X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=78c956b43439b413f4e35d9371b22ae5def133a6;hb=dd4cc875a15a345a7245083fba46ce6013d8cff9;hp=dd4ff383f2136c2e2a356af56a3826fcc61657fc;hpb=baf71a063ac6499b4f9dc8a03aa0f8bd60394dbe;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index dd4ff38..78c956b 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -101,75 +101,94 @@ public class AlignFrame extends GAlignFrame
   Stack redoList = new Stack();
 
   void updateEditMenuBar()
-  {
-    if(historyList.size()>0)
+   {
+     if(historyList.size()>0)
+      {
+        undoMenuItem.setEnabled(true);
+        HistoryItem hi = (HistoryItem)historyList.peek();
+        undoMenuItem.setLabel("Undo "+hi.getDescription());
+      }
+     else
      {
-       undoMenuItem.setEnabled(true);
-       Object [] history = (Object[])historyList.elementAt(0);
-       undoMenuItem.setLabel("Undo "+history[0]);
+       undoMenuItem.setEnabled(false);
+       undoMenuItem.setLabel("Undo");
      }
-    else
-    {
-      undoMenuItem.setEnabled(false);
-      undoMenuItem.setLabel("Undo");
-    }
 
-    if(redoList.size()>0)
+     if(redoList.size()>0)
+      {
+        redoMenuItem.setEnabled(true);
+        HistoryItem hi = (HistoryItem)redoList.peek();
+        redoMenuItem.setLabel("Redo "+hi.getDescription());
+      }
+     else
      {
-       redoMenuItem.setEnabled(true);
-       Object [] history = (Object[])redoList.elementAt(0);
-       redoMenuItem.setLabel("Redo "+history[0]);
+       redoMenuItem.setEnabled(false);
+       redoMenuItem.setLabel("Redo");
      }
-    else
-    {
-      redoMenuItem.setEnabled(false);
-      redoMenuItem.setLabel("Redo");
-    }
-  }
+   }
 
-  public void addHistoryItem(String type)
-  {
-    // must make sure we add new sequence objects her, not refs to the existing sequences
-    redoList.removeAllElements();
-    SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
-    for(int i=0; i<viewport.getAlignment().getHeight(); i++)
-    {
-      seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
-                             viewport.getAlignment().getSequenceAt(i).getSequence());
-    }
+   public void addHistoryItem(HistoryItem hi)
+   {
+     historyList.push(hi);
+     updateEditMenuBar();
+   }
 
-    historyList.addElement(new Object[]{type,  seq} );
-    updateEditMenuBar();
-  }
+   protected void undoMenuItem_actionPerformed(ActionEvent e)
+   {
+       HistoryItem hi = (HistoryItem)historyList.pop();
+       redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE));
+       restoreHistoryItem(hi);
+   }
 
-  protected void undoMenuItem_actionPerformed(ActionEvent e)
-  {
-    Object [] history = (Object[])historyList.elementAt(0);
-    historyList.removeElementAt(0);
-    // add the redo state before continuing!!
-    SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
-    for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
-    {
-      seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
-                            viewport.getAlignment().getSequenceAt(i).
-                            getSequence());
-    }
-    /////////
+   protected void redoMenuItem_actionPerformed(ActionEvent e)
+   {
+      HistoryItem hi = (HistoryItem)redoList.pop();
+      restoreHistoryItem(hi);
+      updateEditMenuBar();
+      viewport.updateConsensus();
+      alignPanel.repaint();
+      alignPanel.repaint();
+   }
 
-    redoList.addElement(new Object[] {history[0], seq});
 
-      seq = (SequenceI[]) history[1];
+   // used by undo and redo
+   void restoreHistoryItem(HistoryItem hi)
+   {
+      if(hi.getType()== HistoryItem.SORT)
+      {
+           for(int i=0; i<hi.getSequences().size(); i++)
+             viewport.alignment.getSequences().setElementAt(hi.getSequences().elementAt(i), i);
+      }
+      else
+      {
+        for (int i = 0; i < hi.getSequences().size(); i++)
+        {
+          SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
+          if(restore.getLength()==0)
+          {
+            // log.System.out.println(hi.getHidden().elementAt(i));
+            restore.setSequence(hi.getHidden().elementAt(i).toString());
+            viewport.alignment.getSequences().insertElementAt(
+               restore,
+               hi.getAlignIndex(i));
+          }
+          else
+            restore.setSequence(hi.getHidden().elementAt(i).toString());
+        }
+        if(hi.getType()==HistoryItem.PASTE)
+        {
+          for(int i=viewport.alignment.getHeight()-1;i>hi.getSequences().size()-1; i--)
+            viewport.alignment.deleteSequence(i);
+        }
+      }
 
