X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=de19fd8bfdf9f428e8ca5ae5d41befea3dd2ff23;hb=6d58edc047af16d3d632842be665ff990de74607;hp=604da7b405a585062b0fcd0e0d8621d96d102202;hpb=22b7f97726482cb0ee32389811126e62aaead61d;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 604da7b..de19fd8 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -425,9 +425,16 @@ public class AlignFrame extends Frame implements ActionListener,
         break;
 
       case KeyEvent.VK_U:
+        if (evt.isControlDown())
+        {
+          this.deleteGroups_actionPerformed();
+        }
+      break;
+
+    case KeyEvent.VK_T:
       if (evt.isControlDown())
       {
-       this.deleteGroups_actionPerformed();
+       newView();
       }
       break;
 
@@ -447,21 +454,24 @@ public void itemStateChanged(ItemEvent evt)
     else if(evt.getSource()==wrapMenuItem)
             wrapMenuItem_actionPerformed();
     else if(evt.getSource()==scaleAbove)
-            scaleAbove_actionPerformed();
+            viewport.setScaleAboveWrapped(scaleAbove.getState());
     else if(evt.getSource()==scaleLeft)
-            scaleLeft_actionPerformed();
+            viewport.setScaleLeftWrapped(scaleLeft.getState());
     else if(evt.getSource()==scaleRight)
-            scaleRight_actionPerformed();
+            viewport.setScaleRightWrapped(scaleRight.getState());
      else if(evt.getSource()==seqLimits)
       seqLimits_itemStateChanged();
     else if(evt.getSource()==viewBoxesMenuItem)
-            viewBoxesMenuItem_actionPerformed();
+            viewport.setShowBoxes(viewBoxesMenuItem.getState());
     else if(evt.getSource()==viewTextMenuItem)
-            viewTextMenuItem_actionPerformed();
+            viewport.setShowText(viewTextMenuItem.getState());
     else if(evt.getSource()==renderGapsMenuItem)
-            renderGapsMenuItem_actionPerformed();
+            viewport.setRenderGaps(renderGapsMenuItem.getState());
     else if(evt.getSource()==annotationPanelMenuItem)
-            annotationPanelMenuItem_actionPerformed();
+    {
+      viewport.setShowAnnotation(annotationPanelMenuItem.getState());
+      alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
+    }
       else if(evt.getSource()==sequenceFeatures)
       {
            viewport.showSequenceFeatures(sequenceFeatures.getState());
@@ -471,10 +481,12 @@ public void itemStateChanged(ItemEvent evt)
             conservationMenuItem_actionPerformed();
       else if(evt.getSource()==abovePIDThreshold)
             abovePIDThreshold_actionPerformed();
-          else if(evt.getSource()==applyToAllGroups)
-            applyToAllGroups_actionPerformed();
+      else if(evt.getSource()==applyToAllGroups)
+            viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
       else if(evt.getSource()==autoCalculate)
           viewport.autocalculateConsensus = autoCalculate.getState();
+
+      alignPanel.repaint();
   }
  public void actionPerformed(ActionEvent evt)
  {
@@ -533,7 +545,9 @@ public void itemStateChanged(ItemEvent evt)
     else if(source==findMenuItem)
             findMenuItem_actionPerformed();
     else if(source==font)
-            font_actionPerformed();
+            new FontChooser(alignPanel);
+    else if (source == newView)
+      newView();
     else if(source==showColumns)
     {
       viewport.showAllHiddenColumns(); alignPanel.repaint();
@@ -551,39 +565,43 @@ public void itemStateChanged(ItemEvent evt)
       viewport.hideAllSelectedSeqs();
     }
     else if(source==featureSettings)
-            featureSettings_actionPerformed();
+            new FeatureSettings(alignPanel);
     else if(source==overviewMenuItem)
             overviewMenuItem_actionPerformed();
     else if(source==noColourmenuItem)
-            noColourmenuItem_actionPerformed();
+            changeColour(null);
     else if(source==clustalColour)
-            clustalColour_actionPerformed();
+    {
+      abovePIDThreshold.setState(false);
+      changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
+                                            viewport.alignment.getWidth()));
+  }
     else if(source==zappoColour)
-            zappoColour_actionPerformed();
+            changeColour(new ZappoColourScheme());
     else if(source==taylorColour)
-            taylorColour_actionPerformed();
+            changeColour(new TaylorColourScheme());
     else if(source==hydrophobicityColour)
-            hydrophobicityColour_actionPerformed();
+            changeColour(new HydrophobicColourScheme());
     else if(source==helixColour)
-            helixColour_actionPerformed();
+            changeColour(new HelixColourScheme());
     else if(source==strandColour)
-            strandColour_actionPerformed();
+            changeColour(new StrandColourScheme());
     else if(source==turnColour)
-            turnColour_actionPerformed();
+            changeColour(new TurnColourScheme());
     else if(source==buriedColour)
-            buriedColour_actionPerformed();
+            changeColour(new BuriedColourScheme());
     else if(source==nucleotideColour)
-            nucleotideColour_actionPerformed();
+            changeColour(new NucleotideColourScheme());
     else if(source==modifyPID)
             modifyPID_actionPerformed();
     else if(source==modifyConservation)
             modifyConservation_actionPerformed();
     else if(source==userDefinedColour)
-            userDefinedColour_actionPerformed();
+            new UserDefinedColours(alignPanel, null);
     else if(source==PIDColour)
-            PIDColour_actionPerformed();
+            changeColour(new PIDColourScheme());
     else if(source==BLOSUM62Colour)
-            BLOSUM62Colour_actionPerformed();
+            changeColour(new Blosum62ColourScheme());
     else if(source==annotationColour)
            new AnnotationColourChooser(viewport, alignPanel);
     else if(source==sortPairwiseMenuItem)
@@ -705,7 +723,10 @@ public void itemStateChanged(ItemEvent evt)
 
