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 jalview.analysis.*;
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23 import jalview.datamodel.*;
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25 import jalview.io.*;
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27 import jalview.jbgui.*;
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29 import jalview.schemes.*;
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31 import jalview.ws.*;
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34 import java.awt.datatransfer.*;
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35 import java.awt.event.*;
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36 import java.awt.print.*;
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40 import java.beans.*;
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44 import javax.swing.*;
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45 import javax.swing.event.*;
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52 * @version $Revision$
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54 public class AlignFrame extends GAlignFrame
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56 /** DOCUMENT ME!! */
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57 public static final int NEW_WINDOW_WIDTH = 700;
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59 /** DOCUMENT ME!! */
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60 public static final int NEW_WINDOW_HEIGHT = 500;
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61 final AlignmentPanel alignPanel;
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62 final AlignViewport viewport;
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64 /** DOCUMENT ME!! */
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65 public String currentFileFormat = null;
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66 Stack historyList = new Stack();
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67 Stack redoList = new Stack();
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68 private int treeCount = 0;
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71 * Creates a new AlignFrame object.
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73 * @param al DOCUMENT ME!
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75 public AlignFrame(AlignmentI al)
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77 viewport = new AlignViewport(al);
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79 alignPanel = new AlignmentPanel(this, viewport);
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80 alignPanel.annotationPanel.adjustPanelHeight();
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81 alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
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82 alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
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83 alignPanel.setAnnotationVisible(viewport.getShowAnnotation());
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85 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
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87 addInternalFrameListener(new InternalFrameAdapter()
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89 public void internalFrameActivated(InternalFrameEvent evt)
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91 javax.swing.SwingUtilities.invokeLater(new Runnable()
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95 alignPanel.requestFocus();
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106 * @param e DOCUMENT ME!
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108 public void parseGroupsFile(String file)
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111 BufferedReader in = new BufferedReader(new FileReader(file));
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112 SequenceI seq=null;
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113 String line, text, token;
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114 UserColourScheme ucs;
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115 int index, start, end;
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116 StringTokenizer st;
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118 while( (line = in.readLine())!=null)
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120 st = new StringTokenizer(line, "\t");
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121 if(st.countTokens()!=6)
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123 System.out.println("Groups file "+file+" is invalid. Read help file.");
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127 while(st.hasMoreElements())
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129 text = st.nextToken();
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130 token = st.nextToken();
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131 if(!token.equals("ID_NOT_SPECIFIED"))
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133 index = viewport.alignment.findIndex(viewport.alignment.findName(
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138 index = Integer.parseInt( st.nextToken() );
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140 start=Integer.parseInt( st.nextToken() );
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141 end = Integer.parseInt( st.nextToken() );
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142 ucs = new UserColourScheme(st.nextToken());
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144 seq = viewport.alignment.getSequenceAt(index);
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145 start = seq.findIndex(start)-1;
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146 end = seq.findIndex(end)-1;
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148 sg = new SequenceGroup(text,ucs,true,true,false,start,end);
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149 sg.addSequence( seq,true);
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151 viewport.alignment.addGroup(sg);
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155 }catch(Exception ex){System.out.println("Error parsing groups file: "+ex);}
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161 * @param e DOCUMENT ME!
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163 public void saveAlignmentMenu_actionPerformed(ActionEvent e)
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165 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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169 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
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174 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
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175 }, currentFileFormat);
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177 chooser.setAcceptAllFileFilterUsed(false);
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178 chooser.setFileView(new JalviewFileView());
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179 chooser.setDialogTitle("Save Alignment to file");
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180 chooser.setToolTipText("Save");
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182 int value = chooser.showSaveDialog(this);
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184 if (value == JalviewFileChooser.APPROVE_OPTION)
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186 currentFileFormat = chooser.getSelectedFormat();
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187 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
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188 currentFileFormat);
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190 String choice = chooser.getSelectedFile().getPath();
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191 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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193 saveAlignment(choice, currentFileFormat);
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197 public boolean saveAlignment(String file, String format)
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199 if (format.equalsIgnoreCase("Jalview"))
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201 String shortName = title;
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203 if (shortName.indexOf(java.io.File.separatorChar) > -1)
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205 shortName = shortName.substring(shortName.lastIndexOf(
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206 java.io.File.separatorChar) + 1);
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209 Jalview2XML.SaveAlignment(this, file, shortName);
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211 // USE Jalview2XML to save this file
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216 String output = FormatAdapter.formatSequences(format,
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217 viewport.getAlignment().
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224 java.io.PrintWriter out = new java.io.PrintWriter(
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225 new java.io.FileWriter(file));
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226 out.println(output);
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230 catch (Exception ex)
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232 ex.printStackTrace();
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242 * @param e DOCUMENT ME!
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244 protected void outputText_actionPerformed(ActionEvent e)
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246 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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247 Desktop.addInternalFrame(cap,
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248 "Alignment output - " + e.getActionCommand(), 600, 500);
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249 cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),
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250 viewport.getAlignment().getSequences()));
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256 * @param e DOCUMENT ME!
