          type, pwType, 0, viewport.alignment.getWidth());
     }