From 2f8b445a1c306a3566454bf5fcf87db6b22da683 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 10 Feb 2005 17:52:35 +0000
Subject: [PATCH] Cut and paste implemented

---
 src/jalview/gui/AlignFrame.java    |  131 +++++++++++++++++++++++++++++++++---
 src/jalview/jbgui/GAlignFrame.java |   86 +++++++++++++++++++++++
 2 files changed, 206 insertions(+), 11 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index f3d0d99..83f7ba0 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -23,7 +23,8 @@ import java.awt.print.*;
 import javax.swing.*;
 import javax.swing.event.*;
 import java.util.*;
-import jalview.datamodel.SequenceI;
+import  java.awt.datatransfer.*;
+
 
 public class AlignFrame extends GAlignFrame
 {
@@ -38,7 +39,20 @@ public class AlignFrame extends GAlignFrame
     fontNameMenuItem.setText(viewport.getFont().getName());
     fontSizeMenuItem.setText(viewport.getFont().getSize()+"");
 
-    AlignmentUtil.fetchSequenceFeatures(al, alignPanel);
+    addInternalFrameListener(new InternalFrameAdapter()
+   {
+     public void internalFrameActivated(InternalFrameEvent evt)
+     {
+          javax.swing.SwingUtilities.invokeLater(new Runnable()
+          {
+            public void run()
+            {      alignPanel.requestFocus();    }
+          });
+
+     }
+   });
+
+   AlignmentUtil.fetchSequenceFeatures(al, alignPanel);
   }
 
   protected void saveAs_actionPerformed(ActionEvent e)
@@ -183,6 +197,110 @@ public class AlignFrame extends GAlignFrame
       alignPanel.RefreshPanels();
   }
 
+  protected void copy_actionPerformed(ActionEvent e)
+  {
+   if(viewport.getRubberbandGroup()==null)
+     return;
+
+   SequenceGroup sg = viewport.getRubberbandGroup();
+
+     Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+     StringBuffer buffer= new StringBuffer();
+
+       for(int i=0; i<sg.getSize(); i++)
+       {
+         SequenceI seq = sg.getSequenceAt(i);
+         buffer.append( seq.getName()+"\t"+seq.getStart() +"\t"+seq.getEnd()+"\t"
+                        +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
+       }
+     c.setContents( new StringSelection( buffer.toString()) , null ) ;
+
+  }
+
+
+  protected void pasteNew_actionPerformed(ActionEvent e)
+  {
+    paste(true);
+  }
+
+  protected void pasteThis_actionPerformed(ActionEvent e)
+  {
+    paste(false);
+  }
+
+  void paste(boolean newAlignment)
+  {
+    try{
+      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+      Transferable contents = c.getContents(this);
+      if (contents == null)
+        return;
+
+      String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
+      StringTokenizer st = new StringTokenizer(str);
+      ArrayList seqs = new ArrayList();
+      while (st.hasMoreElements())
+      {
+        String name = st.nextToken();
+        int start = Integer.parseInt(st.nextToken());
+        int end = Integer.parseInt(st.nextToken());
+
+        Sequence sequence = new Sequence(name, st.nextToken(), start, end);
+        if(!newAlignment)
+          viewport.alignment.addSequence(sequence);
+        else
+          seqs.add(sequence);
+      }
+
+      if(newAlignment)
+      {
+        SequenceI[] newSeqs = new SequenceI[seqs.size()];
+        seqs.toArray(newSeqs);
+        AlignFrame af = new AlignFrame(new Alignment(newSeqs));
+        int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;
+        if (newHeight > 500)
+          newHeight = 500;
+        Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
+      }
+      else
+      {
+        viewport.setEndSeq(viewport.alignment.getHeight());
+        viewport.alignment.getWidth();
+        alignPanel.RefreshPanels();
+      }
+
+    }catch(Exception ex){}// could be anything being pasted in here
+
+  }
+
+
+  protected void cut_actionPerformed(ActionEvent e)
+  {
+    copy_actionPerformed(null);
+    delete_actionPerformed(null);
+  }
+
+  protected void delete_actionPerformed(ActionEvent e)
+  {
+    if (viewport.getRubberbandGroup() == null)
+      return;
+
+     SequenceGroup sg = viewport.getRubberbandGroup();
+     for (int i=0;i < sg.sequences.size(); i++)
+             viewport.getAlignment().deleteSequence(sg.getSequenceAt(i));
+
+     viewport.alignment.deleteGroup(sg);
+     viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
+     if(viewport.getAlignment().getHeight()<1)
+     try
+     {
+       this.setClosed(true);
+     }catch(Exception ex){}
+     alignPanel.RefreshPanels();
+
+  }
+
+
 
   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
@@ -904,13 +1022,4 @@ public class AlignFrame extends GAlignFrame
          g.drawString("Clustal Alignment Web Service running", 30,30);
        }
   }
-
-
-  public void doKeyPressed(KeyEvent evt)
-  {
-    if(evt.isControlDown() && evt.getKeyChar()=='f')
-      findMenuItem_actionPerformed(null);
-  }
-
-
 }
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 764f5cf..5c6494e 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -83,6 +83,12 @@ public class GAlignFrame extends JInternalFrame
   protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
   JMenuItem deleteGroups = new JMenuItem();
+  JMenuItem delete = new JMenuItem();
+  JMenuItem copy = new JMenuItem();
+  JMenuItem cut = new JMenuItem();
+  JMenu jMenu1 = new JMenu();
+  JMenuItem pasteNew = new JMenuItem();
+  JMenuItem pasteThis = new JMenuItem();
   public GAlignFrame()
   {
 
@@ -619,6 +625,52 @@ public class GAlignFrame extends JInternalFrame
         deleteGroups_actionPerformed(e);
       }
     });
+    copy.setText("Copy");
+    copy.setMnemonic(KeyEvent.VK_C);
+
+    copy.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        copy_actionPerformed(e);
+      }
+    });
+   // pasteNew.setText("Paste (as new alignment)");
+    cut.setText("Cut");
+    cut.setMnemonic(KeyEvent.VK_X);
+    cut.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cut_actionPerformed(e);
+      }
+    });
+    delete.setText("Delete");
+    delete.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        delete_actionPerformed(e);
+      }
+    });
+    jMenu1.setMnemonic('V');
+    jMenu1.setText("Paste");
+    pasteNew.setText("as new alignment");
+    pasteNew.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pasteNew_actionPerformed(e);
+      }
+    });
+    pasteThis.setText("add to this alignment");
+    pasteThis.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pasteThis_actionPerformed(e);
+      }
+    });
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
@@ -633,6 +685,11 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(printMenuItem);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
+    editMenu.add(copy);
+    editMenu.add(jMenu1);
+    editMenu.add(cut);
+    editMenu.add(delete);
+    editMenu.addSeparator();
     editMenu.add(undoMenuItem);
     editMenu.add(redoMenuItem);
     editMenu.addSeparator();
@@ -693,6 +750,8 @@ public class GAlignFrame extends JInternalFrame
     alignMenu.add(clustalAlignMenuItem);
     alignMenu.add(pdbTest);
     this.getContentPane().add(statusBar, BorderLayout.SOUTH);
+    jMenu1.add(pasteNew);
+    jMenu1.add(pasteThis);
   }
 
   protected void saveAs_actionPerformed(ActionEvent e)
@@ -1007,5 +1066,32 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
+ protected void copy_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+
+  protected void cut_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  protected void delete_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  protected void pasteNew_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  protected void pasteThis_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+
 
 }
-- 
1.7.10.2