2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 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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19 package jalview.gui;
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21 import java.beans.*;
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25 import java.awt.datatransfer.*;
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26 import java.awt.event.*;
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27 import java.awt.print.*;
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28 import javax.swing.*;
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29 import javax.swing.event.*;
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31 import jalview.analysis.*;
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32 import jalview.datamodel.*;
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33 import jalview.io.*;
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34 import jalview.jbgui.*;
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35 import jalview.schemes.*;
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36 import jalview.ws.*;
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38 public class AlignFrame
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41 public static final int NEW_WINDOW_WIDTH = 700;
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42 public static final int NEW_WINDOW_HEIGHT = 500;
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43 final AlignmentPanel alignPanel;
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44 final AlignViewport viewport;
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45 public String currentFileFormat = "Jalview";
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46 Stack historyList = new Stack();
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47 Stack redoList = new Stack();
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48 private int treeCount = 0;
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50 public AlignFrame(AlignmentI al)
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52 viewport = new AlignViewport(al);
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54 alignPanel = new AlignmentPanel(this, viewport);
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55 alignPanel.annotationPanel.adjustPanelHeight();
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56 alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.
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57 annotationPanel.getPreferredSize());
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58 alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.
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59 getPreferredSize());
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60 alignPanel.setAnnotationVisible(viewport.getShowAnnotation());
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62 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
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64 addInternalFrameListener(new InternalFrameAdapter()
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66 public void internalFrameActivated(InternalFrameEvent evt)
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68 javax.swing.SwingUtilities.invokeLater(new Runnable()
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72 alignPanel.requestFocus();
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79 public void saveAlignmentMenu_actionPerformed(ActionEvent e)
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81 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
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86 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
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91 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
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92 }, currentFileFormat);
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94 chooser.setAcceptAllFileFilterUsed(false);
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95 chooser.setFileView(new JalviewFileView());
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96 chooser.setDialogTitle("Save Alignment to file");
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97 chooser.setToolTipText("Save");
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99 int value = chooser.showSaveDialog(this);
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101 if (value == JalviewFileChooser.APPROVE_OPTION)
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103 currentFileFormat = chooser.getSelectedFormat();
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104 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
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105 currentFileFormat);
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107 if (currentFileFormat.equals("Jalview"))
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109 String shortName = title;
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111 if (shortName.indexOf(java.io.File.separatorChar) > -1)
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113 shortName = shortName.substring(shortName.lastIndexOf(
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114 java.io.File.separatorChar) + 1);
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117 String choice = chooser.getSelectedFile().getPath();
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118 Jalview2XML.SaveAlignment(this, choice, shortName);
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120 // USE Jalview2XML to save this file
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124 String choice = chooser.getSelectedFile().getPath();
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125 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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127 String output = FormatAdapter.formatSequences(currentFileFormat,
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128 viewport.getAlignment().getSequences());
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132 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.
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135 out.println(output);
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138 catch (Exception ex)
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144 protected void outputText_actionPerformed(ActionEvent e)
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146 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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147 Desktop.addInternalFrame(cap,
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148 "Alignment output - " + e.getActionCommand(), 600,
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150 cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
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151 viewport.getAlignment().
