Conservation colour in place

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8af52d0..b504538 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -19,11 +19,12 @@ import jalview.io.*;
 import java.awt.event.*;\r
 import java.awt.*;\r
 import javax.swing.*;\r
+import java.util.*;\r
 \r
 public class AlignFrame extends GAlignFrame\r
 {\r
-  AlignmentPanel alignPanel;\r
-  AlignViewport viewport;\r
+  final AlignmentPanel alignPanel;\r
+  final AlignViewport viewport;\r
   public AlignFrame(AlignmentI al)\r
   {\r
     super();\r
@@ -83,14 +84,96 @@ public class AlignFrame extends GAlignFrame
     }catch(Exception ex){}\r
   }\r
 \r
-  public void groupsMenuItem_actionPerformed(ActionEvent e)\r
+  ArrayList  historyList = new ArrayList();\r
+  ArrayList redoList = new ArrayList();\r
+\r
+  void updateEditMenuBar()\r
   {\r
+    if(historyList.size()>0)\r
+     {\r
+       undoMenuItem.setEnabled(true);\r
+       Object [] history = (Object[])historyList.get(0);\r
+       undoMenuItem.setText("Undo "+history[0]);\r
+     }\r
+    else\r
+    {\r
+      undoMenuItem.setEnabled(false);\r
+      undoMenuItem.setText("Undo");\r
+    }\r
 \r
+    if(redoList.size()>0)\r
+     {\r
+       redoMenuItem.setEnabled(true);\r
+       Object [] history = (Object[])redoList.get(0);\r
+       redoMenuItem.setText("Redo "+history[0]);\r
+     }\r
+    else\r
+    {\r
+      redoMenuItem.setEnabled(false);\r
+      redoMenuItem.setText("Redo");\r
+    }\r
   }\r
 \r
-  public void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
+  public void addHistoryItem(String type)\r
+  {\r
+    // must make sure we add new sequence objects her, not refs to the existing sequences\r
+    redoList.clear();\r
+    SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
+    for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
+    {\r
+      seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
+                             viewport.getAlignment().getSequenceAt(i).getSequence());\r
+    }\r
+\r
+    historyList.add(0, new Object[]{type,  seq} );\r
+    updateEditMenuBar();\r
+  }\r
+\r
+  protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+    Object [] history = (Object[])historyList.remove(0);\r
+    // add the redo state before continuing!!\r
+    SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
+    for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
+    {\r
+      seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
+                            viewport.getAlignment().getSequenceAt(i).\r
+                            getSequence());\r
+    }\r
+    /////////\r
+\r
+    redoList.add(0, new Object[] {history[0], seq});\r
+\r
+      seq = (SequenceI[]) history[1];\r
+      viewport.setAlignment( new Alignment(seq) );\r
+      updateEditMenuBar();\r
+      alignPanel.RefreshPanels();\r
+  }\r
+\r
+\r
+  protected void redoMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+     Object [] history = (Object[])redoList.remove(0);\r
+     SequenceI[] seq = (SequenceI[]) history[1];\r
+     viewport.setAlignment( new Alignment(seq) );\r
+     updateEditMenuBar();\r
+     alignPanel.RefreshPanels();\r
+  }\r
+\r
+\r
+\r
+  public void groupsMenuItem_actionPerformed(ActionEvent e)\r
   {\r
+    GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
+    JInternalFrame frame = new JInternalFrame();\r
+    frame.setContentPane(geditor);\r
+    Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
+    frame.setResizable(false);\r
+  }\r
 \r
+  public void groupEditingMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setGroupEdit( groupEditingMenuItem.isSelected() );\r
   }\r
 \r
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
@@ -122,6 +205,8 @@ public class AlignFrame extends GAlignFrame
 \r
   public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)\r
   {\r
+    addHistoryItem("delete selection");\r
+\r
     for (int i=0;i < viewport.getSelection().size(); i++)\r
             viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));\r
 \r
@@ -147,7 +232,6 @@ public class AlignFrame extends GAlignFrame
      s[i] = new Sequence(viewport.getSelection().sequenceAt(i));\r
     }\r
     AlignFrame af = new AlignFrame(new Alignment(s));\r
-\r
     int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
     if(newHeight>500)\r
       newHeight=500;\r
@@ -162,6 +246,7 @@ public class AlignFrame extends GAlignFrame
 \r
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
   {\r
+    addHistoryItem("delete columns");\r
     ColumnSelection colSel = viewport.getColumnSelection();\r
     if (colSel.size() > 0)\r
     {\r
@@ -174,6 +259,7 @@ public class AlignFrame extends GAlignFrame
 \r
   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
   {\r
+    addHistoryItem("delete columns");\r
     ColumnSelection colSel = viewport.getColumnSelection();\r
     if (colSel.size() > 0)\r
     {\r
@@ -188,12 +274,14 @@ public class AlignFrame extends GAlignFrame
 \r
   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
   {\r
+    addHistoryItem("delete gapped columns");\r
     viewport.getAlignment().removeGaps();\r
     alignPanel.RefreshPanels();\r
   }\r
 \r
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
   {\r
+    addHistoryItem("delete all gaps");\r
     SequenceI current;\r
     int jSize;\r
     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
@@ -297,6 +385,13 @@ public class AlignFrame extends GAlignFrame
 \r
   }\r
 \r
+  protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
+    alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
+  }\r
+\r
+\r
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
   {\r
     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
@@ -336,13 +431,19 @@ public class AlignFrame extends GAlignFrame
