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 alignPanel.annotationPanel.activeRes=null;
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575 PaintRefresher.Refresh(null, viewport.alignment);
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578 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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580 SequenceGroup sg = viewport.getSelectionGroup();
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583 selectAllSequenceMenuItem_actionPerformed(null);
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587 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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590 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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593 PaintRefresher.Refresh(null, viewport.alignment);
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596 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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598 ColumnSelection colSel = viewport.getColumnSelection();
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600 if (colSel.size() > 0)
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602 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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603 HistoryItem.HIDE));
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605 int min = colSel.getMin();
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606 viewport.getAlignment().trimLeft(min);
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607 colSel.compensateForEdit(0, min);
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609 if (viewport.getSelectionGroup() != null)
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611 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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614 Vector groups = viewport.alignment.getGroups();
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616 for (int i = 0; i < groups.size(); i++)
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618 SequenceGroup sg = (SequenceGroup) groups.get(i);
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620 if (!sg.adjustForRemoveLeft(min))
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622 viewport.alignment.deleteGroup(sg);
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626 alignPanel.repaint();
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630 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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632 ColumnSelection colSel = viewport.getColumnSelection();
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634 if (colSel.size() > 0)
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636 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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637 HistoryItem.HIDE));
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639 int max = colSel.getMax();
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640 viewport.getAlignment().trimRight(max);
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642 if (viewport.getSelectionGroup() != null)
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644 viewport.getSelectionGroup().adjustForRemoveRight(max);
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647 Vector groups = viewport.alignment.getGroups();
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649 for (int i = 0; i < groups.size(); i++)
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651 SequenceGroup sg = (SequenceGroup) groups.get(i);
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653 if (!sg.adjustForRemoveRight(max))
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655 viewport.alignment.deleteGroup(sg);
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659 alignPanel.repaint();
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663 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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665 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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666 viewport.alignment, HistoryItem.HIDE));
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668 viewport.getAlignment().removeGaps();
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669 viewport.updateConservation();
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670 viewport.updateConsensus();
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671 alignPanel.repaint();
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674 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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676 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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677 HistoryItem.HIDE));
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684 int start=0, end = viewport.alignment.getWidth();
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686 if(viewport.getSelectionGroup()!=null)
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688 seqs = viewport.getSelectionGroup().sequences;
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689 start = viewport.getSelectionGroup().getStartRes();
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690 end = viewport.getSelectionGroup().getEndRes();
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693 seqs = viewport.alignment.getSequences();
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695 for (int i = 0; i <seqs.size(); i++)
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697 current = (SequenceI)seqs.elementAt(i);
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698 jSize = current.getLength();
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703 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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705 current.deleteCharAt(j);
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714 viewport.updateConservation();
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715 viewport.updateConsensus();
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716 alignPanel.repaint();
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719 public void padGapsMenuitem_actionPerformed(ActionEvent e)
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721 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
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722 HistoryItem.HIDE));
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725 int Width = viewport.getAlignment().getWidth();
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727 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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730 current = viewport.getAlignment().getSequenceAt(i);
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732 if (current.getLength() < Width)
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734 current.insertCharAt(Width-1, viewport.getGapCharacter());
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738 viewport.updateConservation();
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739 viewport.updateConsensus();
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740 alignPanel.repaint();
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743 public void findMenuItem_actionPerformed(ActionEvent e)
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745 JInternalFrame frame = new JInternalFrame();
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746 Finder finder = new Finder(viewport, alignPanel, frame);
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747 frame.setContentPane(finder);
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748 Desktop.addInternalFrame(frame, "Find", 340, 110);
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749 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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752 public void font_actionPerformed(ActionEvent e)
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754 FontChooser fc = new FontChooser(alignPanel);
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757 protected void fullSeqId_actionPerformed(ActionEvent e)
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759 viewport.setShowFullId(fullSeqId.isSelected());
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761 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
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762 alignPanel.repaint();
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765 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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767 viewport.setColourText(colourTextMenuItem.isSelected());
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768 alignPanel.repaint();
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771 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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773 viewport.setWrapAlignment(wrapMenuItem.isSelected());
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774 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
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775 scaleAbove.setVisible(wrapMenuItem.isSelected());
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776 scaleLeft.setVisible(wrapMenuItem.isSelected());
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777 scaleRight.setVisible(wrapMenuItem.isSelected());
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778 alignPanel.repaint();
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781 protected void scaleAbove_actionPerformed(ActionEvent e)
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783 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
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784 alignPanel.repaint();
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787 protected void scaleLeft_actionPerformed(ActionEvent e)
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789 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
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790 alignPanel.repaint();
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793 protected void scaleRight_actionPerformed(ActionEvent e)
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795 viewport.setScaleRightWrapped(scaleRight.isSelected());
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796 alignPanel.repaint();
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799 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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801 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
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802 alignPanel.repaint();
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805 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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807 viewport.setShowText(viewTextMenuItem.isSelected());
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808 alignPanel.repaint();
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811 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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813 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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814 alignPanel.repaint();
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817 public void sequenceFeatures_actionPerformed(ActionEvent evt)
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819 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
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821 if (viewport.showSequenceFeatures &&
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822 ! ( (Alignment) viewport.alignment).featuresAdded)
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824 SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.