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258 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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260 new HTMLOutput(viewport);
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263 public void createImageMap(File file, String image)
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265 alignPanel.makePNGImageMap(file, image);
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271 * @param e DOCUMENT ME!
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273 public void createPNG(File f)
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275 alignPanel.makePNG(f);
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281 * @param e DOCUMENT ME!
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283 public void createEPS(File f)
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285 alignPanel.makeEPS(f);
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291 * @param e DOCUMENT ME!
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293 public void printMenuItem_actionPerformed(ActionEvent e)
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295 //Putting in a thread avoids Swing painting problems
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296 PrintThread thread = new PrintThread();
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303 * @param e DOCUMENT ME!
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305 public void closeMenuItem_actionPerformed(ActionEvent e)
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309 this.setClosed(true);
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311 catch (Exception ex)
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319 void updateEditMenuBar()
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321 if (historyList.size() > 0)
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323 undoMenuItem.setEnabled(true);
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325 HistoryItem hi = (HistoryItem) historyList.peek();
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326 undoMenuItem.setText("Undo " + hi.getDescription());
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330 undoMenuItem.setEnabled(false);
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331 undoMenuItem.setText("Undo");
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334 if (redoList.size() > 0)
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336 redoMenuItem.setEnabled(true);
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338 HistoryItem hi = (HistoryItem) redoList.peek();
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339 redoMenuItem.setText("Redo " + hi.getDescription());
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343 redoMenuItem.setEnabled(false);
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344 redoMenuItem.setText("Redo");
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351 * @param hi DOCUMENT ME!
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353 public void addHistoryItem(HistoryItem hi)
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355 historyList.push(hi);
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356 updateEditMenuBar();
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362 * @param e DOCUMENT ME!
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364 protected void undoMenuItem_actionPerformed(ActionEvent e)
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366 HistoryItem hi = (HistoryItem) historyList.pop();
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367 redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,
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368 HistoryItem.HIDE));
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369 restoreHistoryItem(hi);
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375 * @param e DOCUMENT ME!
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377 protected void redoMenuItem_actionPerformed(ActionEvent e)
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379 HistoryItem hi = (HistoryItem) redoList.pop();
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380 restoreHistoryItem(hi);
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381 updateEditMenuBar();
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382 viewport.updateConsensus();
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383 alignPanel.repaint();
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384 alignPanel.repaint();
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387 // used by undo and redo
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388 void restoreHistoryItem(HistoryItem hi)
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390 if (hi.getType() == HistoryItem.SORT)
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392 for (int i = 0; i < hi.getSequences().size(); i++)
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394 viewport.alignment.getSequences().setElementAt(hi.getSequences()
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401 for (int i = 0; i < hi.getSequences().size(); i++)
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403 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
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405 if (restore.getLength() == 0)
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407 restore.setSequence(hi.getHidden().elementAt(i).toString());
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408 viewport.alignment.getSequences().insertElementAt(restore,
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409 hi.getAlignIndex(i));
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413 restore.setSequence(hi.getHidden().elementAt(i).toString());
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417 if (hi.getType() == HistoryItem.PASTE)
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419 for (int i = viewport.alignment.getHeight() - 1;
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420 i > (hi.getSequences().size() - 1); i--)
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422 viewport.alignment.deleteSequence(i);
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427 updateEditMenuBar();
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429 viewport.updateConsensus();
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430 viewport.updateConservation();
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431 alignPanel.repaint();
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432 viewport.firePropertyChange("alignment", null,
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433 viewport.getAlignment().getSequences());
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439 * @param up DOCUMENT ME!
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441 public void moveSelectedSequences(boolean up)
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443 SequenceGroup sg = viewport.getSelectionGroup();
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452 for (int i = 1; i < viewport.alignment.getHeight(); i++)
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454 SequenceI seq = viewport.alignment.getSequenceAt(i);
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456 if (!sg.sequences.contains(seq))
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461 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
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463 if (sg.sequences.contains(temp))
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468 viewport.alignment.getSequences().setElementAt(temp, i);
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469 viewport.alignment.getSequences().setElementAt(seq, i - 1);
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474 for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
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476 SequenceI seq = viewport.alignment.getSequenceAt(i);
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478 if (!sg.sequences.contains(seq))
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483 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
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485 if (sg.sequences.contains(temp))
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490 viewport.alignment.getSequences().setElementAt(temp, i);
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491 viewport.alignment.getSequences().setElementAt(seq, i + 1);
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495 alignPanel.repaint();
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501 * @param e DOCUMENT ME!
