-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
-package jalview.appletgui;\r
-\r
-import jalview.jbappletgui.GCutAndPasteTransfer;\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-public class CutAndPasteTransfer extends GCutAndPasteTransfer\r
-{\r
- public CutAndPasteTransfer(boolean forImport)\r
- {\r
- super();\r
-\r
- if(!forImport)\r
- {\r
- buttonPanel.setVisible(false);\r
- }\r
- }\r
-\r
-\r
- public String getText()\r
- {\r
- return textarea.getText();\r
- }\r
-\r
- public void setText(String text)\r
- {\r
- textarea.setText(text);\r
- }\r
-\r
-\r
- protected void ok_actionPerformed(ActionEvent e)\r
- {\r
- String text = getText();\r
- SequenceI[] sequences = null;\r
-\r
- String format = IdentifyFile.Identify(text, "Paste");\r
- sequences = FormatAdapter.readFile(text, "Paste", format);\r
-\r
- if (sequences != null)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
- jalview.bin.JalviewLite.addFrame(af, "Cut & Paste input - " + format,\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
- af.statusBar.setText("Successfully pasted alignment file");\r
- }\r
-\r
- Frame frame = (Frame)this.getParent();\r
- frame.setVisible(false);\r
- }\r
-\r
- protected void cancel_actionPerformed(ActionEvent e) {\r
- Frame frame = (Frame)this.getParent();\r
- frame.setVisible(false);\r
- }\r
-\r
-\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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;
+ 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;
+ pdbImport = true;
+ }
+
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ if(evt.getSource()==ok)
+ ok_actionPerformed();
+ else if(evt.getSource()==cancel)
+ cancel_actionPerformed();
+ }
+
+ protected void ok_actionPerformed()
+ {
+ 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(alignFrame!=null)
+ {
+ SequenceI[] sequences = null;
+
+ String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);
+ try{
+ sequences = new AppletFormatAdapter().readFile(text, AppletFormatAdapter.PASTE, format);
+ }catch(java.io.IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ if (sequences != null)
+ {
+ AlignFrame af = new AlignFrame(new Alignment(sequences), alignFrame.viewport.applet,
+ "Cut & Paste input - " + format,
+ false);
+ af.statusBar.setText("Successfully pasted alignment file");
+ }
+ }
+
+ if(this.getParent() instanceof Frame)
+ ((Frame)this.getParent()).setVisible(false);
+ else
+ ((Dialog)this.getParent()).setVisible(false);
+ }
+
+ protected void cancel_actionPerformed()
+ {
+ textarea.setText("");
+ if(this.getParent() instanceof Frame)
+ ((Frame)this.getParent()).setVisible(false);
+ else
+ ((Dialog)this.getParent()).setVisible(false);
+ }
+
+ protected TextArea textarea = new TextArea();
+ Button ok = new Button();
+ Button cancel = new Button();
+ 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);
+ ok.setLabel("OK");
+ ok.addActionListener(this);
+ cancel.setLabel("Cancel");
+ cancel.addActionListener(this);
+ this.add(buttonPanel, BorderLayout.SOUTH);
+ buttonPanel.add(ok, null);
+ 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){}
+}
git://source.jalview.org / jalview.git / blobdiff