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155 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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157 new HTMLOutput(viewport);
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160 protected void createPNG_actionPerformed(ActionEvent e)
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162 alignPanel.makePNG();
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165 protected void epsFile_actionPerformed(ActionEvent e)
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167 alignPanel.makeEPS();
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170 public void printMenuItem_actionPerformed(ActionEvent e)
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172 //Putting in a thread avoids Swing painting problems
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173 PrintThread thread = new PrintThread();
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177 public void closeMenuItem_actionPerformed(ActionEvent e)
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181 this.setClosed(true);
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183 catch (Exception ex)
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188 void updateEditMenuBar()
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190 if (historyList.size() > 0)
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192 undoMenuItem.setEnabled(true);
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194 HistoryItem hi = (HistoryItem) historyList.peek();
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195 undoMenuItem.setText("Undo " + hi.getDescription());
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199 undoMenuItem.setEnabled(false);
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200 undoMenuItem.setText("Undo");
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203 if (redoList.size() > 0)
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205 redoMenuItem.setEnabled(true);
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207 HistoryItem hi = (HistoryItem) redoList.peek();
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208 redoMenuItem.setText("Redo " + hi.getDescription());
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212 redoMenuItem.setEnabled(false);
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213 redoMenuItem.setText("Redo");
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217 public void addHistoryItem(HistoryItem hi)
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219 historyList.push(hi);
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220 updateEditMenuBar();
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223 protected void undoMenuItem_actionPerformed(ActionEvent e)
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225 HistoryItem hi = (HistoryItem) historyList.pop();
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226 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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227 HistoryItem.HIDE));
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228 restoreHistoryItem(hi);
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231 protected void redoMenuItem_actionPerformed(ActionEvent e)
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233 HistoryItem hi = (HistoryItem) redoList.pop();
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234 restoreHistoryItem(hi);
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235 updateEditMenuBar();
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236 viewport.updateConsensus();
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237 alignPanel.repaint();
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238 alignPanel.repaint();
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241 // used by undo and redo
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242 void restoreHistoryItem(HistoryItem hi)
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244 if (hi.getType() == HistoryItem.SORT)
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246 for (int i = 0; i < hi.getSequences().size(); i++)
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248 viewport.alignment.getSequences().setElementAt(hi.getSequences()
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255 for (int i = 0; i < hi.getSequences().size(); i++)
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257 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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259 if (restore.getLength() == 0)
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261 restore.setSequence(hi.getHidden().elementAt(i).toString());
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262 viewport.alignment.getSequences().insertElementAt(restore,
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263 hi.getAlignIndex(i));
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267 restore.setSequence(hi.getHidden().elementAt(i).toString());
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271 if (hi.getType() == HistoryItem.PASTE)
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273 for (int i = viewport.alignment.getHeight() - 1;
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274 i > (hi.getSequences().size() - 1); i--)
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276 viewport.alignment.deleteSequence(i);
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281 updateEditMenuBar();
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283 viewport.updateConsensus();
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284 viewport.updateConservation();
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285 alignPanel.repaint();
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286 viewport.firePropertyChange("alignment", null,
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287 viewport.getAlignment().getSequences());
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290 public void moveSelectedSequences(boolean up)
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292 SequenceGroup sg = viewport.getSelectionGroup();
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301 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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303 SequenceI seq = viewport.alignment.getSequenceAt(i);
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305 if (!sg.sequences.contains(seq))
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310 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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312 if (sg.sequences.contains(temp))
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317 viewport.alignment.getSequences().setElementAt(temp, i);
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318 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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323 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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325 SequenceI seq = viewport.alignment.getSequenceAt(i);
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327 if (!sg.sequences.contains(seq))
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332 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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334 if (sg.sequences.contains(temp))
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339 viewport.alignment.getSequences().setElementAt(temp, i);
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340 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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344 alignPanel.repaint();
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347 protected void copy_actionPerformed(ActionEvent e)
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349 if (viewport.getSelectionGroup() == null)
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354 SequenceGroup sg = viewport.getSelectionGroup();
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356 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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357 StringBuffer buffer = new StringBuffer();
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359 Hashtable orderedSeqs = new Hashtable();
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361 for (int i = 0; i < sg.getSize(); i++)
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363 SequenceI seq = sg.getSequenceAt(i);
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364 int index = viewport.alignment.findIndex(seq);
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365 orderedSeqs.put(index + "", seq);
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370 for (int i = 0; i < sg.getSize(); i++)
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372 SequenceI seq = null;
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374 while (seq == null)
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376 if (orderedSeqs.containsKey(index + ""))
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378 seq = (SequenceI) orderedSeqs.get(index + "");
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389 buffer.append(seq.getName() + "\t" +
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390 seq.findPosition(sg.getStartRes()) + "\t" +
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391 seq.findPosition(sg.getEndRes()) + "\t" +
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392 sg.getSequenceAt(i).getSequence(sg.getStartRes(),
