X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=ec75ee5cb8397f4eee494846054f5bebf4e5e848;hb=57d6a9e73c82ce2663a56dde4e70d997198f9e12;hp=8af52d0e4dcc028acb9f6b9c9cd602aa6463400f;hpb=a9770d55354408173fddcf91fb90059c73497448;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8af52d0..ec75ee5 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -16,14 +16,18 @@ import jalview.schemes.*;
 import jalview.datamodel.*;
 import jalview.analysis.*;
 import jalview.io.*;
-import java.awt.event.*;
+import MCview.*;
 import java.awt.*;
+import java.awt.event.*;
+import java.awt.print.*;
 import javax.swing.*;
+import javax.swing.event.*;
+import java.util.*;
 
 public class AlignFrame extends GAlignFrame
 {
-  AlignmentPanel alignPanel;
-  AlignViewport viewport;
+  final AlignmentPanel alignPanel;
+  final AlignViewport viewport;
   public AlignFrame(AlignmentI al)
   {
     super();
@@ -67,15 +71,42 @@ public class AlignFrame extends GAlignFrame
 
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    HTMLOutput htmlOutput = new HTMLOutput(viewport.getAlignment(), alignPanel.seqPanel.getColourScheme());
+    HTMLOutput htmlOutput = new HTMLOutput(viewport);
     htmlOutput = null;
   }
 
-  public void saveAsPostscriptMenuItem_actionPerformed(ActionEvent e)
+  public void printMenuItem_actionPerformed(ActionEvent e)
+  {
+    //Putting in a thread avoids Swing painting problems
+    PrintThread thread = new PrintThread();
+    thread.start();
+  }
+
+  class PrintThread extends Thread
   {
+    public void run()
+    {
+      PrinterJob printJob = PrinterJob.getPrinterJob();
+      PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+      printJob.setPrintable(alignPanel, pf);
+      if (printJob.printDialog())
+      {
+        try
+        {
+          printJob.print();
+        }
+        catch (Exception PrintException)
+        {
+          PrintException.printStackTrace();
+        }
+      }
+    }
 
   }
 
+
+
+
   public void closeMenuItem_actionPerformed(ActionEvent e)
   {
     try{
@@ -83,16 +114,93 @@ public class AlignFrame extends GAlignFrame
     }catch(Exception ex){}
   }
 
-  public void groupsMenuItem_actionPerformed(ActionEvent e)
+  ArrayList  historyList = new ArrayList();
+  ArrayList redoList = new ArrayList();
+
+  void updateEditMenuBar()
   {
+    if(historyList.size()>0)
+     {
+       undoMenuItem.setEnabled(true);
+       Object [] history = (Object[])historyList.get(0);
+       undoMenuItem.setText("Undo "+history[0]);
+     }
+    else
+    {
+      undoMenuItem.setEnabled(false);
+      undoMenuItem.setText("Undo");
+    }
 
+    if(redoList.size()>0)
+     {
+       redoMenuItem.setEnabled(true);
+       Object [] history = (Object[])redoList.get(0);
+       redoMenuItem.setText("Redo "+history[0]);
+     }
+    else
+    {
+      redoMenuItem.setEnabled(false);
+      redoMenuItem.setText("Redo");
+    }
   }
 
-  public void groupEditingMenuItem_actionPerformed(ActionEvent e)
+  public void addHistoryItem(String type)
   {
+    // must make sure we add new sequence objects her, not refs to the existing sequences
+    redoList.clear();
+    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());
+    }
 
+    historyList.add(0, new Object[]{type,  seq} );
+    updateEditMenuBar();
   }
 
+  protected void undoMenuItem_actionPerformed(ActionEvent e)
+  {
+    Object [] history = (Object[])historyList.remove(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());
+    }
+    /////////
+
+    redoList.add(0, new Object[] {history[0], seq});
+
+      seq = (SequenceI[]) history[1];
+      viewport.setAlignment( new Alignment(seq) );
+      updateEditMenuBar();
+      alignPanel.RefreshPanels();
+  }
+
+
+  protected void redoMenuItem_actionPerformed(ActionEvent e)
+  {
+     Object [] history = (Object[])redoList.remove(0);
+     SequenceI[] seq = (SequenceI[]) history[1];
+     viewport.setAlignment( new Alignment(seq) );
+     updateEditMenuBar();
+     alignPanel.RefreshPanels();
+  }
+
+
+  public void groupsMenuItem_actionPerformed(ActionEvent e)
+  {
+    GroupEditor geditor = new GroupEditor(viewport, alignPanel);
+    JInternalFrame frame = new JInternalFrame();
+    frame.setContentPane(geditor);
+    Desktop.addInternalFrame(frame, "Group editor", 710, 410);
+    frame.setResizable(false);
+  }
+
+
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     Selection sel = viewport.getSelection();
@@ -120,39 +228,6 @@ public class AlignFrame extends GAlignFrame
     PaintRefresher.Refresh(null);
   }
 
