2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 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 extends Panel implements ActionListener, MouseListener
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30 boolean pdbImport = false;
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31 boolean treeImport = false;
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32 boolean annotationImport = false;
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34 AlignFrame alignFrame;
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36 public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
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40 } catch (Exception e) {
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41 e.printStackTrace();
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44 this.alignFrame = alignFrame;
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48 buttonPanel.setVisible(false);
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52 public String getText()
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54 return textarea.getText();
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57 public void setText(String text)
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59 textarea.setText(text);
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62 public void setPDBImport(Sequence seq)
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65 accept.setLabel("Accept");
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66 addSequences.setVisible(false);
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70 public void setTreeImport()
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73 accept.setLabel("Accept");
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74 addSequences.setVisible(false);
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77 public void setAnnotationImport()
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79 annotationImport = true;
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80 accept.setLabel("Accept");
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81 addSequences.setVisible(false);
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85 public void actionPerformed(ActionEvent evt)
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87 if(evt.getSource()==accept)
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89 else if(evt.getSource() == addSequences)
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91 else if(evt.getSource() == cancel)
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95 protected void ok(boolean newWindow)
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97 String text = getText();
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98 int length = text.length();
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99 textarea.append("\n");
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100 if(textarea.getText().length()==length)
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102 String warning = "\n\n#################################################\n"
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103 +"WARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n"
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104 +"\nCAN'T INPUT FULL ALIGNMENT"
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105 +"\n\nYOU MUST DELETE THIS WARNING TO CONTINUE"
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106 +"\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE"
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107 +"\n#################################################\n";
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108 textarea.setText(text.substring(0, text.length()-warning.length())
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111 textarea.setCaretPosition(text.length());
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116 new MCview.AppletPDBViewer(text, AppletFormatAdapter.PASTE,
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118 alignFrame.getSeqcanvas());
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120 else if(treeImport)
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123 jalview.io.NewickFile fin = new jalview.io.NewickFile(textarea.getText(),
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127 if(fin.getTree()!=null)
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128 alignFrame.loadTree(fin, "Pasted tree file");
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131 catch (Exception ex)
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133 textarea.setText("Could not parse Newick file!\n" + ex);
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137 else if(annotationImport)
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139 if (new AnnotationFile().readAnnotationFile(
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140 alignFrame.viewport.alignment, textarea.getText(),
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141 jalview.io.AppletFormatAdapter.PASTE))
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143 alignFrame.alignPanel.fontChanged();
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144 alignFrame.alignPanel.setScrollValues(0, 0);
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149 alignFrame.parseFeaturesFile(textarea.getText(),
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150 jalview.io.AppletFormatAdapter.PASTE);
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153 else if(alignFrame!=null)
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155 Alignment al = null;
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157 String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);
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159 al = new AppletFormatAdapter().readFile(text, AppletFormatAdapter.PASTE, format);
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160 }catch(java.io.IOException ex)
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162 ex.printStackTrace();
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171 AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet,
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172 "Cut & Paste input - " + format,
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174 af.statusBar.setText("Successfully pasted alignment file");
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177 alignFrame.addSequences(al.getSequencesArray());
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181 if(this.getParent() instanceof Frame)
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182 ((Frame)this.getParent()).setVisible(false);
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184 ((Dialog)this.getParent()).setVisible(false);
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187 protected void cancel()
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189 textarea.setText("");
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190 if(this.getParent() instanceof Frame)
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191 ((Frame)this.getParent()).setVisible(false);
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193 ((Dialog)this.getParent()).setVisible(false);
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196 protected TextArea textarea = new TextArea();
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197 Button accept = new Button("New Window");
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198 Button addSequences = new Button("Add to Current Alignment");
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199 Button cancel = new Button("Close");
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201 protected Panel buttonPanel = new Panel();
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202 BorderLayout borderLayout1 = new BorderLayout();
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205 private void jbInit() throws Exception {
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206 textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));
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207 textarea.setText("Paste your alignment file here");
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208 textarea.addMouseListener(this);
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209 this.setLayout(borderLayout1);
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210 accept.addActionListener(this);
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211 addSequences.addActionListener(this);
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212 cancel.addActionListener(this);
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213 this.add(buttonPanel, BorderLayout.SOUTH);
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214 buttonPanel.add(accept, null);
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215 buttonPanel.add(addSequences);
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216 buttonPanel.add(cancel, null);
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217 this.add(textarea, java.awt.BorderLayout.CENTER);
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220 public void mousePressed(MouseEvent evt) {
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221 if (textarea.getText().startsWith("Paste your")) {
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222 textarea.setText("");
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225 public void mouseReleased(MouseEvent evt){}
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226 public void mouseClicked(MouseEvent evt){}
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227 public void mouseEntered(MouseEvent evt){}
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228 public void mouseExited(MouseEvent evt){}
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