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827 ( (Alignment) viewport.alignment).featuresAdded = true;
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830 alignPanel.repaint();
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833 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
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835 if (annotationPanelMenuItem.isSelected() &&
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836 viewport.getWrapAlignment())
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838 annotationPanelMenuItem.setSelected(false);
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843 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
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844 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
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847 public void overviewMenuItem_actionPerformed(ActionEvent e)
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849 if (alignPanel.overviewPanel != null)
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854 JInternalFrame frame = new JInternalFrame();
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855 OverviewPanel overview = new OverviewPanel(alignPanel);
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856 frame.setContentPane(overview);
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857 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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858 frame.getWidth(), frame.getHeight());
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860 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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861 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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863 public void internalFrameClosed(
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864 javax.swing.event.InternalFrameEvent evt)
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866 alignPanel.setOverviewPanel(null);
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871 alignPanel.setOverviewPanel(overview);
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874 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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876 changeColour(null);
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879 public void clustalColour_actionPerformed(ActionEvent e)
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881 changeColour(new ClustalxColourScheme(
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882 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
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885 public void zappoColour_actionPerformed(ActionEvent e)
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887 changeColour(new ZappoColourScheme());
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890 public void taylorColour_actionPerformed(ActionEvent e)
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892 changeColour(new TaylorColourScheme());
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895 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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897 changeColour(new HydrophobicColourScheme());
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900 public void helixColour_actionPerformed(ActionEvent e)
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902 changeColour(new HelixColourScheme());
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905 public void strandColour_actionPerformed(ActionEvent e)
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907 changeColour(new StrandColourScheme());
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910 public void turnColour_actionPerformed(ActionEvent e)
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912 changeColour(new TurnColourScheme());
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915 public void buriedColour_actionPerformed(ActionEvent e)
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917 changeColour(new BuriedColourScheme());
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920 public void nucleotideColour_actionPerformed(ActionEvent e)
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922 changeColour(new NucleotideColourScheme());
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925 protected void applyToAllGroups_actionPerformed(ActionEvent e)
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927 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
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930 void changeColour(ColourSchemeI cs)
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934 if (viewport.getAbovePIDThreshold())
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936 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
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939 if (cs instanceof ResidueColourScheme)