-  public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)
-  {
-    for (int i=0;i < viewport.getSelection().size(); i++)
-            viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));
-
-    viewport.getSelection().clear();
-    viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
-    alignPanel.RefreshPanels();
-  }
-
-  public void moveSelectedMenuItem_actionPerformed(ActionEvent e)
-  {
-    copySelectedMenuItem_actionPerformed(null);
-    deleteSelectedMenuItem_actionPerformed(null);
-    alignPanel.repaint();
-  }
-
-  public void copySelectedMenuItem_actionPerformed(ActionEvent e)
-  {
-    if(viewport.getSelection().size()==0)
-      return;
-
-   SequenceI[] s = new Sequence[viewport.getSelection().size()];
-   for (int i=0; i < viewport.getSelection().size(); i++) {
-     s[i] = new Sequence(viewport.getSelection().sequenceAt(i));
-    }
-    AlignFrame af = new AlignFrame(new Alignment(s));
-
-    int newHeight = s.length * af.viewport.getCharHeight() + 200;
-    if(newHeight>500)
-      newHeight=500;
-    Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);
-  }
 
   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
   {
@@ -162,6 +237,7 @@ public class AlignFrame extends GAlignFrame
 
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
+    addHistoryItem("delete columns");
     ColumnSelection colSel = viewport.getColumnSelection();
     if (colSel.size() > 0)
     {
@@ -174,6 +250,7 @@ public class AlignFrame extends GAlignFrame
 
   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
+    addHistoryItem("delete columns");
     ColumnSelection colSel = viewport.getColumnSelection();
     if (colSel.size() > 0)
     {
@@ -188,12 +265,14 @@ public class AlignFrame extends GAlignFrame
 
   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
+    addHistoryItem("delete gapped columns");
     viewport.getAlignment().removeGaps();
     alignPanel.RefreshPanels();
   }
 
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
+    addHistoryItem("delete all gaps");
     SequenceI current;
     int jSize;
     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
@@ -214,24 +293,36 @@ public class AlignFrame extends GAlignFrame
 
   public void setGapCharMenuItem_actionPerformed(ActionEvent e)
   {
-    String thisChar = "-";
-    String nextChar = ".";
-    if(viewport.getGapCharacter().equals("-"))
+    char thisChar = '-';
+    char nextChar = '.';
+    if(viewport.getGapCharacter()=='-')
     {
-      thisChar = ".";
-      nextChar = "-";
+      thisChar = '.';
+      nextChar = '-';
     }
     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
     viewport.setGapCharacter(thisChar);
+    alignPanel.RefreshPanels();
+  }
+
+  public void findMenuItem_actionPerformed(ActionEvent e)
+  {
+    JOptionPane op = new JOptionPane();
+    JInternalFrame frame =  op.createInternalFrame(this, "Find");
+    Finder finder = new Finder(viewport, alignPanel, frame);
+    frame.setContentPane(finder);
+    frame.setSize(300,110);
+    frame.setVisible(true);
   }
 
 
+
   public void fontNameMenuItem_actionPerformed(ActionEvent e)
   {
     String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 
 
-    String selection = JOptionPane.showInputDialog(this,
+    String selection = JOptionPane.showInternalInputDialog(this,
                                 "Select font",
                                 "Font selection",
                                 JOptionPane.QUESTION_MESSAGE,
@@ -247,7 +338,7 @@ public class AlignFrame extends GAlignFrame
 
   public void fontSizeMenuItem_actionPerformed(ActionEvent e)
   {
-    String selection = JOptionPane.showInputDialog(this,
+    String selection = JOptionPane.showInternalInputDialog(this,
                                 "Select font size",
                                 "Font size",
                                 JOptionPane.QUESTION_MESSAGE,
@@ -262,7 +353,7 @@ public class AlignFrame extends GAlignFrame
 
   public void fontStyleMenuItem_actionPerformed(ActionEvent e)
   {
-    String selection = JOptionPane.showInputDialog(this,
+    String selection = JOptionPane.showInternalInputDialog(this,
                                 "Select font style",
                                 "Font style",
                                 JOptionPane.QUESTION_MESSAGE,
@@ -278,8 +369,8 @@ public class AlignFrame extends GAlignFrame
 
