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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524 int index = 0, startRes, endRes;
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527 for (int i = 0; i < sg.getSize(); i++)
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529 SequenceI seq = null;
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531 while (seq == null)
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533 if (orderedSeqs.containsKey(index + ""))
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535 seq = (SequenceI) orderedSeqs.get(index + "");
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547 //Returns residue following index if gap
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548 startRes = seq.findPosition(sg.getStartRes());
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551 //Need to find the residue preceeding index if gap
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554 for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)
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556 ch = seq.getCharAt(j);
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557 if (!jalview.util.Comparison.isGap( (ch)))
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565 endRes += seq.getStart() -1;
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568 buffer.append(seq.getName() + "\t" +
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571 seq.getSequence(sg.getStartRes(),
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572 sg.getEndRes() + 1) + "\n");
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575 c.setContents(new StringSelection(buffer.toString()), null);
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581 * @param e DOCUMENT ME!
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583 protected void pasteNew_actionPerformed(ActionEvent e)
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591 * @param e DOCUMENT ME!
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593 protected void pasteThis_actionPerformed(ActionEvent e)
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595 addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,
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596 HistoryItem.PASTE));
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603 * @param newAlignment DOCUMENT ME!
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605 void paste(boolean newAlignment)
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609 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
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610 Transferable contents = c.getContents(this);
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612 if (contents == null)
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617 String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
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618 StringTokenizer st = new StringTokenizer(str);
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619 ArrayList seqs = new ArrayList();
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621 while (st.hasMoreElements())
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623 String name = st.nextToken();
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624 int start = Integer.parseInt(st.nextToken());
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625 int end = Integer.parseInt(st.nextToken());
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626 Sequence sequence = new Sequence(name, st.nextToken(), start,
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631 viewport.alignment.addSequence(sequence);
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635 seqs.add(sequence);
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641 SequenceI[] newSeqs = new SequenceI[seqs.size()];
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642 seqs.toArray(newSeqs);
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644 AlignFrame af = new AlignFrame(new Alignment(newSeqs));
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645 String newtitle = new String("Copied sequences");
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647 if (title.startsWith("Copied sequences"))
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653 newtitle = newtitle.concat("- from " + title);
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656 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
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657 NEW_WINDOW_HEIGHT);
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661 viewport.firePropertyChange("alignment", null,
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662 viewport.getAlignment().getSequences());
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663 viewport.setEndSeq(viewport.alignment.getHeight());
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664 viewport.alignment.getWidth();
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665 viewport.updateConservation();
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666 viewport.updateConsensus();
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667 alignPanel.repaint();
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670 catch (Exception ex)
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674 // could be anything being pasted in here
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680 * @param e DOCUMENT ME!
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682 protected void cut_actionPerformed(ActionEvent e)
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684 copy_actionPerformed(null);
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685 delete_actionPerformed(null);
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691 * @param e DOCUMENT ME!
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693 protected void delete_actionPerformed(ActionEvent e)
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695 boolean seqsdeleted = false;
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697 if (viewport.getSelectionGroup() == null)
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702 addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
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703 HistoryItem.HIDE));
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705 SequenceGroup sg = viewport.getSelectionGroup();
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706 boolean allSequences = false;
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707 if(sg.sequences.size()==viewport.alignment.getHeight())
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708 allSequences = true;
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710 for (int i = 0; i < sg.sequences.size(); i++)
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712 SequenceI seq = sg.getSequenceAt(i);
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713 int index = viewport.getAlignment().findIndex(seq);
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714 seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
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716 // If the cut affects all sequences, remove highlighted columns
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719 viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes()+1);
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723 if (seq.getSequence().length() < 1)
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725 seqsdeleted = true;
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726 viewport.getAlignment().deleteSequence(seq);
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730 viewport.getAlignment().getSequences().setElementAt(seq, index);
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734 viewport.setSelectionGroup(null);
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735 viewport.alignment.deleteGroup(sg);
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739 viewport.firePropertyChange("alignment", null,
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740 viewport.getAlignment().getSequences());
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743 viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());
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745 if (viewport.getAlignment().getHeight() < 1)
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749 this.setClosed(true);
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751 catch (Exception ex)
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756 viewport.updateConservation();
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757 viewport.updateConsensus();
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758 alignPanel.repaint();
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764 * @param e DOCUMENT ME!
