X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=7289fc44b0c9fd1dec87c7d6404e717a07b798b3;hb=064f2fdaa463367f8bf7e6aea5e7fc6a32170138;hp=f1ecd6af3df3c258b9257bb049692b2aeb87a951;hpb=8ed0e40c3fcba8396c749d2250a4221a5099ed29;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index f1ecd6a..7289fc4 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -39,14 +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();
-  }
 
   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)
   {
@@ -57,7 +49,6 @@ public class AlignFrame
     alignPanel.validate();
 
     String treeFile = applet.getParameter("treeFile");
-    TreePanel treepanel = null;
     if (treeFile != null)
     {
       try
@@ -82,12 +73,38 @@ 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)
+          {
+            closeMenuItem_actionPerformed(null);
+          }
+    });
+
+    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);
@@ -95,7 +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,
@@ -108,6 +125,7 @@ public class AlignFrame
 
   public void closeMenuItem_actionPerformed(ActionEvent e)
   {
+    PaintRefresher.components.remove(viewport.alignment);
     dispose();
   }
 
@@ -153,6 +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)
@@ -160,9 +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
@@ -206,9 +223,7 @@ public class AlignFrame
 
     updateEditMenuBar();
 
-    viewport.updateConsensus();
-    viewport.updateConservation();
-    alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   public void moveSelectedSequences(boolean up)
@@ -399,9 +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());
       }
 
     }
@@ -467,9 +480,7 @@ public class AlignFrame
       catch (Exception ex)
       {}
     }
-    viewport.updateConservation();
-    viewport.updateConsensus();
-    alignPanel.repaint();
+    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
 
   }
 
@@ -488,10 +499,10 @@ 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);
+    PaintRefresher.Refresh(null, viewport.alignment);
   }
 
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
@@ -499,7 +510,8 @@ public class AlignFrame
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
-    PaintRefresher.Refresh(null);
+    alignPanel.repaint();
+    PaintRefresher.Refresh(null, viewport.alignment);
   }
 
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
@@ -510,7 +522,7 @@ public class AlignFrame
       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
     }
 
-    PaintRefresher.Refresh(null);
+    PaintRefresher.Refresh(null, viewport.alignment);
   }
 
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
@@ -538,8 +550,7 @@ public class AlignFrame
           viewport.alignment.deleteGroup(sg);
         }
       }
-
-      alignPanel.repaint();
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     }
   }
 
@@ -566,8 +577,7 @@ public class AlignFrame
           viewport.alignment.deleteGroup(sg);
         }
       }
-
-      alignPanel.repaint();
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
     }
 
   }
@@ -577,10 +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)
@@ -588,6 +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;
 
@@ -625,11 +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)
   {
@@ -804,53 +873,48 @@ public class AlignFrame
   {
     int threshold = 0;
 
-    if (viewport.getAbovePIDThreshold())
+    if(cs!=null)
     {
-      threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
-
-      if (cs instanceof ResidueColourScheme)
+      if (viewport.getAbovePIDThreshold())
       {
-        ( (ResidueColourScheme) cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-      }
+        threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");
 
-      viewport.setGlobalColourScheme(cs);
-    }
-    else if (cs instanceof ResidueColourScheme)
-    {
-      ( (ResidueColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());
-    }
+        cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
 
-    if (viewport.getConservationSelected())
-    {
-      ConservationColourScheme ccs = null;
+        viewport.setGlobalColourScheme(cs);
+      }
+      else
+      {
+        cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+      }
 
-      Alignment al = (Alignment) viewport.alignment;
-      Conservation c = new Conservation("All",
-                                        ResidueProperties.propHash, 3,
-                                        al.getSequences(), 0,
-                                        al.getWidth() - 1);
+      if (viewport.getConservationSelected())
+      {
 