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setColourText( colourTextMenuItem.isSelected() );
-    alignPanel.RefreshPanels();
+      viewport.setColourText( colourTextMenuItem.isSelected() );
+      alignPanel.RefreshPanels();
   }
 
   void SetFont()
@@ -297,6 +388,13 @@ public class AlignFrame extends GAlignFrame
 
   }
 
+  protected void wrapMenuItem_actionPerformed(ActionEvent e)
+  {
+    viewport.setWrapAlignment( wrapMenuItem.isSelected() );
+    alignPanel.RefreshPanels();
+  }
+
+
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
@@ -310,6 +408,13 @@ public class AlignFrame extends GAlignFrame
   }
 
 
+  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+  {
+    viewport.setRenderGaps(renderGapsMenuItem.isSelected());
+    alignPanel.RefreshPanels();
+  }
+
+
   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
   {
     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
@@ -336,76 +441,108 @@ public class AlignFrame extends GAlignFrame
 
   }catch(java.lang.OutOfMemoryError ex)
    {
-     JOptionPane.showMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!",
+     JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
+                                   +"\nTry reducing the font size.",
                                    "Out of memory", JOptionPane.WARNING_MESSAGE);
    }
 
 
   }
 
+  protected void noColourmenuItem_actionPerformed(ActionEvent e)
+  {
+    viewport.setGlobalColourScheme( null );
+    alignPanel.setColourScheme();
+  }
+
 
   public void clustalColour_actionPerformed(ActionEvent e)
   {
-   // alignPanel.setColourScheme( new ClustalxColourScheme() );
+    viewport.setGlobalColourScheme(new ClustalxColourScheme( ));
+    alignPanel.setColourScheme(  );
   }
 
   public void zappoColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new ZappoColourScheme() );
+    viewport.setGlobalColourScheme(new ZappoColourScheme() );
+    alignPanel.setColourScheme(  );
   }
 
   public void taylorColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new TaylorColourScheme() );
+    viewport.setGlobalColourScheme(new TaylorColourScheme() );
+    alignPanel.setColourScheme(  );
   }
 
 
   public void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new HydrophobicColourScheme() );
+    viewport.setGlobalColourScheme( new HydrophobicColourScheme() );
+    alignPanel.setColourScheme( );
   }
 
   public void helixColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.seqPanel.setColourScheme( new HelixColourScheme() );
+    viewport.setGlobalColourScheme( new HelixColourScheme()  );
+    alignPanel.setColourScheme();
   }
 
+
   public void strandColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new StrandColourScheme() );
+    viewport.setGlobalColourScheme(new StrandColourScheme() );
+    alignPanel.setColourScheme(  );
   }
 
+
   public void turnColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new TurnColourScheme() );
+    viewport.setGlobalColourScheme(new TurnColourScheme() );
+    alignPanel.setColourScheme(  );
   }
 
+
   public void buriedColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new BuriedColourScheme() );
+    viewport.setGlobalColourScheme( new BuriedColourScheme() );
+    alignPanel.setColourScheme( );
   }
 
-  public void conservationColour_actionPerformed(ActionEvent e)
+
+  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
   {
+    viewport.setConservationSelected(conservationMenuItem.isSelected());
+    alignPanel.setColourScheme();
 
+    if(conservationMenuItem.isSelected())
+    {
+      SliderPanel sp = new SliderPanel(alignPanel, 30, true, viewport.getGlobalColourScheme());
+      JInternalFrame frame = new JInternalFrame();
+      frame.setContentPane(sp);
+      Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400, 90);
+      frame.setMaximizable(false);
+    }
   }
 
-  public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
- {
-
- }
 
-
-  public void abovePIDColour_actionPerformed(ActionEvent e)
+  public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new PIDColourScheme() );
+    if(abovePIDThreshold.isSelected())
+    {
+      SliderPanel sp = new SliderPanel(alignPanel, 70, false,
+                                       viewport.getGlobalColourScheme());
+      JInternalFrame frame = new JInternalFrame();
+      frame.setContentPane(sp);
+      Desktop.addInternalFrame(frame, "Percentage Identity Threshold", 400, 90);
+      frame.setMaximizable(false);
+    }
   }
 