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503 protected void copy_actionPerformed(ActionEvent e)
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505 if (viewport.getSelectionGroup() == null)
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510 SequenceGroup sg = viewport.getSelectionGroup();
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512 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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513 StringBuffer buffer = new StringBuffer();
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515 Hashtable orderedSeqs = new Hashtable();
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517 for (int i = 0; i < sg.getSize(); i++)
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519 SequenceI seq = sg.getSequenceAt(i);
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520 int index = viewport.alignment.findIndex(seq);
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521 orderedSeqs.put(index + "", seq);
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526 for (int i = 0; i < sg.getSize(); i++)
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528 SequenceI seq = null;
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530 while (seq == null)
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532 if (orderedSeqs.containsKey(index + ""))
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534 seq = (SequenceI) orderedSeqs.get(index + "");
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545 buffer.append(seq.getName() + "\t" +
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546 seq.findPosition(sg.getStartRes()) + "\t" +
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547 seq.findPosition(sg.getEndRes()) + "\t" +
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548 sg.getSequenceAt(i).getSequence(sg.getStartRes(),
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549 sg.getEndRes() + 1) + "\n");
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552 c.setContents(new StringSelection(buffer.toString()), null);
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558 * @param e DOCUMENT ME!
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560 protected void pasteNew_actionPerformed(ActionEvent e)
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568 * @param e DOCUMENT ME!
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570 protected void pasteThis_actionPerformed(ActionEvent e)
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572 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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573 HistoryItem.PASTE));
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580 * @param newAlignment DOCUMENT ME!
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582 void paste(boolean newAlignment)
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586 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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587 Transferable contents = c.getContents(this);
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589 if (contents == null)
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594 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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595 StringTokenizer st = new StringTokenizer(str);
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596 ArrayList seqs = new ArrayList();
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598 while (st.hasMoreElements())
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600 String name = st.nextToken();
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601 int start = Integer.parseInt(st.nextToken());
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602 int end = Integer.parseInt(st.nextToken());
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603 Sequence sequence = new Sequence(name, st.nextToken(), start,
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608 viewport.alignment.addSequence(sequence);
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612 seqs.add(sequence);
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618 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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619 seqs.toArray(newSeqs);
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621 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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622 String newtitle = new String("Copied sequences");
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624 if (title.startsWith("Copied sequences"))
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630 newtitle = newtitle.concat("- from " + title);
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633 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
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634 NEW_WINDOW_HEIGHT);
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638 viewport.firePropertyChange("alignment", null,
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639 viewport.getAlignment().getSequences());
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640 viewport.setEndSeq(viewport.alignment.getHeight());
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641 viewport.alignment.getWidth();
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642 viewport.updateConservation();
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643 viewport.updateConsensus();
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644 alignPanel.repaint();
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647 catch (Exception ex)
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651 // could be anything being pasted in here
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657 * @param e DOCUMENT ME!
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659 protected void cut_actionPerformed(ActionEvent e)
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661 copy_actionPerformed(null);
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662 delete_actionPerformed(null);
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668 * @param e DOCUMENT ME!
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670 protected void delete_actionPerformed(ActionEvent e)
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672 boolean seqsdeleted = false;
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674 if (viewport.getSelectionGroup() == null)
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679 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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680 HistoryItem.HIDE));
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682 SequenceGroup sg = viewport.getSelectionGroup();
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683 boolean allSequences = false;
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684 if(sg.sequences.size()==viewport.alignment.getHeight())
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685 allSequences = true;
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687 for (int i = 0; i < sg.sequences.size(); i++)
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689 SequenceI seq = sg.getSequenceAt(i);
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690 int index = viewport.getAlignment().findIndex(seq);
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691 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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693 // If the cut affects all sequences, remove highlighted columns
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696 viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes()+1);
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700 if (seq.getSequence().length() < 1)
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702 seqsdeleted = true;
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703 viewport.getAlignment().deleteSequence(seq);
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707 viewport.getAlignment().getSequences().setElementAt(seq, index);
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711 viewport.setSelectionGroup(null);
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712 viewport.alignment.deleteGroup(sg);
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716 viewport.firePropertyChange("alignment", null,
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717 viewport.getAlignment().getSequences());
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720 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
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722 if (viewport.getAlignment().getHeight() < 1)
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726 this.setClosed(true);
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728 catch (Exception ex)
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733 viewport.updateConservation();
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734 viewport.updateConsensus();
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735 alignPanel.repaint();
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741 * @param e DOCUMENT ME!
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743 protected void deleteGroups_actionPerformed(ActionEvent e)
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745 viewport.alignment.deleteAllGroups();
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746 viewport.setSelectionGroup(null);
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747 alignPanel.repaint();
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753 * @param e DOCUMENT ME!
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755 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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757 SequenceGroup sg = new SequenceGroup();
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759 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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762 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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765 sg.setEndRes(viewport.alignment.getWidth());
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766 viewport.setSelectionGroup(sg);
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767 PaintRefresher.Refresh(null, viewport.alignment);
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773 * @param e DOCUMENT ME!
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775 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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777 viewport.setSelectionGroup(null);
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778 viewport.getColumnSelection().clear();
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779 viewport.setSelectionGroup(null);
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780 alignPanel.annotationPanel.activeRes = null;
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781 PaintRefresher.Refresh(null, viewport.alignment);
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787 * @param e DOCUMENT ME!