-      c.calculate();
-      c.verdict(false, viewport.ConsPercGaps);
+        Alignment al = (Alignment) viewport.alignment;
+        Conservation c = new Conservation("All",
+                                          ResidueProperties.propHash, 3,
+                                          al.getSequences(), 0,
+                                          al.getWidth() - 1);
 
-      ccs = new ConservationColourScheme(c, cs);
+        c.calculate();
+        c.verdict(false, viewport.ConsPercGaps);
 
-      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      ccs.setConsensus(viewport.vconsensus);
-      viewport.setGlobalColourScheme(ccs);
+        cs.setConservation(c);
 
-      SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
+        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,
+            "Background"));
 
-    }
-    else
-    {
-      // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-      if (cs != null)
+      }
+      else
       {
-        cs.setConsensus(viewport.vconsensus);
+        cs.setConservation(null);
       }
-      viewport.setGlobalColourScheme(cs);
+
+      cs.setConsensus(viewport.vconsensus);
+
     }
+    viewport.setGlobalColourScheme(cs);
 
     if (viewport.getColourAppliesToAllGroups())
     {
@@ -866,9 +930,7 @@ public class AlignFrame
         }
         if (cs instanceof ClustalxColourScheme)
         {
-          ClustalxColourScheme cxs = (ClustalxColourScheme) cs;
-          cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());
-          sg.cs = cxs;
+          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
         }
         else
         {
@@ -883,15 +945,15 @@ public class AlignFrame
           }
         }
 
-        if (viewport.getAbovePIDThreshold())
+        if (viewport.getAbovePIDThreshold()
+            || cs instanceof PIDColourScheme
+            || cs instanceof Blosum62ColourScheme)
         {
-          if (sg.cs instanceof ResidueColourScheme)
-          {
-            ( (ResidueColourScheme) sg.cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-          }
-
+          sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
         }
+        else
+          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
 
         if (viewport.getConservationSelected())
         {
@@ -901,22 +963,17 @@ public class AlignFrame
                                             viewport.alignment.getWidth() - 1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
-          ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
-
-          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-          ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
-          sg.cs = ccs;
+          sg.cs.setConservation(c);
         }
         else
         {
-          // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
-          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
+          sg.cs.setConservation(null);
+          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
         }
 
       }
     }
 
-    updateCSConsensus();
 
     if (alignPanel.getOverviewPanel() != null)
     {
@@ -926,15 +983,11 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
-  public void updateCSConsensus()
-  {
-    //Colour schemes must have their consensus updated
 
-  }
 
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
-    if (viewport.getAbovePIDThreshold())
+    if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)
     {
       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),
                                      "Background");
@@ -944,7 +997,7 @@ public class AlignFrame
 
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
-    if (viewport.getConservationSelected())
+    if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)
     {
       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,
                                         "Background");
@@ -959,15 +1012,7 @@ public class AlignFrame
     viewport.setAbovePIDThreshold(false);
     abovePIDThreshold.setState(false);
 
-    ColourSchemeI cs = viewport.getGlobalColourScheme();
-    if (cs instanceof ConservationColourScheme)
-    {
-      changeColour( ( (ConservationColourScheme) cs).cs);
-    }
-    else
-    {
-      changeColour(cs);
-    }
+    changeColour(viewport.getGlobalColourScheme());
 
     modifyConservation_actionPerformed(null);
   }
@@ -979,16 +1024,7 @@ public class AlignFrame
     conservationMenuItem.setState(false);
     viewport.setConservationSelected(false);
 
-    ColourSchemeI cs = viewport.getGlobalColourScheme();
-
-    if (cs instanceof ConservationColourScheme)
-    {
-      changeColour( ( (ConservationColourScheme) cs).cs);
-    }
-    else
-    {
-      changeColour(cs);
-    }
+    changeColour(viewport.getGlobalColourScheme());
 
     modifyPID_actionPerformed(null);
   }
@@ -1049,7 +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);
     }
   }
@@ -1125,13 +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());
     }