X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FCutAndPasteTransfer.java;h=2506752e4548389bcefabf63553077726168ac5a;hb=1146ae7f678127be7796772b228d5fc6823435d4;hp=9f12b873c7d7c1b573fabdc8d93bcd1dcc73ccde;hpb=dab5d2d84c25fdb88d1a454eeb263f7dc767ce17;p=jalview.git

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 9f12b87..2506752 100755
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -25,20 +25,24 @@ import java.awt.event.*;
 import jalview.datamodel.*;
 import jalview.io.*;
 
-public class CutAndPasteTransfer extends Panel implements ActionListener, MouseListener
+public class CutAndPasteTransfer
+    extends Panel implements ActionListener, MouseListener
 {
   boolean pdbImport = false;
   boolean treeImport = false;
   boolean annotationImport = false;
-  Sequence seq;
+  Sequence  seq;
   AlignFrame alignFrame;
 
   public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
   {
-    try {
-        jbInit();
-    } catch (Exception e) {
-        e.printStackTrace();
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
     }
 
     this.alignFrame = alignFrame;
@@ -81,15 +85,20 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, MouseL
     addSequences.setVisible(false);
   }
 
-
   public void actionPerformed(ActionEvent evt)
   {
-    if(evt.getSource()==accept)
+    if (evt.getSource() == accept)
+    {
       ok(true);
-    else if(evt.getSource() == addSequences)
+    }
+    else if (evt.getSource() == addSequences)
+    {
       ok(false);
-    else if(evt.getSource() == cancel)
+    }
+    else if (evt.getSource() == cancel)
+    {
       cancel();
+    }
   }
 
   protected void ok(boolean newWindow)
@@ -97,35 +106,53 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, MouseL
     String text = getText();
     int length = text.length();
     textarea.append("\n");
-    if(textarea.getText().length()==length)
+    if (textarea.getText().length() == length)
     {
-      String warning = "\n\n#################################################\n"
-          +"WARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n"
-          +"\nCAN'T INPUT FULL ALIGNMENT"
-          +"\n\nYOU MUST DELETE THIS WARNING TO CONTINUE"
-          +"\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE"
-          +"\n#################################################\n";
-      textarea.setText(text.substring(0, text.length()-warning.length())
-          +warning);
+      String warning =
+          "\n\n#################################################\n"
+          + "WARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n"
+          + "\nCAN'T INPUT FULL ALIGNMENT"
+          + "\n\nYOU MUST DELETE THIS WARNING TO CONTINUE"
+          + "\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE"
+          + "\n#################################################\n";
+      textarea.setText(text.substring(0, text.length() - warning.length())
+                       + warning);
 
       textarea.setCaretPosition(text.length());
     }
 
-    if(pdbImport)
+    if (pdbImport)
     {
-      new MCview.AppletPDBViewer(text, AppletFormatAdapter.PASTE,
-                                 seq,
-                                 alignFrame.getSeqcanvas());
+      PDBEntry pdb = new PDBEntry();
+      pdb.setFile(text);
+
+      if ( alignFrame.alignPanel.av.applet.jmolAvailable )
+        new jalview.appletgui.AppletJmol(pdb,
+                                         new Sequence[]
+                                         {seq},
+                                         alignFrame.alignPanel,
+                                         AppletFormatAdapter.PASTE);
+      else
+
+        new MCview.AppletPDBViewer(pdb,
+                                   new Sequence[]
+                                   {seq},
+                                   alignFrame.alignPanel,
+                                   AppletFormatAdapter.PASTE);
+
     }
-    else if(treeImport)
+    else if (treeImport)
     {
-      try{
+      try
+      {
         jalview.io.NewickFile fin = new jalview.io.NewickFile(textarea.getText(),
             "Paste");
 
         fin.parse();
-        if(fin.getTree()!=null)
+        if (fin.getTree() != null)
+        {
           alignFrame.loadTree(fin, "Pasted tree file");
+        }
 
       }
       catch (Exception ex)
@@ -134,7 +161,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, MouseL
         return;
       }
     }
-    else if(annotationImport)
+    else if (annotationImport)
     {
       if (new AnnotationFile().readAnnotationFile(
           alignFrame.viewport.alignment, textarea.getText(),
@@ -150,23 +177,25 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, MouseL
                                      jalview.io.AppletFormatAdapter.PASTE);
       }
     }
-    else if(alignFrame!=null)
+    else if (alignFrame != null)
     {
       Alignment al = null;
 