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789 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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791 SequenceGroup sg = viewport.getSelectionGroup();
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795 selectAllSequenceMenuItem_actionPerformed(null);
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800 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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803 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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806 PaintRefresher.Refresh(null, viewport.alignment);
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812 * @param e DOCUMENT ME!
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814 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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816 ColumnSelection colSel = viewport.getColumnSelection();
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818 if (colSel.size() > 0)
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820 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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821 HistoryItem.HIDE));
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823 int min = colSel.getMin();
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824 viewport.getAlignment().trimLeft(min);
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825 colSel.compensateForEdit(0, min);
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827 if (viewport.getSelectionGroup() != null)
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829 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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832 Vector groups = viewport.alignment.getGroups();
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834 for (int i = 0; i < groups.size(); i++)
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836 SequenceGroup sg = (SequenceGroup) groups.get(i);
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838 if (!sg.adjustForRemoveLeft(min))
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840 viewport.alignment.deleteGroup(sg);
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844 alignPanel.repaint();
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851 * @param e DOCUMENT ME!
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853 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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855 ColumnSelection colSel = viewport.getColumnSelection();
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857 if (colSel.size() > 0)
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859 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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860 HistoryItem.HIDE));
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862 int max = colSel.getMax();
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863 viewport.getAlignment().trimRight(max);
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865 if (viewport.getSelectionGroup() != null)
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867 viewport.getSelectionGroup().adjustForRemoveRight(max);
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870 Vector groups = viewport.alignment.getGroups();
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872 for (int i = 0; i < groups.size(); i++)
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874 SequenceGroup sg = (SequenceGroup) groups.get(i);
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876 if (!sg.adjustForRemoveRight(max))
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878 viewport.alignment.deleteGroup(sg);
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882 alignPanel.repaint();
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889 * @param e DOCUMENT ME!
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891 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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893 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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894 viewport.alignment, HistoryItem.HIDE));
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896 viewport.getAlignment().removeGaps();
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897 viewport.updateConservation();
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898 viewport.updateConsensus();
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899 alignPanel.repaint();
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905 * @param e DOCUMENT ME!
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907 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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909 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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910 HistoryItem.HIDE));
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915 Vector seqs = null;
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918 int end = viewport.alignment.getWidth();
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920 if (viewport.getSelectionGroup() != null)
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922 seqs = viewport.getSelectionGroup().sequences;
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923 start = viewport.getSelectionGroup().getStartRes();
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924 end = viewport.getSelectionGroup().getEndRes();
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928 seqs = viewport.alignment.getSequences();
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931 for (int i = 0; i < seqs.size(); i++)
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933 current = (SequenceI) seqs.elementAt(i);
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934 jSize = current.getLength();
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940 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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942 current.deleteCharAt(j);
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949 while (j < end && j < jSize);
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952 viewport.updateConservation();
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953 viewport.updateConsensus();
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954 alignPanel.repaint();
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960 * @param e DOCUMENT ME!
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962 public void padGapsMenuitem_actionPerformed(ActionEvent e)
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964 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
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965 HistoryItem.HIDE));
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968 int Width = viewport.getAlignment().getWidth();
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970 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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973 current = viewport.getAlignment().getSequenceAt(i);
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975 if (current.getLength() < Width)
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977 current.insertCharAt(Width - 1, viewport.getGapCharacter());
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981 viewport.updateConservation();
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982 viewport.updateConsensus();
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983 alignPanel.repaint();
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989 * @param e DOCUMENT ME!
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991 public void findMenuItem_actionPerformed(ActionEvent e)
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993 JInternalFrame frame = new JInternalFrame();
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994 Finder finder = new Finder(viewport, alignPanel, frame);
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995 frame.setContentPane(finder);
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996 Desktop.addInternalFrame(frame, "Find", 340, 110);
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997 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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1003 * @param e DOCUMENT ME!
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1005 public void font_actionPerformed(ActionEvent e)
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1007 FontChooser fc = new FontChooser(alignPanel);
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1013 * @param e DOCUMENT ME!
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1015 protected void fullSeqId_actionPerformed(ActionEvent e)
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1017 viewport.setShowFullId(fullSeqId.isSelected());
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1019 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
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1020 alignPanel.repaint();
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1026 * @param e DOCUMENT ME!
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1028 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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1030 viewport.setColourText(colourTextMenuItem.isSelected());
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1031 alignPanel.repaint();
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1037 * @param e DOCUMENT ME!
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1039 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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1041 viewport.setWrapAlignment(wrapMenuItem.isSelected());
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1042 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
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1043 scaleAbove.setVisible(wrapMenuItem.isSelected());
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1044 scaleLeft.setVisible(wrapMenuItem.isSelected());
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1045 scaleRight.setVisible(wrapMenuItem.isSelected());
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1046 alignPanel.repaint();
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1052 * @param e DOCUMENT ME!
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1054 protected void scaleAbove_actionPerformed(ActionEvent e)
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1056 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
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1057 alignPanel.repaint();
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1063 * @param e DOCUMENT ME!
