X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=ced0622244db3d32248e96f839e6bf19a8650b4c;hb=237972562c84b83dbd287071cdd839d97aaf7d4b;hp=ff7646f76e9b245e38e7ad8b9c187b44033c5538;hpb=3e3378e2ccfea39a2b161600c5a2029716acd1b7;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index ff7646f..ced0622 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -208,9 +208,9 @@ public class AlignFrame extends Frame implements ActionListener,
         }
         break;
       case KeyEvent.VK_V:
-        if (evt.isControlDown() || evt.isMetaDown())
+        if (evt.isControlDown())
         {
-          paste(true);
+          paste(evt.isShiftDown());
         }
         break;
       case KeyEvent.VK_A:
@@ -266,8 +266,7 @@ public class AlignFrame extends Frame implements ActionListener,
         {
           alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
                                                 || evt.isShiftDown()
-                                                || evt.isAltDown()
-              );
+                                                || evt.isAltDown());
         }
        else
         {
@@ -319,7 +318,6 @@ public class AlignFrame extends Frame implements ActionListener,
          alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
          alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
        }
-       alignPanel.seqPanel.seqCanvas.repaint();
        break;
 
       case KeyEvent.VK_F:
@@ -328,6 +326,7 @@ public class AlignFrame extends Frame implements ActionListener,
           findMenuItem_actionPerformed();
         }
         break;
+
       case KeyEvent.VK_H:
       {
         boolean toggleSeqs = !evt.isControlDown();
@@ -357,10 +356,9 @@ public class AlignFrame extends Frame implements ActionListener,
           else if (!hide)
             viewport.showAllHiddenColumns();
         }
-
-        alignPanel.repaint();
         break;
       }
+
       case KeyEvent.VK_PAGE_UP:
         if (viewport.wrapAlignment)
           alignPanel.scrollUp(true);
@@ -369,6 +367,7 @@ public class AlignFrame extends Frame implements ActionListener,
                                      viewport.startSeq
                                      - viewport.endSeq + viewport.startSeq);
         break;
+
       case KeyEvent.VK_PAGE_DOWN:
         if (viewport.wrapAlignment)
           alignPanel.scrollUp(false);
@@ -377,7 +376,71 @@ public class AlignFrame extends Frame implements ActionListener,
                                      viewport.startSeq
                                      + viewport.endSeq - viewport.startSeq);
         break;
+
+      case KeyEvent.VK_Z:
+        if (evt.isControlDown())
+        {
+          undoMenuItem_actionPerformed();
+        }
+        break;
+
+      case KeyEvent.VK_Y:
+        if (evt.isControlDown())
+        {
+          redoMenuItem_actionPerformed();
+        }
+        break;
+
+      case KeyEvent.VK_L:
+        if (evt.isControlDown())
+        {
+          trimAlignment(true);
+        }
+        break;
+
+      case KeyEvent.VK_R:
+        if (evt.isControlDown())
+        {
+          trimAlignment(false);
+        }
+        break;
+
+      case KeyEvent.VK_E:
+        if (evt.isControlDown())
+        {
+          if (evt.isShiftDown())
+            this.removeAllGapsMenuItem_actionPerformed();
+          else
+            removeGappedColumnMenuItem_actionPerformed();
+        }
+        break;
+      case KeyEvent.VK_I:
+        if (evt.isControlDown())
+        {
+          if (evt.isAltDown())
+            viewport.invertColumnSelection();
+          else
+            this.invertSequenceMenuItem_actionPerformed();
+        }
+        break;
+
+      case KeyEvent.VK_U:
+        if (evt.isControlDown())
+        {
+          this.deleteGroups_actionPerformed();
+        }
+      break;
+
+    case KeyEvent.VK_T:
+      if (evt.isControlDown())
+      {
+       newView();
+      }
+      break;
+
+
       }
+      alignPanel.repaint();
   }
   public void keyReleased(KeyEvent evt)
   {}
@@ -391,21 +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());
@@ -415,10 +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)
  {
@@ -477,7 +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();
@@ -495,39 +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)
@@ -649,7 +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);
 
