2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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20 package jalview.appletgui;
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23 import java.awt.event.*;
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25 import jalview.datamodel.*;
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26 import jalview.io.*;
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28 public class CutAndPasteTransfer
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29 extends Panel implements ActionListener, MouseListener
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31 boolean pdbImport = false;
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32 boolean treeImport = false;
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33 boolean annotationImport = false;
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35 AlignFrame alignFrame;
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37 public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
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45 e.printStackTrace();
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48 this.alignFrame = alignFrame;
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52 buttonPanel.setVisible(false);
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56 public String getText()
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58 return textarea.getText();
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61 public void setText(String text)
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63 textarea.setText(text);
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66 public void setPDBImport(Sequence seq)
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69 accept.setLabel("Accept");
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70 addSequences.setVisible(false);
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74 public void setTreeImport()
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77 accept.setLabel("Accept");
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78 addSequences.setVisible(false);
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81 public void setAnnotationImport()
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83 annotationImport = true;
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84 accept.setLabel("Accept");
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85 addSequences.setVisible(false);
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88 public void actionPerformed(ActionEvent evt)
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90 if (evt.getSource() == accept)
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94 else if (evt.getSource() == addSequences)
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98 else if (evt.getSource() == cancel)
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104 protected void ok(boolean newWindow)
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106 String text = getText();
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107 int length = text.length();
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108 textarea.append("\n");
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109 if (textarea.getText().length() == length)
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112 "\n\n#################################################\n"
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113 + "WARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n"
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114 + "\nCAN'T INPUT FULL ALIGNMENT"
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115 + "\n\nYOU MUST DELETE THIS WARNING TO CONTINUE"
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116 + "\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE"
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117 + "\n#################################################\n";
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118 textarea.setText(text.substring(0, text.length() - warning.length())
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121 textarea.setCaretPosition(text.length());
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126 new MCview.AppletPDBViewer(text, AppletFormatAdapter.PASTE,
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128 alignFrame.getSeqcanvas());
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130 else if (treeImport)
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134 jalview.io.NewickFile fin = new jalview.io.NewickFile(textarea.getText(),
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138 if (fin.getTree() != null)
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140 alignFrame.loadTree(fin, "Pasted tree file");
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144 catch (Exception ex)
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146 textarea.setText("Could not parse Newick file!\n" + ex);
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150 else if (annotationImport)
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152 if (new AnnotationFile().readAnnotationFile(
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153 alignFrame.viewport.alignment, textarea.getText(),
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154 jalview.io.AppletFormatAdapter.PASTE))
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156 alignFrame.alignPanel.fontChanged();
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157 alignFrame.alignPanel.setScrollValues(0, 0);
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162 alignFrame.parseFeaturesFile(textarea.getText(),
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163 jalview.io.AppletFormatAdapter.PASTE);
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166 else if (alignFrame != null)
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168 Alignment al = null;
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170 String format = new IdentifyFile().Identify(text,
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171 AppletFormatAdapter.PASTE);
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174 al = new AppletFormatAdapter().readFile(text, AppletFormatAdapter.PASTE,
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177 catch (java.io.IOException ex)
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179 ex.printStackTrace();
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186 AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
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187 "Cut & Paste input - " + format,
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189 af.statusBar.setText("Successfully pasted alignment file");
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193 alignFrame.addSequences(al.getSequencesArray());
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198 if (this.getParent() instanceof Frame)
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200 ( (Frame)this.getParent()).setVisible(false);
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204 ( (Dialog)this.getParent()).setVisible(false);
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208 protected void cancel()
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210 textarea.setText("");
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211 if (this.getParent() instanceof Frame)
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213 ( (Frame)this.getParent()).setVisible(false);
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217 ( (Dialog)this.getParent()).setVisible(false);
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221 protected TextArea textarea = new TextArea();
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222 Button accept = new Button("New Window");
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223 Button addSequences = new Button("Add to Current Alignment");
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224 Button cancel = new Button("Close");
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226 protected Panel buttonPanel = new Panel();
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227 BorderLayout borderLayout1 = new BorderLayout();
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229 private void jbInit()
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232 textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
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233 textarea.setText("Paste your alignment file here");
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234 textarea.addMouseListener(this);
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235 this.setLayout(borderLayout1);
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236 accept.addActionListener(this);
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237 addSequences.addActionListener(this);
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238 cancel.addActionListener(this);
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239 this.add(buttonPanel, BorderLayout.SOUTH);
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240 buttonPanel.add(accept, null);
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241 buttonPanel.add(addSequences);
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242 buttonPanel.add(cancel, null);
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243 this.add(textarea, java.awt.BorderLayout.CENTER);
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246 public void mousePressed(MouseEvent evt)
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248 if (textarea.getText().startsWith("Paste your"))
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250 textarea.setText("");
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254 public void mouseReleased(MouseEvent evt)
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257 public void mouseClicked(MouseEvent evt)
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260 public void mouseEntered(MouseEvent evt)
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263 public void mouseExited(MouseEvent evt)
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