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1065 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1067 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1068 alignPanel.repaint();
\r
1074 * @param e DOCUMENT ME!
\r
1076 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1078 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1079 alignPanel.repaint();
\r
1085 * @param e DOCUMENT ME!
\r
1087 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1089 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1090 alignPanel.repaint();
\r
1096 * @param e DOCUMENT ME!
\r
1098 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1100 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1101 alignPanel.repaint();
\r
1107 * @param e DOCUMENT ME!
\r
1109 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1111 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1112 alignPanel.repaint();
\r
1118 * @param evt DOCUMENT ME!
\r
1120 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1122 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1124 if (viewport.showSequenceFeatures &&
\r
1125 !((Alignment) viewport.alignment).featuresAdded)
\r
1127 SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment,
\r
1129 ((Alignment) viewport.alignment).featuresAdded = true;
\r
1132 alignPanel.repaint();
\r
1138 * @param e DOCUMENT ME!
\r
1140 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1142 if (annotationPanelMenuItem.isSelected() &&
\r
1143 viewport.getWrapAlignment())
\r
1145 annotationPanelMenuItem.setSelected(false);
\r
1150 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1151 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1157 * @param e DOCUMENT ME!
\r
1159 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1161 if (alignPanel.overviewPanel != null)
\r
1166 JInternalFrame frame = new JInternalFrame();
\r
1167 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1168 frame.setContentPane(overview);
\r
1169 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1170 frame.getWidth(), frame.getHeight());
\r
1172 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1173 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1175 public void internalFrameClosed(
\r
1176 javax.swing.event.InternalFrameEvent evt)
\r
1178 alignPanel.setOverviewPanel(null);
\r
1183 alignPanel.setOverviewPanel(overview);
\r
1189 * @param e DOCUMENT ME!
\r
1191 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1193 changeColour(null);
\r
1199 * @param e DOCUMENT ME!
\r
1201 public void clustalColour_actionPerformed(ActionEvent e)
\r
1203 changeColour(new ClustalxColourScheme(
\r
1204 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1210 * @param e DOCUMENT ME!
\r
1212 public void zappoColour_actionPerformed(ActionEvent e)
\r
1214 changeColour(new ZappoColourScheme());
\r
1220 * @param e DOCUMENT ME!
\r
1222 public void taylorColour_actionPerformed(ActionEvent e)
\r
1224 changeColour(new TaylorColourScheme());
\r
1230 * @param e DOCUMENT ME!
\r
1232 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1234 changeColour(new HydrophobicColourScheme());
\r
1240 * @param e DOCUMENT ME!
\r
1242 public void helixColour_actionPerformed(ActionEvent e)
\r
1244 changeColour(new HelixColourScheme());
\r
1250 * @param e DOCUMENT ME!
\r
1252 public void strandColour_actionPerformed(ActionEvent e)
\r
1254 changeColour(new StrandColourScheme());
\r
1260 * @param e DOCUMENT ME!
\r
1262 public void turnColour_actionPerformed(ActionEvent e)
\r
1264 changeColour(new TurnColourScheme());
\r
1270 * @param e DOCUMENT ME!
\r
1272 public void buriedColour_actionPerformed(ActionEvent e)
\r
1274 changeColour(new BuriedColourScheme());
\r
1280 * @param e DOCUMENT ME!
\r
1282 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1284 changeColour(new NucleotideColourScheme());
\r
1290 * @param e DOCUMENT ME!
\r
1292 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1294 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1300 * @param cs DOCUMENT ME!
\r
1302 void changeColour(ColourSchemeI cs)
\r
1304 int threshold = 0;
\r
1306 if (viewport.getAbovePIDThreshold())
\r
1308 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1311 if (cs instanceof ResidueColourScheme)
\r
1313 ((ResidueColourScheme) cs).setThreshold(threshold);
\r
1315 else if (cs instanceof ScoreColourScheme)
\r
1317 ((ScoreColourScheme) cs).setThreshold(threshold);
\r
1320 viewport.setGlobalColourScheme(cs);
\r
1322 else if (cs instanceof ResidueColourScheme)
\r
1324 ((ResidueColourScheme) cs).setThreshold(0);
\r
1326 else if (cs instanceof ScoreColourScheme)
\r
1328 ((ScoreColourScheme) cs).setThreshold(0);
\r
1331 if (viewport.getConservationSelected())
\r
1333 ConservationColourScheme ccs = null;
\r
1335 Alignment al = (Alignment) viewport.alignment;
\r
1336 Conservation c = new Conservation("All",
\r
1337 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
1338 al.getWidth() - 1);
\r
1341 c.verdict(false, viewport.ConsPercGaps);
\r
1343 ccs = new ConservationColourScheme(c, cs);
\r
1345 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
1346 ccs.setConsensus(viewport.vconsensus);
\r
1347 viewport.setGlobalColourScheme(ccs);
\r
1349 ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,
\r
1354 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
1357 cs.setConsensus(viewport.vconsensus);
\r
1360 viewport.setGlobalColourScheme(cs);
\r
1363 if (viewport.getColourAppliesToAllGroups())
\r
1365 Vector groups = viewport.alignment.getGroups();
\r
1367 for (int i = 0; i < groups.size(); i++)
\r
1369 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1375 else if (cs instanceof ClustalxColourScheme)
\r
1377 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1379 else if (cs instanceof UserColourScheme)
\r
1381 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
\r
1387 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1389 catch (Exception ex)
\r
1394 if (viewport.getAbovePIDThreshold())
\r
1396 if (sg.cs instanceof ResidueColourScheme)
\r
1398 ((ResidueColourScheme) sg.cs).setThreshold(threshold);
\r
1400 else if (sg.cs instanceof ScoreColourScheme)
\r
1402 ((ScoreColourScheme) sg.cs).setThreshold(threshold);
\r
1405 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1409 if (viewport.getConservationSelected())
\r
1411 Conservation c = new Conservation("Group",
\r
1412 ResidueProperties.propHash, 3, sg.sequences, 0,
\r
1413 viewport.alignment.getWidth() - 1);
\r
1415 c.verdict(false, viewport.ConsPercGaps);
\r
1417 ConservationColourScheme ccs = new ConservationColourScheme(c,
\r
1420 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
1421 ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1425 else if (cs != null)
\r
1427 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
1428 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1434 if (alignPanel.getOverviewPanel() != null)
\r
1436 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1439 alignPanel.repaint();
\r
1445 * @param e DOCUMENT ME!