-      AlignmentAnnotation[] old = viewport.alignment.getAlignmentAnnotation();
-      viewport.setAlignment(new Alignment(seq));
-      updateEditMenuBar();
-      for (int i = 0; i < old.length; i++)
-        viewport.alignment.addAnnotation(old[i]);
+       updateEditMenuBar();
+
+       viewport.updateConsensus();
+       viewport.updateConservation();
+       alignPanel.repaint();
+   }
 
-      viewport.updateConservation();
-      viewport.updateConsensus();
-      alignPanel.repaint();
-  }
 
   public void moveSelectedSequences(boolean up)
   {
@@ -261,7 +280,7 @@ public class AlignFrame extends GAlignFrame
 
   protected void pasteThis_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("Paste");
+    addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE));
     paste(false);
   }
 
@@ -322,7 +341,7 @@ public class AlignFrame extends GAlignFrame
 
   protected void delete_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("Delete");
+    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
     if (viewport.getSelectionGroup() == null)
       return;
 
@@ -355,23 +374,6 @@ public class AlignFrame extends GAlignFrame
 
 
 
-  protected void redoMenuItem_actionPerformed(ActionEvent e)
-  {
-     Object [] history = (Object[])redoList.pop();
-     SequenceI[] seq = (SequenceI[]) history[1];
-
-     AlignmentAnnotation[] old = viewport.alignment.getAlignmentAnnotation();
-     viewport.setAlignment(new Alignment(seq));
-     for (int i = 0; i < old.length; i++)
-       viewport.alignment.addAnnotation(old[i]);
-
-     viewport.updateConservation();
-     viewport.updateConsensus();
-     updateEditMenuBar();
-     alignPanel.repaint();
-  }
-
-
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
     viewport.alignment.deleteAllGroups();
@@ -412,10 +414,11 @@ public class AlignFrame extends GAlignFrame
 
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete columns");
     ColumnSelection colSel = viewport.getColumnSelection();
     if (colSel.size() > 0)
     {
+      addHistoryItem(new HistoryItem("Remove Left",viewport.alignment,
+                                     HistoryItem.HIDE));
       int min = colSel.getMin();
       viewport.getAlignment().trimLeft(min);
       colSel.compensateForEdit(0,min);
@@ -437,10 +440,11 @@ public class AlignFrame extends GAlignFrame
 
   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete columns");
     ColumnSelection colSel = viewport.getColumnSelection();
     if (colSel.size() > 0)
     {
+      addHistoryItem(new HistoryItem("Remove Right",viewport.alignment,
+                                     HistoryItem.HIDE));
       int max = colSel.getMax();
       viewport.getAlignment().trimRight(max);
       if(viewport.getSelectionGroup()!=null)
@@ -463,7 +467,9 @@ public class AlignFrame extends GAlignFrame
 
   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete gapped columns");
+    addHistoryItem(new HistoryItem("Remove Gapped Columns",
+                                   viewport.alignment,
+                                   HistoryItem.HIDE));
     viewport.getAlignment().removeGaps();
     viewport.updateConservation();
     viewport.updateConsensus();
@@ -472,7 +478,9 @@ public class AlignFrame extends GAlignFrame
 
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("delete all gaps");
+    addHistoryItem(new HistoryItem("Remove Gaps",
+                                   viewport.alignment,
+                                   HistoryItem.HIDE));
     SequenceI current;
     int jSize;
     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
@@ -860,21 +868,21 @@ public class AlignFrame extends GAlignFrame
 
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("sort");
+    addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT));
     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
     alignPanel.repaint();
   }
 
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("sort");
+    addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT));
     AlignmentSorter.sortByID( viewport.getAlignment() );
     alignPanel.repaint();
   }
 
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
-    addHistoryItem("sort");
+    addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT));
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     AlignmentSorter.sortGroups(viewport.getAlignment());
     alignPanel.repaint();
@@ -976,7 +984,8 @@ public class AlignFrame extends GAlignFrame
     {
       public void actionPerformed(ActionEvent e)
       {
-        addHistoryItem("sort");
+        addHistoryItem(new HistoryItem("Sort", viewport.alignment,
+                                       HistoryItem.SORT));
         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());
         alignPanel.repaint();
       }