 \r
   }catch(java.lang.OutOfMemoryError ex)\r
    {\r
-     JOptionPane.showMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!",\r
+     JOptionPane.showMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
+                                   +"\nTry reducing the font size.",\r
                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
    }\r
 \r
 \r
   }\r
 \r
+  protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+    alignPanel.setColourScheme(null, false);\r
+  }\r
+\r
 \r
   public void clustalColour_actionPerformed(ActionEvent e)\r
   {\r
@@ -351,54 +452,65 @@ public class AlignFrame extends GAlignFrame
 \r
   public void zappoColour_actionPerformed(ActionEvent e)\r
   {\r
-    alignPanel.setColourScheme( new ZappoColourScheme() );\r
+    alignPanel.setColourScheme( new ZappoColourScheme(), conservationMenuItem.isSelected() );\r
   }\r
 \r
   public void taylorColour_actionPerformed(ActionEvent e)\r
   {\r
-    alignPanel.setColourScheme( new TaylorColourScheme() );\r
+    alignPanel.setColourScheme( new TaylorColourScheme(),conservationMenuItem.isSelected() );\r
   }\r
 \r
 \r
   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
   {\r
-    alignPanel.setColourScheme( new HydrophobicColourScheme() );\r
+    alignPanel.setColourScheme( new HydrophobicColourScheme(),conservationMenuItem.isSelected() );\r
   }\r
 \r
   public void helixColour_actionPerformed(ActionEvent e)\r
   {\r
-    alignPanel.seqPanel.setColourScheme( new HelixColourScheme() );\r
+    alignPanel.setColourScheme( new HelixColourScheme(),conservationMenuItem.isSelected() );\r
   }\r
 \r
+\r
   public void strandColour_actionPerformed(ActionEvent e)\r
   {\r
-    alignPanel.setColourScheme( new StrandColourScheme() );\r
+    alignPanel.setColourScheme( new StrandColourScheme() ,conservationMenuItem.isSelected() );\r
   }\r
 \r
+\r
   public void turnColour_actionPerformed(ActionEvent e)\r
   {\r
-    alignPanel.setColourScheme( new TurnColourScheme() );\r
+    alignPanel.setColourScheme( new TurnColourScheme() ,conservationMenuItem.isSelected() );\r
   }\r
 \r
+\r
   public void buriedColour_actionPerformed(ActionEvent e)\r
   {\r
-    alignPanel.setColourScheme( new BuriedColourScheme() );\r
+    alignPanel.setColourScheme( new BuriedColourScheme() ,conservationMenuItem.isSelected() );\r
   }\r
 \r
-  public void conservationColour_actionPerformed(ActionEvent e)\r
-  {\r
 \r
+  protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+    alignPanel.setColourScheme ( alignPanel.seqPanel.getColourScheme(),conservationMenuItem.isSelected() );\r
+    conservationColourIncMenuItem.setEnabled( conservationMenuItem.isSelected() );\r
   }\r
 \r
+\r
+\r
   public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
  {\r
-\r
+   ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);\r
+   JInternalFrame frame = new JInternalFrame();\r
+   frame.setContentPane(cip);\r
+   Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);\r
+   frame.setMaximizable(false);\r
  }\r
 \r
 \r
   public void abovePIDColour_actionPerformed(ActionEvent e)\r
   {\r
-    alignPanel.setColourScheme( new PIDColourScheme() );\r
+    alignPanel.setColourScheme( new PIDColourScheme() ,conservationMenuItem.isSelected() );\r
   }\r
 \r
 \r
@@ -415,15 +527,17 @@ public class AlignFrame extends GAlignFrame
 \r
   public void PIDColour_actionPerformed(ActionEvent e)\r
   {\r
-    alignPanel.setColourScheme( new PIDColourScheme() );\r
+    alignPanel.setColourScheme( new PIDColourScheme(),conservationMenuItem.isSelected() );\r
   }\r
 \r
+\r
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
   {\r
-    alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) );\r
+    alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) ,conservationMenuItem.isSelected() );\r
   }\r
 \r
 \r
+\r
   protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
   {\r
     ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() );\r
@@ -433,18 +547,21 @@ public class AlignFrame extends GAlignFrame
 \r
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
   {\r
+    addHistoryItem("sort");\r
     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
     alignPanel.RefreshPanels();\r
   }\r
 \r
   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
   {\r
+    addHistoryItem("sort");\r
     AlignmentSorter.sortByID( viewport.getAlignment() );\r
     alignPanel.RefreshPanels();\r
   }\r
 \r
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
   {\r
+    addHistoryItem("sort");\r
     AlignmentSorter.sortGroups(viewport.getAlignment());\r
     AlignmentSorter.sortGroups(viewport.getAlignment());\r
     alignPanel.RefreshPanels();\r
@@ -452,6 +569,7 @@ public class AlignFrame extends GAlignFrame
 \r
   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
   {\r
+    addHistoryItem("sort");\r
     if(viewport.getCurrentTree()==null)\r
       return;\r
 \r
@@ -488,10 +606,18 @@ public class AlignFrame extends GAlignFrame
       return;\r
     }\r
 \r
-    PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
-    JInternalFrame frame = new JInternalFrame();\r
-    frame.setContentPane(pcaPanel);\r
-    Desktop.addInternalFrame(frame, "Principal component analysis", 400,400);\r
+    try{\r
+      PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
+      JInternalFrame frame = new JInternalFrame();\r
+      frame.setContentPane(pcaPanel);\r
+      Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
+   }catch(java.lang.OutOfMemoryError ex)\r
+   {\r
+     JOptionPane.showMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
+                                   "Out of memory", JOptionPane.WARNING_MESSAGE);\r
+   }\r
+\r
+\r
   }\r
 \r
   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r