X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=bed10a1d09841453881aadef0953e7eb57461e6d;hb=beaa65409fc4cf865392c4e6e57116b64af37dfc;hp=f1ecd6af3df3c258b9257bb049692b2aeb87a951;hpb=8ed0e40c3fcba8396c749d2250a4221a5099ed29;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index f1ecd6a..bed10a1 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -46,8 +46,18 @@ public class AlignFrame
     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)
   {
     this.applet = applet;
@@ -57,7 +67,6 @@ public class AlignFrame
     alignPanel.validate();
 
     String treeFile = applet.getParameter("treeFile");
-    TreePanel treepanel = null;
     if (treeFile != null)
     {
       try
@@ -82,6 +91,15 @@ public class AlignFrame
       }
     }
 
+    this.addWindowListener(new WindowAdapter()
+    {
+      public void windowClosing(WindowEvent e)
+          {
+            closeMenuItem_actionPerformed(null);
+          }
+    });
+
+
 
   }
 
@@ -108,6 +126,7 @@ public class AlignFrame
 
   public void closeMenuItem_actionPerformed(ActionEvent e)
   {
+    PaintRefresher.components.remove(viewport.alignment);
     dispose();
   }
 
@@ -153,6 +172,7 @@ public class AlignFrame
     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
                                   HistoryItem.HIDE));
     restoreHistoryItem(hi);
+    resetAllColourSchemes();
   }
 
   protected void redoMenuItem_actionPerformed(ActionEvent e)
@@ -161,6 +181,7 @@ public class AlignFrame
     restoreHistoryItem(hi);
     updateEditMenuBar();
     viewport.updateConsensus();
+    resetAllColourSchemes();
     alignPanel.repaint();
     alignPanel.repaint();
   }
@@ -401,6 +422,7 @@ public class AlignFrame
         viewport.alignment.getWidth();
         viewport.updateConservation();
         viewport.updateConsensus();
+        resetAllColourSchemes();
         alignPanel.repaint();
       }
 
@@ -469,6 +491,7 @@ public class AlignFrame
     }
     viewport.updateConservation();
     viewport.updateConsensus();
+    resetAllColourSchemes();
     alignPanel.repaint();
 
   }
@@ -488,10 +511,10 @@ 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 +522,7 @@ public class AlignFrame
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
-    PaintRefresher.Refresh(null);
+    PaintRefresher.Refresh(null, viewport.alignment);
   }
 
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
@@ -510,7 +533,7 @@ public class AlignFrame
       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
     }
 
-    PaintRefresher.Refresh(null);
+    PaintRefresher.Refresh(null, viewport.alignment);
   }
 
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
@@ -538,7 +561,7 @@ public class AlignFrame
           viewport.alignment.deleteGroup(sg);
         }
       }
-
+      resetAllColourSchemes();
       alignPanel.repaint();
     }
   }
@@ -566,7 +589,7 @@ public class AlignFrame
           viewport.alignment.deleteGroup(sg);
         }
       }
-
+      resetAllColourSchemes();
       alignPanel.repaint();
     }
 
@@ -577,9 +600,19 @@ 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.setStartRes(seq.findIndex(startRes)-1);
+
     viewport.updateConservation();
     viewport.updateConsensus();
+    resetAllColourSchemes();
     alignPanel.repaint();
   }
 
@@ -588,6 +621,11 @@ 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 +663,56 @@ public class AlignFrame
       while(j < end && j < jSize) ;
     }
 
+    viewport.setStartRes(seq.findIndex(startRes)-1);
     viewport.updateConservation();
     viewport.updateConsensus();
+    resetAllColourSchemes();
     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);
+
+          cs.setConservation(c);
+        }
+    }
+
+    if(viewport.getGlobalColourScheme()!=null
+       && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)
+    {
+      ((ClustalxColourScheme)viewport.getGlobalColourScheme()).
+          resetClustalX(viewport.alignment.getSequences(),
+                        viewport.alignment.getWidth());
+    }
+
+    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 +887,48 @@ 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 +944,7 @@ 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 +959,15 @@ 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 +977,17 @@ 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 +997,11 @@ 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 +1011,7 @@ 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 +1026,7 @@ 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 +1038,7 @@ 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);
   }