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393 sg.getEndRes() + 1) + "\n");
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396 c.setContents(new StringSelection(buffer.toString()), null);
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399 protected void pasteNew_actionPerformed(ActionEvent e)
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404 protected void pasteThis_actionPerformed(ActionEvent e)
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406 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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407 HistoryItem.PASTE));
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411 void paste(boolean newAlignment)
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415 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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416 Transferable contents = c.getContents(this);
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418 if (contents == null)
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423 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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424 StringTokenizer st = new StringTokenizer(str);
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425 ArrayList seqs = new ArrayList();
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427 while (st.hasMoreElements())
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429 String name = st.nextToken();
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430 int start = Integer.parseInt(st.nextToken());
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431 int end = Integer.parseInt(st.nextToken());
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432 Sequence sequence = new Sequence(name, st.nextToken(), start,
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437 viewport.alignment.addSequence(sequence);
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441 seqs.add(sequence);
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447 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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448 seqs.toArray(newSeqs);
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450 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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451 String newtitle = new String("Copied sequences");
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453 if (title.startsWith("Copied sequences"))
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459 newtitle = newtitle.concat("- from " + title);
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462 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
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463 NEW_WINDOW_HEIGHT);
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467 viewport.firePropertyChange("alignment", null,
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468 viewport.getAlignment().getSequences());
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469 viewport.setEndSeq(viewport.alignment.getHeight());
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470 viewport.alignment.getWidth();
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471 viewport.updateConservation();
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472 viewport.updateConsensus();
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473 alignPanel.repaint();
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476 catch (Exception ex)
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480 // could be anything being pasted in here
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483 protected void cut_actionPerformed(ActionEvent e)
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485 copy_actionPerformed(null);
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486 delete_actionPerformed(null);
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489 protected void delete_actionPerformed(ActionEvent e)
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491 boolean seqsdeleted = false;
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493 if (viewport.getSelectionGroup() == null)
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498 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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499 HistoryItem.HIDE));
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501 SequenceGroup sg = viewport.getSelectionGroup();
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503 for (int i = 0; i < sg.sequences.size(); i++)
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505 SequenceI seq = sg.getSequenceAt(i);
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506 int index = viewport.getAlignment().findIndex(seq);
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507 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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509 if (seq.getSequence().length() < 1)
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511 seqsdeleted = true;
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512 viewport.getAlignment().deleteSequence(seq);
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516 viewport.getAlignment().getSequences().setElementAt(seq, index);
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520 viewport.setSelectionGroup(null);
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521 viewport.alignment.deleteGroup(sg);
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525 viewport.firePropertyChange("alignment", null,
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526 viewport.getAlignment().getSequences());
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529 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
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531 if (viewport.getAlignment().getHeight() < 1)
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535 this.setClosed(true);
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537 catch (Exception ex)
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542 viewport.updateConservation();
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543 viewport.updateConsensus();
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544 alignPanel.repaint();
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547 protected void deleteGroups_actionPerformed(ActionEvent e)
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549 viewport.alignment.deleteAllGroups();
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550 viewport.setSelectionGroup(null);
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551 alignPanel.repaint();
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554 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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556 SequenceGroup sg = new SequenceGroup();
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558 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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561 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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564 sg.setEndRes(viewport.alignment.getWidth());
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565 viewport.setSelectionGroup(sg);
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566 PaintRefresher.Refresh(null, viewport.alignment);
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569 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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571 viewport.setSelectionGroup(null);
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572 viewport.getColumnSelection().clear();
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573 viewport.setSelectionGroup(null);
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574 PaintRefresher.Refresh(null, viewport.alignment);
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577 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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579 SequenceGroup sg = viewport.getSelectionGroup();
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582 selectAllSequenceMenuItem_actionPerformed(null);
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586 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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589 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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592 PaintRefresher.Refresh(null, viewport.alignment);
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595 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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597 ColumnSelection colSel = viewport.getColumnSelection();
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599 if (colSel.size() > 0)
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601 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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602 HistoryItem.HIDE));
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604 int min = colSel.getMin();
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605 viewport.getAlignment().trimLeft(min);
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606 colSel.compensateForEdit(0, min);
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608 if (viewport.getSelectionGroup() != null)
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610 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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613 Vector groups = viewport.alignment.getGroups();