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941 ( (ResidueColourScheme) cs).setThreshold(threshold);
\r
943 else if (cs instanceof ScoreColourScheme)
\r
945 ( (ScoreColourScheme) cs).setThreshold(threshold);
\r
948 viewport.setGlobalColourScheme(cs);
\r
950 else if (cs instanceof ResidueColourScheme)
\r
952 ( (ResidueColourScheme) cs).setThreshold(0);
\r
954 else if (cs instanceof ScoreColourScheme)
\r
956 ( (ScoreColourScheme) cs).setThreshold(0);
\r
959 if (viewport.getConservationSelected())
\r
961 ConservationColourScheme ccs = null;
\r
963 Alignment al = (Alignment) viewport.alignment;
\r
964 Conservation c = new Conservation("All",
\r
965 ResidueProperties.propHash, 3,
\r
966 al.getSequences(), 0,
\r
967 al.getWidth() - 1);
\r
970 c.verdict(false, viewport.ConsPercGaps);
\r
972 ccs = new ConservationColourScheme(c, cs);
\r
974 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
975 ccs.setConsensus(viewport.vconsensus);
\r
976 viewport.setGlobalColourScheme(ccs);
\r
978 ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,
\r
983 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
986 cs.setConsensus(viewport.vconsensus);
\r
989 viewport.setGlobalColourScheme(cs);
\r
992 if (viewport.getColourAppliesToAllGroups())
\r
994 Vector groups = viewport.alignment.getGroups();
\r
996 for (int i = 0; i < groups.size(); i++)
\r
998 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1004 else if (cs instanceof ClustalxColourScheme)
\r
1006 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1008 else if (cs instanceof UserColourScheme)
\r
1010 sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());
\r
1016 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1018 catch (Exception ex)
\r
1023 if (viewport.getAbovePIDThreshold())
\r
1025 if (sg.cs instanceof ResidueColourScheme)
\r
1027 ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
\r
1029 else if (sg.cs instanceof ScoreColourScheme)
\r
1031 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
\r
1034 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1038 if (viewport.getConservationSelected())
\r
1040 Conservation c = new Conservation("Group",
\r
1041 ResidueProperties.propHash, 3,
\r
1043 viewport.alignment.getWidth() - 1);
\r
1045 c.verdict(false, viewport.ConsPercGaps);
\r
1047 ConservationColourScheme ccs = new ConservationColourScheme(c,
\r
1050 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
1051 ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1055 else if (cs != null)
\r
1057 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
1058 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1064 if (alignPanel.getOverviewPanel() != null)
\r
1066 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1069 alignPanel.repaint();
\r
1072 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1074 if (viewport.getAbovePIDThreshold())
\r
1076 SliderPanel.setPIDSliderSource(alignPanel,
\r
1077 viewport.getGlobalColourScheme(),
\r
1079 SliderPanel.showPIDSlider();
\r
1083 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1085 if (viewport.getConservationSelected())
\r
1087 SliderPanel.setConservationSlider(alignPanel,
\r
1088 viewport.globalColourScheme,
\r
1090 SliderPanel.showConservationSlider();
\r
1094 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1096 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1098 viewport.setAbovePIDThreshold(false);
\r
1099 abovePIDThreshold.setSelected(false);
\r
1101 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
1103 if (cs instanceof ConservationColourScheme)
\r
1105 changeColour( ( (ConservationColourScheme) cs).cs);
\r
1112 modifyConservation_actionPerformed(null);
\r
1115 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1117 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1119 conservationMenuItem.setSelected(false);
\r
1120 viewport.setConservationSelected(false);
\r
1122 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
1124 if (cs instanceof ConservationColourScheme)
\r
1126 changeColour( ( (ConservationColourScheme) cs).cs);
\r
1133 modifyPID_actionPerformed(null);
\r
1136 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1138 new UserDefinedColours(alignPanel, null);
\r
1141 public void PIDColour_actionPerformed(ActionEvent e)
\r
1143 changeColour(new PIDColourScheme());
\r
1146 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1148 changeColour(new Blosum62ColourScheme());
\r
1151 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1153 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1154 HistoryItem.SORT));
\r
1155 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1156 viewport.getAlignment().getSequenceAt(0));
\r
1157 alignPanel.repaint();
\r
1160 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1162 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1163 HistoryItem.SORT));
\r
1164 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1165 alignPanel.repaint();
\r
1168 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1170 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1171 HistoryItem.SORT));