-      String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);
-      try{
-        al = new AppletFormatAdapter().readFile(text, AppletFormatAdapter.PASTE, format);
-      }catch(java.io.IOException ex)
+      String format = new IdentifyFile().Identify(text,
+                                                  AppletFormatAdapter.PASTE);
+      try
+      {
+        al = new AppletFormatAdapter().readFile(text, AppletFormatAdapter.PASTE,
+                                                format);
+      }
+      catch (java.io.IOException ex)
       {
         ex.printStackTrace();
       }
 
-
-
       if (al != null)
       {
-        if(newWindow)
+        if (newWindow)
         {
           AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
                                          "Cut & Paste input - " + format,
@@ -174,23 +203,33 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, MouseL
           af.statusBar.setText("Successfully pasted alignment file");
         }
         else
+        {
           alignFrame.addSequences(al.getSequencesArray());
+        }
       }
     }
 
-   if(this.getParent() instanceof Frame)
-    ((Frame)this.getParent()).setVisible(false);
-   else
-     ((Dialog)this.getParent()).setVisible(false);
+    if (this.getParent() instanceof Frame)
+    {
+      ( (Frame)this.getParent()).setVisible(false);
+    }
+    else
+    {
+      ( (Dialog)this.getParent()).setVisible(false);
+    }
   }
 
   protected void cancel()
   {
     textarea.setText("");
-    if(this.getParent() instanceof Frame)
-     ((Frame)this.getParent()).setVisible(false);
+    if (this.getParent() instanceof Frame)
+    {
+      ( (Frame)this.getParent()).setVisible(false);
+    }
     else
-     ((Dialog)this.getParent()).setVisible(false);
+    {
+      ( (Dialog)this.getParent()).setVisible(false);
+    }
   }
 
   protected TextArea textarea = new TextArea();
@@ -201,29 +240,40 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, MouseL
   protected Panel buttonPanel = new Panel();
   BorderLayout borderLayout1 = new BorderLayout();
 
-
-  private void jbInit() throws Exception {
-      textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
-      textarea.setText("Paste your alignment file here");
-      textarea.addMouseListener(this);
-      this.setLayout(borderLayout1);
-      accept.addActionListener(this);
-      addSequences.addActionListener(this);
-      cancel.addActionListener(this);
-      this.add(buttonPanel, BorderLayout.SOUTH);
-      buttonPanel.add(accept, null);
-      buttonPanel.add(addSequences);
-      buttonPanel.add(cancel, null);
-      this.add(textarea, java.awt.BorderLayout.CENTER);
+  private void jbInit()
+      throws Exception
+  {
+    textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
+    textarea.setText("Paste your alignment file here");
+    textarea.addMouseListener(this);
+    this.setLayout(borderLayout1);
+    accept.addActionListener(this);
+    addSequences.addActionListener(this);
+    cancel.addActionListener(this);
+    this.add(buttonPanel, BorderLayout.SOUTH);
+    buttonPanel.add(accept, null);
+    buttonPanel.add(addSequences);
+    buttonPanel.add(cancel, null);
+    this.add(textarea, java.awt.BorderLayout.CENTER);
   }
 
-  public void mousePressed(MouseEvent evt) {
-      if (textarea.getText().startsWith("Paste your")) {
-          textarea.setText("");
-     }
+  public void mousePressed(MouseEvent evt)
+  {
+    if (textarea.getText().startsWith("Paste your"))
+    {
+      textarea.setText("");
+    }
   }
-  public void mouseReleased(MouseEvent evt){}
-  public void mouseClicked(MouseEvent evt){}
-  public void mouseEntered(MouseEvent evt){}
-  public void mouseExited(MouseEvent evt){}
+
+  public void mouseReleased(MouseEvent evt)
+  {}
+
+  public void mouseClicked(MouseEvent evt)
+  {}
+
+  public void mouseEntered(MouseEvent evt)
+  {}
+
+  public void mouseExited(MouseEvent evt)
+  {}
 }