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615 for (int i = 0; i < groups.size(); i++)
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617 SequenceGroup sg = (SequenceGroup) groups.get(i);
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619 if (!sg.adjustForRemoveLeft(min))
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621 viewport.alignment.deleteGroup(sg);
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625 alignPanel.repaint();
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629 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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631 ColumnSelection colSel = viewport.getColumnSelection();
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633 if (colSel.size() > 0)
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635 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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636 HistoryItem.HIDE));
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638 int max = colSel.getMax();
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639 viewport.getAlignment().trimRight(max);
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641 if (viewport.getSelectionGroup() != null)
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643 viewport.getSelectionGroup().adjustForRemoveRight(max);
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646 Vector groups = viewport.alignment.getGroups();
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648 for (int i = 0; i < groups.size(); i++)
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650 SequenceGroup sg = (SequenceGroup) groups.get(i);
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652 if (!sg.adjustForRemoveRight(max))
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654 viewport.alignment.deleteGroup(sg);
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658 alignPanel.repaint();
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662 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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664 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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665 viewport.alignment, HistoryItem.HIDE));
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667 viewport.getAlignment().removeGaps();
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668 viewport.updateConservation();
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669 viewport.updateConsensus();
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670 alignPanel.repaint();
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673 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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675 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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676 HistoryItem.HIDE));
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681 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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684 current = viewport.getAlignment().getSequenceAt(i);
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685 jSize = current.getLength();
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687 for (int j = 0; j < jSize; j++)
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689 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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691 current.deleteCharAt(j);
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698 viewport.updateConservation();
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699 viewport.updateConsensus();
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700 alignPanel.repaint();
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703 public void padGapsMenuitem_actionPerformed(ActionEvent e)
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705 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
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706 HistoryItem.HIDE));
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709 int Width = viewport.getAlignment().getWidth() - 1;
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711 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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714 current = viewport.getAlignment().getSequenceAt(i);
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716 if (current.getLength() < Width)
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718 current.insertCharAt(Width, viewport.getGapCharacter());
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722 viewport.updateConservation();
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723 viewport.updateConsensus();
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724 alignPanel.repaint();
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727 public void findMenuItem_actionPerformed(ActionEvent e)
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729 JInternalFrame frame = new JInternalFrame();
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730 Finder finder = new Finder(viewport, alignPanel, frame);
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731 frame.setContentPane(finder);
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732 Desktop.addInternalFrame(frame, "Find", 340, 110);
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733 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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736 public void font_actionPerformed(ActionEvent e)
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738 FontChooser fc = new FontChooser(alignPanel);
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741 protected void fullSeqId_actionPerformed(ActionEvent e)
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743 viewport.setShowFullId(fullSeqId.isSelected());
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745 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
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746 alignPanel.repaint();
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749 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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751 viewport.setColourText(colourTextMenuItem.isSelected());
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752 alignPanel.repaint();
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755 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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757 viewport.setWrapAlignment(wrapMenuItem.isSelected());
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758 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
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759 scaleAbove.setVisible(wrapMenuItem.isSelected());
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760 scaleLeft.setVisible(wrapMenuItem.isSelected());
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761 scaleRight.setVisible(wrapMenuItem.isSelected());
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762 alignPanel.repaint();
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765 protected void scaleAbove_actionPerformed(ActionEvent e)
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767 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
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768 alignPanel.repaint();
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771 protected void scaleLeft_actionPerformed(ActionEvent e)
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773 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
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774 alignPanel.repaint();
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777 protected void scaleRight_actionPerformed(ActionEvent e)
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779 viewport.setScaleRightWrapped(scaleRight.isSelected());
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780 alignPanel.repaint();
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783 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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785 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
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786 alignPanel.repaint();
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789 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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791 viewport.setShowText(viewTextMenuItem.isSelected());
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792 alignPanel.repaint();
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795 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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797 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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798 alignPanel.repaint();
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801 public void sequenceFeatures_actionPerformed(ActionEvent evt)
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803 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
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805 if (viewport.showSequenceFeatures &&
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806 ! ( (Alignment) viewport.alignment).featuresAdded)
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808 SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.