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766 protected void deleteGroups_actionPerformed(ActionEvent e)
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768 viewport.alignment.deleteAllGroups();
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769 viewport.setSelectionGroup(null);
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770 alignPanel.repaint();
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776 * @param e DOCUMENT ME!
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778 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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780 SequenceGroup sg = new SequenceGroup();
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782 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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785 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
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788 sg.setEndRes(viewport.alignment.getWidth()-1);
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789 viewport.setSelectionGroup(sg);
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790 PaintRefresher.Refresh(null, viewport.alignment);
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796 * @param e DOCUMENT ME!
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798 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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800 viewport.setSelectionGroup(null);
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801 viewport.getColumnSelection().clear();
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802 viewport.setSelectionGroup(null);
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803 alignPanel.annotationPanel.activeRes = null;
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804 PaintRefresher.Refresh(null, viewport.alignment);
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810 * @param e DOCUMENT ME!
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812 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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814 SequenceGroup sg = viewport.getSelectionGroup();
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818 selectAllSequenceMenuItem_actionPerformed(null);
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823 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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826 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
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829 PaintRefresher.Refresh(null, viewport.alignment);
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835 * @param e DOCUMENT ME!
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837 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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839 ColumnSelection colSel = viewport.getColumnSelection();
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841 if (colSel.size() > 0)
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843 addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,
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844 HistoryItem.HIDE));
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846 int min = colSel.getMin();
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847 viewport.getAlignment().trimLeft(min);
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848 colSel.compensateForEdit(0, min);
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850 if (viewport.getSelectionGroup() != null)
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852 viewport.getSelectionGroup().adjustForRemoveLeft(min);
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855 Vector groups = viewport.alignment.getGroups();
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857 for (int i = 0; i < groups.size(); i++)
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859 SequenceGroup sg = (SequenceGroup) groups.get(i);
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861 if (!sg.adjustForRemoveLeft(min))
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863 viewport.alignment.deleteGroup(sg);
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867 alignPanel.repaint();
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874 * @param e DOCUMENT ME!
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876 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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878 ColumnSelection colSel = viewport.getColumnSelection();
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880 if (colSel.size() > 0)
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882 addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,
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883 HistoryItem.HIDE));
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885 int max = colSel.getMax();
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886 viewport.getAlignment().trimRight(max);
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888 if (viewport.getSelectionGroup() != null)
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890 viewport.getSelectionGroup().adjustForRemoveRight(max);
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893 Vector groups = viewport.alignment.getGroups();
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895 for (int i = 0; i < groups.size(); i++)
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897 SequenceGroup sg = (SequenceGroup) groups.get(i);
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899 if (!sg.adjustForRemoveRight(max))
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901 viewport.alignment.deleteGroup(sg);
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905 alignPanel.repaint();
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912 * @param e DOCUMENT ME!
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914 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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916 addHistoryItem(new HistoryItem("Remove Gapped Columns",
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917 viewport.alignment, HistoryItem.HIDE));
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919 viewport.getAlignment().removeGaps();
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920 viewport.updateConservation();
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921 viewport.updateConsensus();
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922 alignPanel.repaint();
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928 * @param e DOCUMENT ME!
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930 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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932 addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,
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933 HistoryItem.HIDE));
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938 Vector seqs = null;
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941 int end = viewport.alignment.getWidth();
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944 if (viewport.getSelectionGroup() != null
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945 && viewport.getSelectionGroup().sequences != null
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946 && viewport.getSelectionGroup().sequences.size()>0)
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948 seqs = viewport.getSelectionGroup().sequences;
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949 start = viewport.getSelectionGroup().getStartRes();
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950 end = viewport.getSelectionGroup().getEndRes();
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954 seqs = viewport.alignment.getSequences();
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957 for (int i = 0; i < seqs.size(); i++)
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959 current = (SequenceI) seqs.elementAt(i);
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960 jSize = current.getLength();
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966 if (jalview.util.Comparison.isGap(current.getCharAt(j)))
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968 current.deleteCharAt(j);
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975 while (j < end && j < jSize);
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978 viewport.updateConservation();
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979 viewport.updateConsensus();
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980 alignPanel.repaint();
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986 * @param e DOCUMENT ME!