\r
1173 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1174 alignPanel.repaint();
\r
1177 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1179 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1180 JInternalFrame frame = new JInternalFrame();
\r
1181 frame.setContentPane(sp);
\r
1182 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1186 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1188 if ( (viewport.getSelectionGroup() == null) ||
\r
1189 (viewport.getSelectionGroup().getSize() < 2))
\r
1191 JOptionPane.showInternalMessageDialog(this,
\r
1192 "You must select at least 2 sequences.",
\r
1193 "Invalid Selection",
\r
1194 JOptionPane.WARNING_MESSAGE);
\r
1198 JInternalFrame frame = new JInternalFrame();
\r
1199 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1200 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1204 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1206 if ( ( (viewport.getSelectionGroup() != null) &&
\r
1207 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1208 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1209 (viewport.getAlignment().getHeight() < 4))
\r
1211 JOptionPane.showInternalMessageDialog(this,
\r
1212 "Principal component analysis must take\n" +
\r
1213 "at least 4 input sequences.",
\r
1214 "Sequence selection insufficient",
\r
1215 JOptionPane.WARNING_MESSAGE);
\r
1222 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
1223 JInternalFrame frame = new JInternalFrame();
\r
1224 frame.setContentPane(pcaPanel);
\r
1225 Desktop.addInternalFrame(frame, "Principal component analysis",
\r
1228 catch (java.lang.OutOfMemoryError ex)
\r
1230 JOptionPane.showInternalMessageDialog(this,
\r
1231 "Too many sequences selected\nfor Principal Component Analysis!!",
\r
1233 JOptionPane.WARNING_MESSAGE);
\r
1237 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1239 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1242 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1244 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1247 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1249 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1252 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1254 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
1257 void NewTreePanel(String type, String pwType, String title)
\r
1259 final TreePanel tp;
\r
1261 if ( (viewport.getSelectionGroup() != null) &&
\r
1262 (viewport.getSelectionGroup().getSize() > 3))
\r
1265 SequenceGroup sg = viewport.getSelectionGroup();
\r
1267 /* Decide if the selection is a column region */
\r
1268 while (s < sg.sequences.size())
\r
1270 if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
\r
1273 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1274 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
1275 "Try using the Pad function in the edit menu,\n" +
\r
1276 "or one of the multiple sequence alignment web services.",
\r
1277 "Sequences in selection are not aligned",
\r
1278 JOptionPane.WARNING_MESSAGE);
\r
1284 title = title + " on region";
\r
1285 tp = new TreePanel(viewport,
\r
1286 viewport.getSelectionGroup().sequences, type, pwType,
\r
1287 sg.getStartRes(), sg.getEndRes());
\r
1291 //are the sequences aligned?
\r
1292 if (!viewport.alignment.isAligned())
\r
1294 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1295 "The sequences must be aligned before creating a tree.\n" +
\r
1296 "Try using the Pad function in the edit menu,\n" +
\r
1297 "or one of the multiple sequence alignment web services.",
\r
1298 "Sequences not aligned",
\r
1299 JOptionPane.WARNING_MESSAGE);
\r
1304 tp = new TreePanel(viewport,
\r
1305 viewport.getAlignment().getSequences(), type, pwType,
\r
1307 viewport.alignment.getWidth());
\r
1310 addTreeMenuItem(tp, title);
\r
1311 viewport.setCurrentTree(tp.getTree());
\r
1313 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
1316 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
1318 final JMenuItem item = new JMenuItem("by " + title);
\r
1320 item.addActionListener(new java.awt.event.ActionListener()
\r
1322 public void actionPerformed(ActionEvent e)
\r
1324 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1325 HistoryItem.SORT));
\r
1327 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
1328 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
1329 alignPanel.repaint();
\r
1334 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1336 final JMenuItem item = new JMenuItem(title);
\r
1340 if (treeCount == 1)
\r
1342 sort.add(sortByTreeMenu);
\r
1345 sortByTreeMenu.add(item);
\r
1346 item.addActionListener(new java.awt.event.ActionListener()
\r
1348 public void actionPerformed(ActionEvent e)
\r
1350 addHistoryItem(new HistoryItem("Tree Sort",
\r
1351 viewport.alignment, HistoryItem.SORT));
\r
1352 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
1353 treePanel.getTree());
\r
1354 alignPanel.repaint();
\r
1358 treePanel.addInternalFrameListener(new javax.swing.event.