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811 ( (Alignment) viewport.alignment).featuresAdded = true;
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814 alignPanel.repaint();
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817 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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819 if (annotationPanelMenuItem.isSelected() &&
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820 viewport.getWrapAlignment())
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822 annotationPanelMenuItem.setSelected(false);
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827 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
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828 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
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831 public void overviewMenuItem_actionPerformed(ActionEvent e)
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833 if (alignPanel.overviewPanel != null)
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838 JInternalFrame frame = new JInternalFrame();
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839 OverviewPanel overview = new OverviewPanel(alignPanel);
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840 frame.setContentPane(overview);
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841 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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842 frame.getWidth(), frame.getHeight());
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844 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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845 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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847 public void internalFrameClosed(
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848 javax.swing.event.InternalFrameEvent evt)
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850 alignPanel.setOverviewPanel(null);
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855 alignPanel.setOverviewPanel(overview);
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858 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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860 changeColour(null);
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863 public void clustalColour_actionPerformed(ActionEvent e)
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865 changeColour(new ClustalxColourScheme(
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866 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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869 public void zappoColour_actionPerformed(ActionEvent e)
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871 changeColour(new ZappoColourScheme());
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874 public void taylorColour_actionPerformed(ActionEvent e)
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876 changeColour(new TaylorColourScheme());
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879 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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881 changeColour(new HydrophobicColourScheme());
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884 public void helixColour_actionPerformed(ActionEvent e)
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886 changeColour(new HelixColourScheme());
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889 public void strandColour_actionPerformed(ActionEvent e)
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891 changeColour(new StrandColourScheme());
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894 public void turnColour_actionPerformed(ActionEvent e)
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896 changeColour(new TurnColourScheme());
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899 public void buriedColour_actionPerformed(ActionEvent e)
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901 changeColour(new BuriedColourScheme());
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904 public void nucleotideColour_actionPerformed(ActionEvent e)
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906 changeColour(new NucleotideColourScheme());
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909 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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911 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
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914 void changeColour(ColourSchemeI cs)
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918 if (viewport.getAbovePIDThreshold())
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920 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
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923 if (cs instanceof ResidueColourScheme)
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925 ( (ResidueColourScheme) cs).setThreshold(threshold);
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927 else if (cs instanceof ScoreColourScheme)
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929 ( (ScoreColourScheme) cs).setThreshold(threshold);
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932 viewport.setGlobalColourScheme(cs);
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934 else if (cs instanceof ResidueColourScheme)
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936 ( (ResidueColourScheme) cs).setThreshold(0);
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938 else if (cs instanceof ScoreColourScheme)
\r
940 ( (ScoreColourScheme) cs).setThreshold(0);
\r
943 if (viewport.getConservationSelected())
\r
945 ConservationColourScheme ccs = null;
\r
947 Alignment al = (Alignment) viewport.alignment;
\r
948 Conservation c = new Conservation("All",
\r
949 ResidueProperties.propHash, 3,
\r
950 al.getSequences(), 0,
\r
951 al.getWidth() - 1);
\r
954 c.verdict(false, viewport.ConsPercGaps);
\r
956 ccs = new ConservationColourScheme(c, cs);
\r
958 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
959 ccs.setConsensus(viewport.vconsensus);
\r
960 viewport.setGlobalColourScheme(ccs);
\r
962 ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,
\r
967 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
970 cs.setConsensus(viewport.vconsensus);
\r
973 viewport.setGlobalColourScheme(cs);
\r
976 if (viewport.getColourAppliesToAllGroups())
\r
978 Vector groups = viewport.alignment.getGroups();
\r
980 for (int i = 0; i < groups.size(); i++)
\r
982 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
988 else if (cs instanceof ClustalxColourScheme)
\r
990 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
992 else if (cs instanceof UserColourScheme)
