X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FCutAndPasteTransfer.java;h=f4b0a1de76d9526544c8ba4143db9f2d90f82a50;hb=1660a4fe03b8dda74b008ae4de2d804f8044a463;hp=b6e74603d82bd2fb2f573878b544bbdf54d247c9;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index b6e7460..f4b0a1d 100755
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -1,265 +1,278 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * 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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
-
-public class CutAndPasteTransfer
-    extends Panel implements ActionListener, MouseListener
-{
-  boolean pdbImport = false;
-  boolean treeImport = false;
-  boolean annotationImport = false;
-  Sequence seq;
-  AlignFrame alignFrame;
-
-  public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-
-    this.alignFrame = alignFrame;
-
-    if (!forImport)
-    {
-      buttonPanel.setVisible(false);
-    }
-  }
-
-  public String getText()
-  {
-    return textarea.getText();
-  }
-
-  public void setText(String text)
-  {
-    textarea.setText(text);
-  }
-
-  public void setPDBImport(Sequence seq)
-  {
-    this.seq = seq;
-    accept.setLabel("Accept");
-    addSequences.setVisible(false);
-    pdbImport = true;
-  }
-
-  public void setTreeImport()
-  {
-    treeImport = true;
-    accept.setLabel("Accept");
-    addSequences.setVisible(false);
-  }
-
-  public void setAnnotationImport()
-  {
-    annotationImport = true;
-    accept.setLabel("Accept");
-    addSequences.setVisible(false);
-  }
-
-  public void actionPerformed(ActionEvent evt)
-  {
-    if (evt.getSource() == accept)
-    {
-      ok(true);
-    }
-    else if (evt.getSource() == addSequences)
-    {
-      ok(false);
-    }
-    else if (evt.getSource() == cancel)
-    {
-      cancel();
-    }
-  }
-
-  protected void ok(boolean newWindow)
-  {
-    String text = getText();
-    int length = text.length();
-    textarea.append("\n");
-    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);
-
-      textarea.setCaretPosition(text.length());
-    }
-
-    if (pdbImport)
-    {
-      new MCview.AppletPDBViewer(text, AppletFormatAdapter.PASTE,
-                                 seq,
-                                 alignFrame.getSeqcanvas());
-    }
-    else if (treeImport)
-    {
-      try
-      {
-        jalview.io.NewickFile fin = new jalview.io.NewickFile(textarea.getText(),
-            "Paste");
-
-        fin.parse();
-        if (fin.getTree() != null)
-        {
-          alignFrame.loadTree(fin, "Pasted tree file");
-        }
-
-      }
-      catch (Exception ex)
-      {
-        textarea.setText("Could not parse Newick file!\n" + ex);
-        return;
-      }
-    }
-    else if (annotationImport)
-    {
-      if (new AnnotationFile().readAnnotationFile(
-          alignFrame.viewport.alignment, textarea.getText(),
-          jalview.io.AppletFormatAdapter.PASTE))
-      {
-        alignFrame.alignPanel.fontChanged();
-        alignFrame.alignPanel.setScrollValues(0, 0);
-
-      }
-      else
-      {
-        alignFrame.parseFeaturesFile(textarea.getText(),
-                                     jalview.io.AppletFormatAdapter.PASTE);
-      }
-    }
-    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)
-      {
-        ex.printStackTrace();
-      }
-
-      if (al != null)
-      {
-        if (newWindow)
-        {
-          AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
-                                         "Cut & Paste input - " + format,
-                                         false);
-          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);
-    }
-  }
-
-  protected void cancel()
-  {
-    textarea.setText("");
-    if (this.getParent() instanceof Frame)
-    {
-      ( (Frame)this.getParent()).setVisible(false);
-    }
-    else
-    {
-      ( (Dialog)this.getParent()).setVisible(false);
-    }
-  }
-
-  protected TextArea textarea = new TextArea();
-  Button accept = new Button("New Window");
-  Button addSequences = new Button("Add to Current Alignment");
-  Button cancel = new Button("Close");