   public void closeMenuItem_actionPerformed()
   {
-    PaintRefresher.components.remove(viewport.alignment);
+    PaintRefresher.RemoveComponent(alignPanel);
+    PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
+    PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
+
     if(PaintRefresher.components.size()==0 && viewport.applet==null)
       System.exit(0);
 
@@ -784,6 +805,9 @@ public void itemStateChanged(ItemEvent evt)
    */
   protected void redoMenuItem_actionPerformed()
   {
+    if(viewport.redoList.size()<1)
+      return;
+
     CommandI command = (CommandI) viewport.redoList.pop();
     viewport.historyList.push(command);
     command.doCommand();
@@ -797,14 +821,15 @@ public void itemStateChanged(ItemEvent evt)
 
   AlignViewport getOriginatingSource(CommandI command)
   {
-    AlignViewport originalSource = viewport;
+    AlignViewport originalSource = null;
     //For sequence removal and addition, we need to fire
    //the property change event FROM the viewport where the
    //original alignment was altered
+   AlignmentI al = null;
     if (command instanceof EditCommand)
     {
       EditCommand editCommand = (EditCommand) command;
-      AlignmentI al = editCommand.getAlignment();
+      al = editCommand.getAlignment();
       Vector comps = (Vector) PaintRefresher.components
           .get(viewport.getSequenceSetId());
       for (int i = 0; i < comps.size(); i++)
@@ -819,6 +844,18 @@ public void itemStateChanged(ItemEvent evt)
         }
       }
     }
+
+    if (originalSource == null)
+    {
+      //The original view is closed, we must validate
+      //the current view against the closed view first
+      if (al != null)
+        PaintRefresher.validateSequences(al, viewport.alignment);
+
+      originalSource = viewport;
+    }
+
+
     return originalSource;
   }
 
@@ -1305,10 +1342,53 @@ public void itemStateChanged(ItemEvent evt)
     new Finder(alignPanel);
   }
 
-  public void font_actionPerformed()
+  public void newView()
   {
-    new FontChooser(alignPanel);
-  }
+    AlignmentI newal;
+    if (viewport.hasHiddenRows)
+      newal = new Alignment(viewport.getAlignment().
+                            getHiddenSequences()
+                            .getFullAlignment().
+                            getSequencesArray());
+    else
+      newal = new Alignment(viewport.alignment.getSequencesArray());
+
+    AlignFrame newaf = new AlignFrame(newal,
+                                      viewport.applet,
+                                      "",
+                                      false);
+
+    newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
+    PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
+    PaintRefresher.Register(newaf.alignPanel,
+                            newaf.alignPanel.av.getSequenceSetId());
+
+    PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
+                            newaf.alignPanel.av.getSequenceSetId());
+    PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
+                            newaf.alignPanel.av.getSequenceSetId());
+
+    Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());
+    int viewSize = -1;
+    for (int i = 0; i < comps.size(); i++)
+    {
+      if (comps.elementAt(i) instanceof AlignmentPanel)
+        viewSize++;
+    }
+
+    String title = new String(this.getTitle());
+    if (title.indexOf("(View") > -1)
+      title = title.substring(0, title.indexOf("(View"));
+
+    title+= "(View "+viewSize+")";
+
+    newaf.setTitle(title.toString());
+
+
+    newaf.viewport.historyList = viewport.historyList;
+    newaf.viewport.redoList = viewport.redoList;
+
+   }
 
 
   public void seqLimits_itemStateChanged()
@@ -1336,53 +1416,6 @@ public void itemStateChanged(ItemEvent evt)
   }
 