\r
994 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
\r
1000 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1002 catch (Exception ex)
\r
1007 if (viewport.getAbovePIDThreshold())
\r
1009 if (sg.cs instanceof ResidueColourScheme)
\r
1011 ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
\r
1013 else if (sg.cs instanceof ScoreColourScheme)
\r
1015 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
\r
1018 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1022 if (viewport.getConservationSelected())
\r
1024 Conservation c = new Conservation("Group",
\r
1025 ResidueProperties.propHash, 3,
\r
1027 viewport.alignment.getWidth() - 1);
\r
1029 c.verdict(false, viewport.ConsPercGaps);
\r
1031 ConservationColourScheme ccs = new ConservationColourScheme(c,
\r
1034 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
1035 ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1039 else if (cs != null)
\r
1041 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
1042 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1048 if (alignPanel.getOverviewPanel() != null)
\r
1050 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1053 alignPanel.repaint();
\r
1056 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1058 if (viewport.getAbovePIDThreshold())
\r
1060 SliderPanel.setPIDSliderSource(alignPanel,
\r
1061 viewport.getGlobalColourScheme(),
\r
1063 SliderPanel.showPIDSlider();
\r
1067 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1069 if (viewport.getConservationSelected())
\r
1071 SliderPanel.setConservationSlider(alignPanel,
\r
1072 viewport.globalColourScheme,
\r
1074 SliderPanel.showConservationSlider();
\r
1078 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1080 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1082 viewport.setAbovePIDThreshold(false);
\r
1083 abovePIDThreshold.setSelected(false);
\r
1085 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
1087 if (cs instanceof ConservationColourScheme)
\r
1089 changeColour( ( (ConservationColourScheme) cs).cs);
\r
1096 modifyConservation_actionPerformed(null);
\r
1099 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1101 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1103 conservationMenuItem.setSelected(false);
\r
1104 viewport.setConservationSelected(false);
\r
1106 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
1108 if (cs instanceof ConservationColourScheme)
\r
1110 changeColour( ( (ConservationColourScheme) cs).cs);
\r
1117 modifyPID_actionPerformed(null);
\r
1120 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1122 new UserDefinedColours(alignPanel, null);
\r
1125 public void PIDColour_actionPerformed(ActionEvent e)
\r
1127 changeColour(new PIDColourScheme());
\r
1130 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1132 changeColour(new Blosum62ColourScheme());
\r
1135 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1137 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1138 HistoryItem.SORT));
\r
1139 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1140 viewport.getAlignment().getSequenceAt(0));
\r
1141 alignPanel.repaint();
\r
1144 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1146 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1147 HistoryItem.SORT));
\r
1148 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1149 alignPanel.repaint();
\r
1152 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1154 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1155 HistoryItem.SORT));
\r
1157 // AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1158 AlignmentSorter.sortGroups(viewport.getAlignment());
\r
1159 alignPanel.repaint();
\r
1162 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1164 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1165 JInternalFrame frame = new JInternalFrame();
\r
1166 frame.setContentPane(sp);
\r
1167 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1171 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1173 if ( (viewport.getSelectionGroup() == null) ||
\r
1174 (viewport.getSelectionGroup().getSize() < 2))
\r
1176 JOptionPane.showInternalMessageDialog(this,
\r
1177 "You must select at least 2 sequences.",
\r
1178 "Invalid Selection",
\r
1179 JOptionPane.WARNING_MESSAGE);
\r
1183 JInternalFrame frame = new JInternalFrame();
\r
1184 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1185 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1189 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1191 if ( ( (viewport.getSelectionGroup() != null) &&
\r
1192 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1193 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1194 (viewport.getAlignment().getHeight() < 4))
\r
1196 JOptionPane.showInternalMessageDialog(this,
\r
1197 "Principal component analysis must take\n" +
\r
1198 "at least 4 input sequences.",
\r
1199 "Sequence selection insufficient",
\r
1200 JOptionPane.WARNING_MESSAGE);
\r
1207 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
1208 JInternalFrame frame = new JInternalFrame();
\r
1209 frame.setContentPane(pcaPanel);
\r
1210 Desktop.addInternalFrame(frame, "Principal component analysis",
\r
1213 catch (java.lang.OutOfMemoryError ex)
\r
1215 JOptionPane.showInternalMessageDialog(this,
\r
1216 "Too many sequences selected\nfor Principal Component Analysis!!",
\r
1218 JOptionPane.WARNING_MESSAGE);
\r
1222 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1224 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1227 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1229 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1232 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1234 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1237 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1239 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
1242 void NewTreePanel(String type, String pwType, String title)
\r
1244 final TreePanel tp;
\r
1246 if ( (viewport.getSelectionGroup() != null) &&
\r
1247 (viewport.getSelectionGroup().getSize() > 3))
\r
1250 SequenceGroup sg = viewport.getSelectionGroup();
\r
1252 /* Decide if the selection is a column region */
\r
1253 while (s < sg.sequences.size())
\r
1255 if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
\r
1258 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1259 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
1260 "Try using the Pad function in the edit menu,\n" +
\r
1261 "or one of the multiple sequence alignment web services.",
\r
1262 "Sequences in selection are not aligned",
\r
1263 JOptionPane.WARNING_MESSAGE);
\r
1269 title = title + " on region";
\r
1270 tp = new TreePanel(viewport,
\r
1271 viewport.getSelectionGroup().sequences, type, pwType,
\r
1272 sg.getStartRes(), sg.getEndRes());
\r
1276 //are the sequences aligned?