\r
1447 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1449 if (viewport.getAbovePIDThreshold())
\r
1451 SliderPanel.setPIDSliderSource(alignPanel,
\r
1452 viewport.getGlobalColourScheme(), "Background");
\r
1453 SliderPanel.showPIDSlider();
\r
1460 * @param e DOCUMENT ME!
\r
1462 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1464 if (viewport.getConservationSelected())
\r
1466 SliderPanel.setConservationSlider(alignPanel,
\r
1467 viewport.globalColourScheme, "Background");
\r
1468 SliderPanel.showConservationSlider();
\r
1475 * @param e DOCUMENT ME!
\r
1477 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1479 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1481 viewport.setAbovePIDThreshold(false);
\r
1482 abovePIDThreshold.setSelected(false);
\r
1484 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
1486 if (cs instanceof ConservationColourScheme)
\r
1488 changeColour(((ConservationColourScheme) cs).cs);
\r
1495 modifyConservation_actionPerformed(null);
\r
1501 * @param e DOCUMENT ME!
\r
1503 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1505 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1507 conservationMenuItem.setSelected(false);
\r
1508 viewport.setConservationSelected(false);
\r
1510 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
1512 if (cs instanceof ConservationColourScheme)
\r
1514 changeColour(((ConservationColourScheme) cs).cs);
\r
1521 modifyPID_actionPerformed(null);
\r
1527 * @param e DOCUMENT ME!
\r
1529 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1531 new UserDefinedColours(alignPanel, null);
\r
1537 * @param e DOCUMENT ME!
\r
1539 public void PIDColour_actionPerformed(ActionEvent e)
\r
1541 changeColour(new PIDColourScheme());
\r
1547 * @param e DOCUMENT ME!
\r
1549 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1551 changeColour(new Blosum62ColourScheme());
\r
1557 * @param e DOCUMENT ME!
\r
1559 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1561 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1562 HistoryItem.SORT));
\r
1563 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1564 viewport.getAlignment().getSequenceAt(0));
\r
1565 alignPanel.repaint();
\r
1571 * @param e DOCUMENT ME!
\r
1573 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1575 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1576 HistoryItem.SORT));
\r
1577 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1578 alignPanel.repaint();
\r
1584 * @param e DOCUMENT ME!
\r
1586 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1588 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1589 HistoryItem.SORT));
\r
1591 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1592 alignPanel.repaint();
\r
1598 * @param e DOCUMENT ME!
\r
1600 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1602 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1603 JInternalFrame frame = new JInternalFrame();
\r
1604 frame.setContentPane(sp);
\r
1605 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1612 * @param e DOCUMENT ME!
\r
1614 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1616 if ((viewport.getSelectionGroup() == null) ||
\r
1617 (viewport.getSelectionGroup().getSize() < 2))
\r
1619 JOptionPane.showInternalMessageDialog(this,
\r
1620 "You must select at least 2 sequences.", "Invalid Selection",
\r
1621 JOptionPane.WARNING_MESSAGE);
\r
1625 JInternalFrame frame = new JInternalFrame();
\r
1626 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1627 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1634 * @param e DOCUMENT ME!