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988 public void padGapsMenuitem_actionPerformed(ActionEvent e)
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990 addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
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991 HistoryItem.HIDE));
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994 int Width = viewport.getAlignment().getWidth();
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996 for (int i = 0; i < viewport.getAlignment().getSequences().size();
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999 current = viewport.getAlignment().getSequenceAt(i);
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1001 if (current.getLength() < Width)
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1003 current.insertCharAt(Width - 1, viewport.getGapCharacter());
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1007 viewport.updateConservation();
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1008 viewport.updateConsensus();
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1009 alignPanel.repaint();
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1015 * @param e DOCUMENT ME!
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1017 public void findMenuItem_actionPerformed(ActionEvent e)
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1019 JInternalFrame frame = new JInternalFrame();
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1020 Finder finder = new Finder(viewport, alignPanel, frame);
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1021 frame.setContentPane(finder);
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1022 Desktop.addInternalFrame(frame, "Find", 340, 110);
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1023 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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1029 * @param e DOCUMENT ME!
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1031 public void font_actionPerformed(ActionEvent e)
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1033 FontChooser fc = new FontChooser(alignPanel);
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1039 * @param e DOCUMENT ME!
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1041 protected void fullSeqId_actionPerformed(ActionEvent e)
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1043 viewport.setShowFullId(fullSeqId.isSelected());
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1045 alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
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1046 alignPanel.repaint();
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1052 * @param e DOCUMENT ME!
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1054 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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1056 viewport.setColourText(colourTextMenuItem.isSelected());
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1057 alignPanel.repaint();
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1063 * @param e DOCUMENT ME!
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1065 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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1067 viewport.setWrapAlignment(wrapMenuItem.isSelected());
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1068 alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
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1069 scaleAbove.setVisible(wrapMenuItem.isSelected());
\r
1070 scaleLeft.setVisible(wrapMenuItem.isSelected());
\r
1071 scaleRight.setVisible(wrapMenuItem.isSelected());
\r
1072 alignPanel.repaint();
\r
1078 * @param e DOCUMENT ME!
\r
1080 protected void scaleAbove_actionPerformed(ActionEvent e)
\r
1082 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
\r
1083 alignPanel.repaint();
\r
1089 * @param e DOCUMENT ME!
\r
1091 protected void scaleLeft_actionPerformed(ActionEvent e)
\r
1093 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
\r
1094 alignPanel.repaint();
\r
1100 * @param e DOCUMENT ME!
\r
1102 protected void scaleRight_actionPerformed(ActionEvent e)
\r
1104 viewport.setScaleRightWrapped(scaleRight.isSelected());
\r
1105 alignPanel.repaint();
\r
1111 * @param e DOCUMENT ME!
\r
1113 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
\r
1115 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
\r
1116 alignPanel.repaint();
\r
1122 * @param e DOCUMENT ME!
\r
1124 public void viewTextMenuItem_actionPerformed(ActionEvent e)
\r
1126 viewport.setShowText(viewTextMenuItem.isSelected());
\r
1127 alignPanel.repaint();
\r
1133 * @param e DOCUMENT ME!
\r
1135 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
\r
1137 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
\r
1138 alignPanel.repaint();
\r
1144 * @param evt DOCUMENT ME!
\r
1146 public void sequenceFeatures_actionPerformed(ActionEvent evt)
\r
1148 viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
1150 if (viewport.showSequenceFeatures &&
\r
1151 !((Alignment) viewport.alignment).featuresAdded)
\r
1153 SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment,
\r
1155 ((Alignment) viewport.alignment).featuresAdded = true;
\r
1158 alignPanel.repaint();
\r
1164 * @param e DOCUMENT ME!
\r
1166 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
\r
1168 if (annotationPanelMenuItem.isSelected() &&
\r
1169 viewport.getWrapAlignment())
\r
1171 annotationPanelMenuItem.setSelected(false);
\r
1176 viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
\r
1177 alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
\r
1183 * @param e DOCUMENT ME!
\r
1185 public void overviewMenuItem_actionPerformed(ActionEvent e)
\r
1187 if (alignPanel.overviewPanel != null)
\r
1192 JInternalFrame frame = new JInternalFrame();
\r
1193 OverviewPanel overview = new OverviewPanel(alignPanel);
\r
1194 frame.setContentPane(overview);
\r
1195 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
\r
1196 frame.getWidth(), frame.getHeight());
\r
1198 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
1199 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1201 public void internalFrameClosed(
\r
1202 javax.swing.event.InternalFrameEvent evt)
\r
1204 alignPanel.setOverviewPanel(null);
\r
1209 alignPanel.setOverviewPanel(overview);
\r
1215 * @param e DOCUMENT ME!