\r
1277 if (!viewport.alignment.isAligned())
\r
1279 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1280 "The sequences must be aligned before creating a tree.\n" +
\r
1281 "Try using the Pad function in the edit menu,\n" +
\r
1282 "or one of the multiple sequence alignment web services.",
\r
1283 "Sequences not aligned",
\r
1284 JOptionPane.WARNING_MESSAGE);
\r
1289 tp = new TreePanel(viewport,
\r
1290 viewport.getAlignment().getSequences(), type, pwType,
\r
1292 viewport.alignment.getWidth());
\r
1295 addTreeMenuItem(tp, title);
\r
1296 viewport.setCurrentTree(tp.getTree());
\r
1298 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
1301 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
1303 final JMenuItem item = new JMenuItem("by " + title);
\r
1305 item.addActionListener(new java.awt.event.ActionListener()
\r
1307 public void actionPerformed(ActionEvent e)
\r
1309 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1310 HistoryItem.SORT));
\r
1312 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
1313 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
1314 alignPanel.repaint();
\r
1319 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1321 final JMenuItem item = new JMenuItem(title);
\r
1325 if (treeCount == 1)
\r
1327 sort.add(sortByTreeMenu);
\r
1330 sortByTreeMenu.add(item);
\r
1331 item.addActionListener(new java.awt.event.ActionListener()
\r
1333 public void actionPerformed(ActionEvent e)
\r
1335 addHistoryItem(new HistoryItem("Tree Sort",
\r
1336 viewport.alignment, HistoryItem.SORT));
\r
1337 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
1338 treePanel.getTree());
\r
1339 alignPanel.repaint();
\r
1343 treePanel.addInternalFrameListener(new javax.swing.event.
\r
1344 InternalFrameAdapter()
\r
1346 public void internalFrameClosed(
\r
1347 javax.swing.event.InternalFrameEvent evt)
\r
1350 sortByTreeMenu.remove(item);
\r
1352 if (treeCount == 0)
\r
1354 sort.remove(sortByTreeMenu);
\r
1359 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
\r
1361 public void propertyChange(PropertyChangeEvent evt)
\r
1363 if (evt.getPropertyName().equals("alignment"))
\r
1365 treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
\r
1366 treePanel.repaint();
\r
1372 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
1374 // TODO:resolve which menu item was actually selected
\r
1375 // Now, check we have enough sequences
\r
1376 SequenceI[] msa = null;
\r
1378 if ( (viewport.getSelectionGroup() != null) &&
\r
1379 (viewport.getSelectionGroup().getSize() > 1))
\r
1381 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1382 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1384 msa = new SequenceI[sz = seqs.getSize()];
\r
1386 for (int i = 0; i < sz; i++)
\r
1388 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1393 Vector seqs = viewport.getAlignment().getSequences();
\r
1395 if (seqs.size() > 1)
\r
1397 msa = new SequenceI[seqs.size()];
\r
1399 for (int i = 0; i < seqs.size(); i++)
\r
1401 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1408 jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
\r
1409 title, msa, false, true);
\r
1413 public void ClustalRealign_actionPerformed(ActionEvent e)
\r
1415 // TODO:resolve which menu item was actually selected
\r
1416 // Now, check we have enough sequences
\r
1417 SequenceI[] msa = null;
\r
1419 if ( (viewport.getSelectionGroup() != null) &&
\r
1420 (viewport.getSelectionGroup().getSize() > 1))
\r
1422 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1423 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1425 msa = new SequenceI[sz = seqs.getSize()];
\r
1427 for (int i = 0; i < sz; i++)
\r
1429 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1434 Vector seqs = viewport.getAlignment().getSequences();
\r
1436 if (seqs.size() > 1)