\r
1636 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1638 if (((viewport.getSelectionGroup() != null) &&
\r
1639 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1640 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1641 (viewport.getAlignment().getHeight() < 4))
\r
1643 JOptionPane.showInternalMessageDialog(this,
\r
1644 "Principal component analysis must take\n" +
\r
1645 "at least 4 input sequences.",
\r
1646 "Sequence selection insufficient", JOptionPane.WARNING_MESSAGE);
\r
1653 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
1654 JInternalFrame frame = new JInternalFrame();
\r
1655 frame.setContentPane(pcaPanel);
\r
1656 Desktop.addInternalFrame(frame, "Principal component analysis",
\r
1659 catch (java.lang.OutOfMemoryError ex)
\r
1661 JOptionPane.showInternalMessageDialog(this,
\r
1662 "Too many sequences selected\nfor Principal Component Analysis!!",
\r
1663 "Out of memory", JOptionPane.WARNING_MESSAGE);
\r
1670 * @param e DOCUMENT ME!
\r
1672 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1674 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1680 * @param e DOCUMENT ME!
\r
1682 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1684 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1690 * @param e DOCUMENT ME!
\r
1692 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1694 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1700 * @param e DOCUMENT ME!
\r
1702 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1704 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
1710 * @param type DOCUMENT ME!
\r
1711 * @param pwType DOCUMENT ME!
\r
1712 * @param title DOCUMENT ME!
\r
1714 void NewTreePanel(String type, String pwType, String title)
\r
1716 final TreePanel tp;
\r
1718 if ((viewport.getSelectionGroup() != null) &&
\r
1719 (viewport.getSelectionGroup().getSize() > 3))
\r
1722 SequenceGroup sg = viewport.getSelectionGroup();
\r
1724 /* Decide if the selection is a column region */
\r
1725 while (s < sg.sequences.size())
\r
1727 if (((SequenceI) sg.sequences.elementAt(s++)).getLength() < sg.getEndRes())
\r
1729 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1730 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
1731 "Try using the Pad function in the edit menu,\n" +
\r
1732 "or one of the multiple sequence alignment web services.",
\r
1733 "Sequences in selection are not aligned",
\r
1734 JOptionPane.WARNING_MESSAGE);
\r
1740 title = title + " on region";
\r
1741 tp = new TreePanel(viewport,
\r
1742 viewport.getSelectionGroup().sequences, type, pwType,
\r
1743 sg.getStartRes(), sg.getEndRes());
\r
1747 //are the sequences aligned?
\r
1748 if (!viewport.alignment.isAligned())
\r
1750 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1751 "The sequences must be aligned before creating a tree.\n" +
\r
1752 "Try using the Pad function in the edit menu,\n" +
\r
1753 "or one of the multiple sequence alignment web services.",
\r
1754 "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
\r
1759 tp = new TreePanel(viewport,
\r
1760 viewport.getAlignment().getSequences(), type, pwType, 0,
\r
1761 viewport.alignment.getWidth());
\r
1764 addTreeMenuItem(tp, title);
\r
1765 viewport.setCurrentTree(tp.getTree());
\r
1767 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
1773 * @param title DOCUMENT ME!
\r
1774 * @param order DOCUMENT ME!
\r
1776 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
1778 final JMenuItem item = new JMenuItem("by " + title);
\r
1780 item.addActionListener(new java.awt.event.ActionListener()
\r
1782 public void actionPerformed(ActionEvent e)
\r
1784 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1785 HistoryItem.SORT));
\r
1787 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
1788 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
1789 alignPanel.repaint();
\r
1797 * @param treePanel DOCUMENT ME!
\r
1798 * @param title DOCUMENT ME!
\r
1800 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1802 final JMenuItem item = new JMenuItem(title);
\r
1806 if (treeCount == 1)
\r
1808 sort.add(sortByTreeMenu);
\r
1811 sortByTreeMenu.add(item);
\r
1812 item.addActionListener(new java.awt.event.ActionListener()
\r
1814 public void actionPerformed(ActionEvent e)
\r
1816 addHistoryItem(new HistoryItem("Tree Sort",
\r
1817 viewport.alignment, HistoryItem.SORT));
\r
1818 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
1819 treePanel.getTree());
\r
1820 alignPanel.repaint();
\r
1824 treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1826 public void internalFrameClosed(
\r
1827 javax.swing.event.InternalFrameEvent evt)
\r
1830 sortByTreeMenu.remove(item);
\r
1832 if (treeCount == 0)
\r
1834 sort.remove(sortByTreeMenu);
\r
1839 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
\r
1841 public void propertyChange(PropertyChangeEvent evt)
\r
1843 if (evt.getPropertyName().equals("alignment"))
\r
1845 treePanel.getTree().UpdatePlaceHolders((Vector) evt.getNewValue());
\r
1846 treePanel.repaint();
\r
1855 * @param e DOCUMENT ME!
\r
1857 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
1859 // TODO:resolve which menu item was actually selected
\r
1860 // Now, check we have enough sequences
\r
1861 SequenceI[] msa = null;
\r
1863 if ((viewport.getSelectionGroup() != null) &&
\r
1864 (viewport.getSelectionGroup().getSize() > 1))
\r
1866 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1867 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1869 msa = new SequenceI[sz = seqs.getSize()];
\r
1871 for (int i = 0; i < sz; i++)
\r
1873 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1878 Vector seqs = viewport.getAlignment().getSequences();
\r
1880 if (seqs.size() > 1)
\r
1882 msa = new SequenceI[seqs.size()];
\r
1884 for (int i = 0; i < seqs.size(); i++)
\r
1886 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1893 jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
\r
1894 title, msa, false, true);
\r
1901 * @param e DOCUMENT ME!