-
-  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);
-  }
-
-  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)
-  {}
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+import jalview.io.*;
+
+public class CutAndPasteTransfer extends Panel implements ActionListener,
+        MouseListener
+{
+  boolean pdbImport = false;
+
+  boolean treeImport = false;
+
+  boolean annotationImport = false;
+
+  Sequence seq;
+
+  AlignFrame alignFrame;
+
+  public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    this.alignFrame = alignFrame;
+
+    if (!forImport)
+    {
+      buttonPanel.setVisible(false);
+    }
+  }
+
+  public String getText()
+  {
+    return textarea.getText();
+  }
+
+  public void setText(String text)
+  {
+    textarea.setText(text);
+  }
+
+  public void setPDBImport(Sequence seq)
+  {
+    this.seq = seq;
+    accept.setLabel("Accept");
+    addSequences.setVisible(false);
+    pdbImport = true;
+  }
+
+  public void setTreeImport()
+  {
+    treeImport = true;
+    accept.setLabel("Accept");
+    addSequences.setVisible(false);
+  }
+
+  public void setAnnotationImport()
+  {
+    annotationImport = true;
+    accept.setLabel("Accept");
+    addSequences.setVisible(false);
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    if (evt.getSource() == accept)
+    {
+      ok(true);
+    }
+    else if (evt.getSource() == addSequences)
+    {
+      ok(false);
+    }
+    else if (evt.getSource() == cancel)
+    {
+      cancel();
+    }
+  }
+
+  protected void ok(boolean newWindow)
+  {
+    String text = getText();
+    int length = text.length();
+    textarea.append("\n");
+    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);
+
+      textarea.setCaretPosition(text.length());
+    }
+
+    if (pdbImport)
+    {
+      PDBEntry pdb = new PDBEntry();
+      pdb.setFile(text);
+
+      if (alignFrame.alignPanel.av.applet.jmolAvailable)
+        new jalview.appletgui.AppletJmol(pdb, new Sequence[]
+        { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+      else
+
+        new MCview.AppletPDBViewer(pdb, new Sequence[]
+        { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
+
+    }
+    else if (treeImport)
+    {
+      try
+      {
+        jalview.io.NewickFile fin = new jalview.io.NewickFile(textarea
+                .getText(), "Paste");
+
+        fin.parse();
+        if (fin.getTree() != null)
+        {
+          alignFrame.loadTree(fin, "Pasted tree file");
+        }
+
+      } catch (Exception ex)
+      {
+        textarea.setText("Could not parse Newick file!\n" + ex);
+        return;
+      }
+    }
+    else if (annotationImport)
+    {
+      if (new AnnotationFile().readAnnotationFile(
+              alignFrame.viewport.alignment, textarea.getText(),
+              jalview.io.AppletFormatAdapter.PASTE))
+      {
+        alignFrame.alignPanel.fontChanged();
+        alignFrame.alignPanel.setScrollValues(0, 0);
+
+      }
+      else
+      {
+        alignFrame.parseFeaturesFile(textarea.getText(),
+                jalview.io.AppletFormatAdapter.PASTE);
+      }
+    }
+    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)
+      {
+        ex.printStackTrace();
+      }
+
+      if (al != null)
+      {
+        if (newWindow)
+        {
+          AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
+                  "Cut & Paste input - " + format, false);
+          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);
+    }
+  }
+
+  protected void cancel()
+  {
+    textarea.setText("");
+    if (this.getParent() instanceof Frame)
+    {
+      ((Frame) this.getParent()).setVisible(false);
+    }
+    else
+    {
+      ((Dialog) this.getParent()).setVisible(false);
+    }
+  }
+
+  protected TextArea textarea = new TextArea();
+
+  Button accept = new Button("New Window");
+
+  Button addSequences = new Button("Add to Current Alignment");
+
+  Button cancel = new Button("Close");
+
+  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);
+  }
+
+  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)
+  {
+  }
+}