\r
1438 msa = new SequenceI[seqs.size()];
\r
1440 for (int i = 0; i < seqs.size(); i++)
\r
1442 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1449 jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
\r
1450 title, msa, true, true);
\r
1454 protected void jpred_actionPerformed(ActionEvent e)
\r
1456 SequenceI seq = null;
\r
1457 SequenceI[] msa = null;
\r
1459 if ( (viewport.getSelectionGroup() != null) &&
\r
1460 (viewport.getSelectionGroup().getSize() > 0))
\r
1462 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1463 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1465 if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
1467 seq = (SequenceI) seqs.getSequenceAt(0);
\r
1472 msa = new SequenceI[sz = seqs.getSize()];
\r
1474 for (int i = 0; i < sz; i++)
\r
1476 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1482 Vector seqs = viewport.getAlignment().getSequences();
\r
1484 if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
\r
1486 seq = (SequenceI) seqs.elementAt(0);
\r
1490 msa = new SequenceI[seqs.size()];
\r
1492 for (int i = 0; i < seqs.size(); i++)
\r
1494 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1501 JPredClient ct = new JPredClient(title, msa);
\r
1503 else if (seq != null)
\r
1505 JPredClient ct = new JPredClient(title, seq);
\r
1510 "JALVIEW ERROR! - Unexpected JPred selection state!\n");
\r
1514 protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
\r
1516 // TODO:resolve which menu item was actually selected
\r
1517 // Now, check we have enough sequences
\r
1518 SequenceI[] msa = null;
\r
1520 if ( (viewport.getSelectionGroup() != null) &&
\r
1521 (viewport.getSelectionGroup().getSize() > 1))
\r
1523 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1524 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1526 msa = new SequenceI[sz = seqs.getSize()];
\r
1528 for (int i = 0; i < sz; i++)
\r
1530 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1535 Vector seqs = viewport.getAlignment().getSequences();
\r
1537 if (seqs.size() > 1)
\r
1539 msa = new SequenceI[seqs.size()];
\r
1541 for (int i = 0; i < seqs.size(); i++)
\r
1543 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1550 MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,
\r
1555 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
1557 // Pick the tree file
\r
1558 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
1560 "LAST_DIRECTORY"));
\r
1561 chooser.setFileView(new JalviewFileView());
\r
1562 chooser.setDialogTitle("Select a newick-like tree file");
\r
1563 chooser.setToolTipText("Load a tree file");
\r
1565 int value = chooser.showOpenDialog(null);
\r
1567 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
1569 String choice = chooser.getSelectedFile().getPath();
\r
1570 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1574 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
1576 viewport.setCurrentTree( ShowNewickTree(fin, choice).getTree() );
\r
1578 catch (Exception ex)
\r
1580 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1581 "Problem reading tree file",
\r
1583 JOptionPane.WARNING_MESSAGE);
\r
1584 ex.printStackTrace();
\r
1589 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
1591 TreePanel tp = null;
\r
1595 if (nf.getTree() != null)
\r
1597 tp = new TreePanel(viewport,
\r
1598 viewport.getAlignment().getSequences(), nf,
\r
1601 Desktop.addInternalFrame(tp, title, 600, 500);
\r
1602 addTreeMenuItem(tp, title);
\r
1605 catch (Exception ex)
\r
1607 ex.printStackTrace();
\r
1617 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
1618 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
1619 printJob.setPrintable(alignPanel, pf);
\r
1621 if (printJob.printDialog())
\r
1627 catch (Exception PrintException)
\r
1629 PrintException.printStackTrace();
\r