 
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
     JInternalFrame frame = new JInternalFrame();
-    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel.seqPanel );
+    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
     frame.setContentPane(chooser);
     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
     frame.setResizable(false);
@@ -415,43 +552,51 @@ public class AlignFrame extends GAlignFrame
 
   public void PIDColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new PIDColourScheme() );
+    viewport.setGlobalColourScheme( new PIDColourScheme() );
+    alignPanel.setColourScheme( );
   }
 
+
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) );
+    viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );
+    alignPanel.setColourScheme();
   }
 
 
+
   protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
   {
-    ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() );
+    ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() );
     Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
   }
 
 
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
+    addHistoryItem("sort");
     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
     alignPanel.RefreshPanels();
   }
 
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
+    addHistoryItem("sort");
     AlignmentSorter.sortByID( viewport.getAlignment() );
     alignPanel.RefreshPanels();
   }
 
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
-    AlignmentSorter.sortGroups(viewport.getAlignment());
+    addHistoryItem("sort");
+    AlignmentSorter.sortByGroup(viewport.getAlignment());
     AlignmentSorter.sortGroups(viewport.getAlignment());
     alignPanel.RefreshPanels();
   }
 
   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
   {
+    addHistoryItem("sort");
     if(viewport.getCurrentTree()==null)
       return;
 
@@ -467,7 +612,7 @@ public class AlignFrame extends GAlignFrame
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
     if(viewport.getSelection().size()<2)
-      JOptionPane.showMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
+      JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
     else
     {
       JInternalFrame frame = new JInternalFrame();
@@ -481,17 +626,25 @@ public class AlignFrame extends GAlignFrame
     if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
        || viewport.getAlignment().getHeight()<4)
     {
-      JOptionPane.showMessageDialog(this, "Principal component analysis must take\n"
+      JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
                                     +"at least 4 input sequences.",
                                     "Sequence selection insufficient",
                                     JOptionPane.WARNING_MESSAGE);
       return;
     }
 
-    PCAPanel pcaPanel = new PCAPanel(viewport, null);
-    JInternalFrame frame = new JInternalFrame();
-    frame.setContentPane(pcaPanel);
-    Desktop.addInternalFrame(frame, "Principal component analysis", 400,400);
+    try{
+      PCAPanel pcaPanel = new PCAPanel(viewport, null);
+      JInternalFrame frame = new JInternalFrame();
+      frame.setContentPane(pcaPanel);
+      Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
+   }catch(java.lang.OutOfMemoryError ex)
+   {
+     JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
+                                   "Out of memory", JOptionPane.WARNING_MESSAGE);
+   }
+
+
   }
 
   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
@@ -539,10 +692,51 @@ public class AlignFrame extends GAlignFrame
 
   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
   {
-    JOptionPane.showMessageDialog(this, "Jalview is currently being reengineered"
+    JOptionPane.showInternalMessageDialog(this, "Jalview is currently being reengineered"
                                   +"\nwithin the Barton Group, Dundee University."
                                   +"\nThis will be available as a web service 2005",
                                   "Web service", JOptionPane.INFORMATION_MESSAGE);
   }
 
+  public void pdbTest_actionPerformed(ActionEvent e)
+  {
+   String reply = JOptionPane.showInternalInputDialog(this, "Enter pdb code", "PDB test viewer", JOptionPane.QUESTION_MESSAGE);
+
+   String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";
+   if (reply.length()>1)
+     url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;
+
+   try
+   {
+     PDBfile pdb = new PDBfile(url,
+                               "URL");
+    Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);
+    seq.setPDBfile(pdb);
+     ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;
+     ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;
+  // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();
+
+     rotCanvas rc = new rotCanvas(pdb);
+     JInternalFrame frame = new JInternalFrame();
+     frame.setContentPane(rc);
+     Desktop.addInternalFrame(frame, url, 400,400);
+   }
+   catch (Exception ex)
+   {
+     ex.printStackTrace();
+   }
+
+  }
+
+
+  public void doKeyPressed(KeyEvent evt)
+  {
+
+    System.out.println(evt.getKeyChar());
+    if(evt.isControlDown() && evt.getKeyChar()=='f')
+      findMenuItem_actionPerformed(null);
+
+  }
+
+
 }