\r
1217 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
1219 changeColour(null);
\r
1225 * @param e DOCUMENT ME!
\r
1227 public void clustalColour_actionPerformed(ActionEvent e)
\r
1229 changeColour(new ClustalxColourScheme(
\r
1230 viewport.alignment.getSequences(), viewport.alignment.getWidth()));
\r
1236 * @param e DOCUMENT ME!
\r
1238 public void zappoColour_actionPerformed(ActionEvent e)
\r
1240 changeColour(new ZappoColourScheme());
\r
1246 * @param e DOCUMENT ME!
\r
1248 public void taylorColour_actionPerformed(ActionEvent e)
\r
1250 changeColour(new TaylorColourScheme());
\r
1256 * @param e DOCUMENT ME!
\r
1258 public void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
1260 changeColour(new HydrophobicColourScheme());
\r
1266 * @param e DOCUMENT ME!
\r
1268 public void helixColour_actionPerformed(ActionEvent e)
\r
1270 changeColour(new HelixColourScheme());
\r
1276 * @param e DOCUMENT ME!
\r
1278 public void strandColour_actionPerformed(ActionEvent e)
\r
1280 changeColour(new StrandColourScheme());
\r
1286 * @param e DOCUMENT ME!
\r
1288 public void turnColour_actionPerformed(ActionEvent e)
\r
1290 changeColour(new TurnColourScheme());
\r
1296 * @param e DOCUMENT ME!
\r
1298 public void buriedColour_actionPerformed(ActionEvent e)
\r
1300 changeColour(new BuriedColourScheme());
\r
1306 * @param e DOCUMENT ME!
\r
1308 public void nucleotideColour_actionPerformed(ActionEvent e)
\r
1310 changeColour(new NucleotideColourScheme());
\r
1316 * @param e DOCUMENT ME!
\r
1318 protected void applyToAllGroups_actionPerformed(ActionEvent e)
\r
1320 viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
\r
1326 * @param cs DOCUMENT ME!
\r
1328 void changeColour(ColourSchemeI cs)
\r
1330 int threshold = 0;
\r
1332 if (viewport.getAbovePIDThreshold())
\r
1334 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
\r
1337 if (cs instanceof ResidueColourScheme)
\r
1339 ((ResidueColourScheme) cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1341 else if (cs instanceof ScoreColourScheme)
\r
1343 ((ScoreColourScheme) cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1346 viewport.setGlobalColourScheme(cs);
\r
1348 else if (cs instanceof ResidueColourScheme)
\r
1350 ((ResidueColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1352 else if (cs instanceof ScoreColourScheme)
\r
1354 ((ScoreColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());
\r
1357 if (viewport.getConservationSelected())
\r
1359 ConservationColourScheme ccs = null;
\r
1361 Alignment al = (Alignment) viewport.alignment;
\r
1362 Conservation c = new Conservation("All",
\r
1363 ResidueProperties.propHash, 3, al.getSequences(), 0,
\r
1364 al.getWidth() - 1);
\r
1367 c.verdict(false, viewport.ConsPercGaps);
\r
1369 ccs = new ConservationColourScheme(c, cs);
\r
1372 viewport.setGlobalColourScheme(ccs);
\r
1374 ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,
\r
1379 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
1382 cs.setConsensus(viewport.vconsensus);
\r
1385 viewport.setGlobalColourScheme(cs);
\r
1388 if (viewport.getColourAppliesToAllGroups())
\r
1390 Vector groups = viewport.alignment.getGroups();
\r
1392 for (int i = 0; i < groups.size(); i++)
\r
1394 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
\r
1400 else if (cs instanceof ClustalxColourScheme)
\r
1402 sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
\r
1404 else if (cs instanceof UserColourScheme)
\r
1406 sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
\r
1412 sg.cs = (ColourSchemeI) cs.getClass().newInstance();
\r
1414 catch (Exception ex)
\r
1419 if (viewport.getAbovePIDThreshold())
\r
1421 if (sg.cs instanceof ResidueColourScheme)
\r
1423 ((ResidueColourScheme) sg.cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1425 else if (sg.cs instanceof ScoreColourScheme)
\r
1427 ((ScoreColourScheme) sg.cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());
\r
1430 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1434 if (viewport.getConservationSelected())
\r
1436 Conservation c = new Conservation("Group",
\r
1437 ResidueProperties.propHash, 3, sg.sequences, 0,
\r
1438 viewport.alignment.getWidth() - 1);
\r
1440 c.verdict(false, viewport.ConsPercGaps);
\r
1442 ConservationColourScheme ccs = new ConservationColourScheme(c,
\r
1445 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
1446 ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1450 else if (cs != null)
\r
1452 // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
\r
1453 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
1459 if (alignPanel.getOverviewPanel() != null)
\r
1461 alignPanel.getOverviewPanel().updateOverviewImage();
\r
1464 alignPanel.repaint();
\r
1470 * @param e DOCUMENT ME!