\r
1359 InternalFrameAdapter()
\r
1361 public void internalFrameClosed(
\r
1362 javax.swing.event.InternalFrameEvent evt)
\r
1365 sortByTreeMenu.remove(item);
\r
1367 if (treeCount == 0)
\r
1369 sort.remove(sortByTreeMenu);
\r
1374 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
\r
1376 public void propertyChange(PropertyChangeEvent evt)
\r
1378 if (evt.getPropertyName().equals("alignment"))
\r
1380 treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
\r
1381 treePanel.repaint();
\r
1387 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
1389 // TODO:resolve which menu item was actually selected
\r
1390 // Now, check we have enough sequences
\r
1391 SequenceI[] msa = null;
\r
1393 if ( (viewport.getSelectionGroup() != null) &&
\r
1394 (viewport.getSelectionGroup().getSize() > 1))
\r
1396 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1397 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1399 msa = new SequenceI[sz = seqs.getSize()];
\r
1401 for (int i = 0; i < sz; i++)
\r
1403 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1408 Vector seqs = viewport.getAlignment().getSequences();
\r
1410 if (seqs.size() > 1)
\r
1412 msa = new SequenceI[seqs.size()];
\r
1414 for (int i = 0; i < seqs.size(); i++)
\r
1416 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1423 jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
\r
1424 title, msa, false, true);
\r
1428 public void ClustalRealign_actionPerformed(ActionEvent e)
\r
1430 // TODO:resolve which menu item was actually selected
\r
1431 // Now, check we have enough sequences
\r
1432 SequenceI[] msa = null;
\r
1434 if ( (viewport.getSelectionGroup() != null) &&
\r
1435 (viewport.getSelectionGroup().getSize() > 1))
\r
1437 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1438 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1440 msa = new SequenceI[sz = seqs.getSize()];
\r
1442 for (int i = 0; i < sz; i++)
\r
1444 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1449 Vector seqs = viewport.getAlignment().getSequences();
\r
1451 if (seqs.size() > 1)
\r
1453 msa = new SequenceI[seqs.size()];
\r
1455 for (int i = 0; i < seqs.size(); i++)
\r
1457 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1464 jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
\r
1465 title, msa, true, true);
\r
1469 protected void jpred_actionPerformed(ActionEvent e)
\r
1471 SequenceI seq = null;
\r
1472 SequenceI[] msa = null;
\r
1474 if ( (viewport.getSelectionGroup() != null) &&
\r
1475 (viewport.getSelectionGroup().getSize() > 0))
\r
1477 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1478 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1480 if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
1482 seq = (SequenceI) seqs.getSequenceAt(0);
\r
1487 msa = new SequenceI[sz = seqs.getSize()];
\r
1489 for (int i = 0; i < sz; i++)
\r
1491 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1497 Vector seqs = viewport.getAlignment().getSequences();
\r
1499 if ( (seqs.size() == 1) || !viewport.alignment.isAligned())
\r
1501 seq = (SequenceI) seqs.elementAt(0);
\r
1505 msa = new SequenceI[seqs.size()];
\r
1507 for (int i = 0; i < seqs.size(); i++)
\r
1509 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1516 JPredClient ct = new JPredClient(title, msa);
\r
1518 else if (seq != null)
\r
1520 JPredClient ct = new JPredClient(title, seq);
\r
1525 "JALVIEW ERROR! - Unexpected JPred selection state!\n");
\r
1529 protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
\r
1531 // TODO:resolve which menu item was actually selected
\r
1532 // Now, check we have enough sequences
\r
1533 SequenceI[] msa = null;
\r
1535 if ( (viewport.getSelectionGroup() != null) &&
\r
1536 (viewport.getSelectionGroup().getSize() > 1))
\r
1538 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1539 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1541 msa = new SequenceI[sz = seqs.getSize()];
\r
1543 for (int i = 0; i < sz; i++)
\r
1545 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1550 Vector seqs = viewport.getAlignment().getSequences();
\r
1552 if (seqs.size() > 1)
\r
1554 msa = new SequenceI[seqs.size()];
\r
1556 for (int i = 0; i < seqs.size(); i++)
\r
1558 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1565 MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,
\r
1570 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
1572 // Pick the tree file
\r
1573 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
1575 "LAST_DIRECTORY"));
\r
1576 chooser.setFileView(new JalviewFileView());
\r
1577 chooser.setDialogTitle("Select a newick-like tree file");
\r
1578 chooser.setToolTipText("Load a tree file");
\r
1580 int value = chooser.showOpenDialog(null);
\r
1582 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
1584 String choice = chooser.getSelectedFile().getPath();
\r
1585 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1589 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
1591 viewport.setCurrentTree( ShowNewickTree(fin, choice).getTree() );
\r
1593 catch (Exception ex)
\r
1595 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1596 "Problem reading tree file",
\r
1598 JOptionPane.WARNING_MESSAGE);
\r
1599 ex.printStackTrace();
\r
1604 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
1606 TreePanel tp = null;
\r
1610 if (nf.getTree() != null)
\r
1612 tp = new TreePanel(viewport,
\r
1613 viewport.getAlignment().getSequences(), nf,
\r
1616 Desktop.addInternalFrame(tp, title, 600, 500);
\r
1617 addTreeMenuItem(tp, title);
\r
1620 catch (Exception ex)
\r
1622 ex.printStackTrace();
\r
1632 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
1633 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
1634 printJob.setPrintable(alignPanel, pf);
\r
1636 if (printJob.printDialog())
\r
1642 catch (Exception PrintException)
\r
1644 PrintException.printStackTrace();
\r