 
-  protected void scaleAbove_actionPerformed()
-  {
-    viewport.setScaleAboveWrapped(scaleAbove.getState());
-    alignPanel.repaint();
-  }
-
-  protected void scaleLeft_actionPerformed()
-  {
-    viewport.setScaleLeftWrapped(scaleLeft.getState());
-    alignPanel.repaint();
-  }
-
-  protected void scaleRight_actionPerformed()
-  {
-    viewport.setScaleRightWrapped(scaleRight.getState());
-    alignPanel.repaint();
-  }
-
-  public void viewBoxesMenuItem_actionPerformed()
-  {
-    viewport.setShowBoxes(viewBoxesMenuItem.getState());
-    alignPanel.repaint();
-  }
-
-  public void viewTextMenuItem_actionPerformed()
-  {
-    viewport.setShowText(viewTextMenuItem.getState());
-    alignPanel.repaint();
-  }
-
-  protected void renderGapsMenuItem_actionPerformed()
-  {
-    viewport.setRenderGaps(renderGapsMenuItem.getState());
-    alignPanel.repaint();
-  }
-
-  public void annotationPanelMenuItem_actionPerformed()
-  {
-    viewport.setShowAnnotation(annotationPanelMenuItem.getState());
-    alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
-  }
-
-  public void featureSettings_actionPerformed()
-  {
-    new FeatureSettings(viewport, alignPanel);
-  }
-
   public void overviewMenuItem_actionPerformed()
   {
     if (alignPanel.overviewPanel != null)
@@ -1411,62 +1444,6 @@ public void itemStateChanged(ItemEvent evt)
 
   }
 
-  protected void noColourmenuItem_actionPerformed()
-  {
-    changeColour(null);
-  }
-
-  public void clustalColour_actionPerformed()
-  {
-    abovePIDThreshold.setState(false);
-    changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),
-                                          viewport.alignment.getWidth()));
-  }
-
-  public void zappoColour_actionPerformed()
-  {
-    changeColour(new ZappoColourScheme());
-  }
-
-  public void taylorColour_actionPerformed()
-  {
-    changeColour(new TaylorColourScheme());
-  }
-
-  public void hydrophobicityColour_actionPerformed()
-  {
-    changeColour(new HydrophobicColourScheme());
-  }
-
-  public void helixColour_actionPerformed()
-  {
-    changeColour(new HelixColourScheme());
-  }
-
-  public void strandColour_actionPerformed()
-  {
-    changeColour(new StrandColourScheme());
-  }
-
-  public void turnColour_actionPerformed()
-  {
-    changeColour(new TurnColourScheme());
-  }
-
-  public void buriedColour_actionPerformed()
-  {
-    changeColour(new BuriedColourScheme());
-  }
-
-  public void nucleotideColour_actionPerformed()
-  {
-    changeColour(new NucleotideColourScheme());
-  }
-
-  protected void applyToAllGroups_actionPerformed()
-  {
-    viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
-  }
 
   void changeColour(ColourSchemeI cs)
   {
@@ -1628,20 +1605,7 @@ public void itemStateChanged(ItemEvent evt)
     modifyPID_actionPerformed();
   }
 
-  public void userDefinedColour_actionPerformed()
-  {
-    new UserDefinedColours(alignPanel, null);
-  }
 
-  public void PIDColour_actionPerformed()
-  {
-    changeColour(new PIDColourScheme());
-  }
-
-  public void BLOSUM62Colour_actionPerformed()
-  {
-    changeColour(new Blosum62ColourScheme());
-  }
 
   public void sortPairwiseMenuItem_actionPerformed()
   {
@@ -2201,6 +2165,8 @@ public void itemStateChanged(ItemEvent evt)
     hideSequences.addActionListener(this);
     formatMenu.setLabel("Format");
     selectMenu.setLabel("Select");
+    newView.setLabel("New View");
+    newView.addActionListener(this);
     alignFrameMenuBar.add(fileMenu);
         alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(selectMenu);
@@ -2228,6 +2194,8 @@ public void itemStateChanged(ItemEvent evt)
         editMenu.add(removeGappedColumnMenuItem);
         editMenu.add(removeAllGapsMenuItem);
         editMenu.add(removeRedundancyMenuItem);
+    viewMenu.add(newView);
+    viewMenu.addSeparator();
     viewMenu.add(menu1);
     viewMenu.add(menu2);
     viewMenu.addSeparator();
@@ -2376,6 +2344,7 @@ public void itemStateChanged(ItemEvent evt)
   MenuItem hideSequences = new MenuItem();
   Menu formatMenu = new Menu();
   Menu selectMenu = new Menu();
+  MenuItem newView = new MenuItem();
 
   public void mousePressed(MouseEvent evt)
   {