\r
1472 protected void modifyPID_actionPerformed(ActionEvent e)
\r
1474 if (viewport.getAbovePIDThreshold())
\r
1476 SliderPanel.setPIDSliderSource(alignPanel,
\r
1477 viewport.getGlobalColourScheme(), "Background");
\r
1478 SliderPanel.showPIDSlider();
\r
1485 * @param e DOCUMENT ME!
\r
1487 protected void modifyConservation_actionPerformed(ActionEvent e)
\r
1489 if (viewport.getConservationSelected())
\r
1491 SliderPanel.setConservationSlider(alignPanel,
\r
1492 viewport.globalColourScheme, "Background");
\r
1493 SliderPanel.showConservationSlider();
\r
1500 * @param e DOCUMENT ME!
\r
1502 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
1504 viewport.setConservationSelected(conservationMenuItem.isSelected());
\r
1506 viewport.setAbovePIDThreshold(false);
\r
1507 abovePIDThreshold.setSelected(false);
\r
1509 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
1511 if (cs instanceof ConservationColourScheme)
\r
1513 changeColour(((ConservationColourScheme) cs).cs);
\r
1520 modifyConservation_actionPerformed(null);
\r
1526 * @param e DOCUMENT ME!
\r
1528 public void abovePIDThreshold_actionPerformed(ActionEvent e)
\r
1530 viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
\r
1532 conservationMenuItem.setSelected(false);
\r
1533 viewport.setConservationSelected(false);
\r
1535 ColourSchemeI cs = viewport.getGlobalColourScheme();
\r
1537 if (cs instanceof ConservationColourScheme)
\r
1539 changeColour(((ConservationColourScheme) cs).cs);
\r
1546 modifyPID_actionPerformed(null);
\r
1552 * @param e DOCUMENT ME!
\r
1554 public void userDefinedColour_actionPerformed(ActionEvent e)
\r
1556 if(e.getActionCommand().equals("User Defined..."))
\r
1557 new UserDefinedColours(alignPanel, null);
\r
1560 UserColourScheme udc = (UserColourScheme)UserDefinedColours.
\r
1561 getUserColourSchemes().get(e.getActionCommand());
\r
1563 changeColour(udc);
\r
1567 public void updateUserColourMenu()
\r
1570 Component [] menuItems = colourMenu.getMenuComponents();
\r
1571 int i, iSize = menuItems.length;
\r
1572 for(i=0; i<iSize; i++)
\r
1574 if( menuItems[i].getName()!=null && menuItems[i].getName().equals("USER_DEFINED"))
\r
1576 colourMenu.remove(menuItems[i]);
\r
1580 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
\r
1582 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
1583 getUserColourSchemes().keys();
\r
1585 while (userColours.hasMoreElements())
\r
1587 JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
\r
1588 nextElement().toString());
\r
1589 radioItem.addActionListener(new ActionListener()
\r
1591 public void actionPerformed(ActionEvent evt)
\r
1593 userDefinedColour_actionPerformed(evt);
\r
1596 colourMenu.insert(radioItem, 15);
\r
1597 colours.add(radioItem);
\r
1605 * @param e DOCUMENT ME!
\r
1607 public void PIDColour_actionPerformed(ActionEvent e)
\r
1609 changeColour(new PIDColourScheme());
\r
1615 * @param e DOCUMENT ME!
\r
1617 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
1619 changeColour(new Blosum62ColourScheme());
\r
1625 * @param e DOCUMENT ME!
\r
1627 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
\r
1629 addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,
\r
1630 HistoryItem.SORT));
\r
1631 AlignmentSorter.sortByPID(viewport.getAlignment(),
\r
1632 viewport.getAlignment().getSequenceAt(0));
\r
1633 alignPanel.repaint();
\r
1639 * @param e DOCUMENT ME!