\r
1903 public void ClustalRealign_actionPerformed(ActionEvent e)
\r
1905 // TODO:resolve which menu item was actually selected
\r
1906 // Now, check we have enough sequences
\r
1907 SequenceI[] msa = null;
\r
1909 if ((viewport.getSelectionGroup() != null) &&
\r
1910 (viewport.getSelectionGroup().getSize() > 1))
\r
1912 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1913 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1915 msa = new SequenceI[sz = seqs.getSize()];
\r
1917 for (int i = 0; i < sz; i++)
\r
1919 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1924 Vector seqs = viewport.getAlignment().getSequences();
\r
1926 if (seqs.size() > 1)
\r
1928 msa = new SequenceI[seqs.size()];
\r
1930 for (int i = 0; i < seqs.size(); i++)
\r
1932 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1939 jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
\r
1940 title, msa, true, true);
\r
1947 * @param e DOCUMENT ME!
\r
1949 protected void jpred_actionPerformed(ActionEvent e)
\r
1951 SequenceI seq = null;
\r
1952 SequenceI[] msa = null;
\r
1954 if ((viewport.getSelectionGroup() != null) &&
\r
1955 (viewport.getSelectionGroup().getSize() > 0))
\r
1957 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1958 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1960 if ((seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
1962 seq = (SequenceI) seqs.getSequenceAt(0);
\r
1967 msa = new SequenceI[sz = seqs.getSize()];
\r
1969 for (int i = 0; i < sz; i++)
\r
1971 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1977 Vector seqs = viewport.getAlignment().getSequences();
\r
1979 if ((seqs.size() == 1) || !viewport.alignment.isAligned())
\r
1981 seq = (SequenceI) seqs.elementAt(0);
\r
1985 msa = new SequenceI[seqs.size()];
\r
1987 for (int i = 0; i < seqs.size(); i++)
\r
1989 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1996 JPredClient ct = new JPredClient(title, msa);
\r
1998 else if (seq != null)
\r
2000 JPredClient ct = new JPredClient(title, seq);
\r
2005 "JALVIEW ERROR! - Unexpected JPred selection state!\n");
\r
2012 * @param e DOCUMENT ME!
\r
2014 protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
\r
2016 // TODO:resolve which menu item was actually selected
\r
2017 // Now, check we have enough sequences
\r
2018 SequenceI[] msa = null;
\r
2020 if ((viewport.getSelectionGroup() != null) &&
\r
2021 (viewport.getSelectionGroup().getSize() > 1))
\r
2023 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2024 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2026 msa = new SequenceI[sz = seqs.getSize()];
\r
2028 for (int i = 0; i < sz; i++)
\r
2030 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2035 Vector seqs = viewport.getAlignment().getSequences();
\r
2037 if (seqs.size() > 1)
\r
2039 msa = new SequenceI[seqs.size()];
\r
2041 for (int i = 0; i < seqs.size(); i++)
\r
2043 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2050 MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,
\r
2058 * @param e DOCUMENT ME!
\r
2060 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2062 // Pick the tree file
\r
2063 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
\r
2064 "LAST_DIRECTORY"));
\r
2065 chooser.setFileView(new JalviewFileView());
\r
2066 chooser.setDialogTitle("Select a newick-like tree file");
\r
2067 chooser.setToolTipText("Load a tree file");
\r
2069 int value = chooser.showOpenDialog(null);
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2071 if (value == JalviewFileChooser.APPROVE_OPTION)
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2073 String choice = chooser.getSelectedFile().getPath();
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2074 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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2078 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
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2080 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
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2082 catch (Exception ex)
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2084 JOptionPane.showMessageDialog(Desktop.desktop,
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2085 "Problem reading tree file", ex.getMessage(),
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2086 JOptionPane.WARNING_MESSAGE);
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2087 ex.printStackTrace();
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2095 * @param nf DOCUMENT ME!
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2096 * @param title DOCUMENT ME!
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2098 * @return DOCUMENT ME!
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2100 public TreePanel ShowNewickTree(NewickFile nf, String title)
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2102 TreePanel tp = null;
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2108 if (nf.getTree() != null)
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2110 tp = new TreePanel(viewport,
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2111 viewport.getAlignment().getSequences(), nf, "FromFile",
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2113 Desktop.addInternalFrame(tp, title, 600, 500);
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2114 addTreeMenuItem(tp, title);
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2117 catch (Exception ex)
\r
2119 ex.printStackTrace();
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2125 class PrintThread extends Thread
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2129 PrinterJob printJob = PrinterJob.getPrinterJob();
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2130 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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2131 printJob.setPrintable(alignPanel, pf);
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2133 if (printJob.printDialog())
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2139 catch (Exception PrintException)
\r
2141 PrintException.printStackTrace();
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