@@ -700,29 +777,83 @@ public void itemStateChanged(ItemEvent evt)
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void undoMenuItem_actionPerformed()
   {
+    if(viewport.historyList.size()<1)
+      return;
+
     CommandI command = (CommandI)viewport.historyList.pop();
     viewport.redoList.push(command);
     command.undoCommand();
 
-    viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+    AlignViewport originalSource = getOriginatingSource(command);
+
+    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
     updateEditMenuBar();
-    viewport.firePropertyChange("alignment", null,
-                                viewport.getAlignment().getSequences());
+    originalSource.firePropertyChange("alignment", null,null);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   protected void redoMenuItem_actionPerformed()
   {
+    if(viewport.redoList.size()<1)
+      return;
+
     CommandI command = (CommandI) viewport.redoList.pop();
     viewport.historyList.push(command);
     command.doCommand();
-    viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
+
+    AlignViewport originalSource = getOriginatingSource(command);
+    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
 
     updateEditMenuBar();
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+    originalSource.firePropertyChange("alignment", null, null);
   }
 
+  AlignViewport getOriginatingSource(CommandI command)
+  {
+    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
+    if (command instanceof EditCommand)
+    {
+      EditCommand editCommand = (EditCommand) command;
+      AlignmentI al = editCommand.getAlignment();
+      Vector comps = (Vector) PaintRefresher.components
+          .get(viewport.getSequenceSetId());
+      for (int i = 0; i < comps.size(); i++)
+      {
+        if (comps.elementAt(i) instanceof AlignmentPanel)
+        {
+          if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)
+          {
+            originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;
+            break;
+          }
+        }
+      }
+      if (originalSource == null && al!=null)
+      {
+        //The original view is closed, we must validate
+        //the current view against the closed view first
+        PaintRefresher.validateSequences(al, viewport.alignment);
+        originalSource = viewport;
+      }
+
+    }
+
+    return originalSource;
+  }
 
   public void moveSelectedSequences(boolean up)
   {
@@ -881,6 +1012,7 @@ public void itemStateChanged(ItemEvent evt)
   {
     try
     {
+
       if (copiedSequences == null)
       {
         return;
@@ -931,6 +1063,11 @@ public void itemStateChanged(ItemEvent evt)
       }
       else
       {
+        for (int i = 0; i < newSeqs.length; i++)
+        {
+          viewport.alignment.addSequence(newSeqs[i]);
+        }
+
         //!newAlignment
         addHistoryItem(new EditCommand(
             "Add sequences",
@@ -943,7 +1080,7 @@ public void itemStateChanged(ItemEvent evt)
 
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
-        viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+        viewport.firePropertyChange("alignment", null, null);
       }
 
     }
@@ -1201,10 +1338,53 @@ 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()
@@ -1232,53 +1412,6 @@ 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)
@@ -1307,62 +1440,6 @@ 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)
   {
@@ -1524,20 +1601,7 @@ 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()
   {
@@ -2097,6 +2161,8 @@ 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);
@@ -2124,6 +2190,8 @@ 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();
@@ -2203,7 +2271,7 @@ public void itemStateChanged(ItemEvent evt)
     embeddedEdit = new Label("Edit");
     embeddedSelect = new Label("Select");
     embeddedView = new Label("View");
-    embeddedFormat = new Label("Label");
+    embeddedFormat = new Label("Format");
     embeddedColour = new Label("Colour");
     embeddedFile = new Label("File");
     embeddedHelp = new Label("Help");
@@ -2259,7 +2327,7 @@ public void itemStateChanged(ItemEvent evt)
 
 
   PopupMenu filePopup, editPopup, searchPopup,
-      viewPopup, colourPopup, calculatePopup, helpPopup;
+      viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;
   MenuItem featureSettings = new MenuItem();
   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
   MenuItem annotationColour = new MenuItem();
@@ -2272,6 +2340,7 @@ 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)
   {
@@ -2295,7 +2364,7 @@ public void itemStateChanged(ItemEvent evt)
     }
     else if (source ==embeddedFormat)
     {
-      popup = viewPopup = genPopupMenu(viewPopup, formatMenu);
+      popup = formatPopup = genPopupMenu(formatPopup, formatMenu);
     }
     else if(source==embeddedColour)
     {