\r
1641 public void sortIDMenuItem_actionPerformed(ActionEvent e)
\r
1643 addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
\r
1644 HistoryItem.SORT));
\r
1645 AlignmentSorter.sortByID(viewport.getAlignment());
\r
1646 alignPanel.repaint();
\r
1652 * @param e DOCUMENT ME!
\r
1654 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
\r
1656 addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,
\r
1657 HistoryItem.SORT));
\r
1659 AlignmentSorter.sortByGroup(viewport.getAlignment());
\r
1660 alignPanel.repaint();
\r
1666 * @param e DOCUMENT ME!
\r
1668 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
\r
1670 RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
\r
1671 JInternalFrame frame = new JInternalFrame();
\r
1672 frame.setContentPane(sp);
\r
1673 Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
\r
1680 * @param e DOCUMENT ME!
\r
1682 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
\r
1684 if ((viewport.getSelectionGroup() == null) ||
\r
1685 (viewport.getSelectionGroup().getSize() < 2))
\r
1687 JOptionPane.showInternalMessageDialog(this,
\r
1688 "You must select at least 2 sequences.", "Invalid Selection",
\r
1689 JOptionPane.WARNING_MESSAGE);
\r
1693 JInternalFrame frame = new JInternalFrame();
\r
1694 frame.setContentPane(new PairwiseAlignPanel(viewport));
\r
1695 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
\r
1702 * @param e DOCUMENT ME!
\r
1704 public void PCAMenuItem_actionPerformed(ActionEvent e)
\r
1706 if (((viewport.getSelectionGroup() != null) &&
\r
1707 (viewport.getSelectionGroup().getSize() < 4) &&
\r
1708 (viewport.getSelectionGroup().getSize() > 0)) ||
\r
1709 (viewport.getAlignment().getHeight() < 4))
\r
1711 JOptionPane.showInternalMessageDialog(this,
\r
1712 "Principal component analysis must take\n" +
\r
1713 "at least 4 input sequences.",
\r
1714 "Sequence selection insufficient", JOptionPane.WARNING_MESSAGE);
\r
1721 PCAPanel pcaPanel = new PCAPanel(viewport, null);
\r
1722 JInternalFrame frame = new JInternalFrame();
\r
1723 frame.setContentPane(pcaPanel);
\r
1724 Desktop.addInternalFrame(frame, "Principal component analysis",
\r
1727 catch (java.lang.OutOfMemoryError ex)
\r
1729 JOptionPane.showInternalMessageDialog(this,
\r
1730 "Too many sequences selected\nfor Principal Component Analysis!!",
\r
1731 "Out of memory", JOptionPane.WARNING_MESSAGE);
\r
1738 * @param e DOCUMENT ME!
\r
1740 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
\r
1742 NewTreePanel("AV", "PID", "Average distance tree using PID");
\r
1748 * @param e DOCUMENT ME!
\r
1750 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
\r
1752 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
\r
1758 * @param e DOCUMENT ME!
\r
1760 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1762 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1768 * @param e DOCUMENT ME!
\r
1770 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
\r
1772 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
\r
1778 * @param type DOCUMENT ME!
\r
1779 * @param pwType DOCUMENT ME!
\r
1780 * @param title DOCUMENT ME!
\r
1782 void NewTreePanel(String type, String pwType, String title)
\r
1784 final TreePanel tp;
\r
1786 if ((viewport.getSelectionGroup() != null) &&
\r
1787 (viewport.getSelectionGroup().getSize() > 3))
\r
1790 SequenceGroup sg = viewport.getSelectionGroup();
\r
1792 /* Decide if the selection is a column region */
\r
1793 while (s < sg.sequences.size())
\r
1795 if (((SequenceI) sg.sequences.elementAt(s++)).getLength() < sg.getEndRes())
\r
1797 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1798 "The selected region to create a tree may\nonly contain residues or gaps.\n" +
\r
1799 "Try using the Pad function in the edit menu,\n" +
\r
1800 "or one of the multiple sequence alignment web services.",
\r
1801 "Sequences in selection are not aligned",
\r
1802 JOptionPane.WARNING_MESSAGE);
\r
1808 title = title + " on region";
\r
1809 tp = new TreePanel(viewport,
\r
1810 viewport.getSelectionGroup().sequences, type, pwType,
\r
1811 sg.getStartRes(), sg.getEndRes());
\r
1815 //are the sequences aligned?
\r
1816 if (!viewport.alignment.isAligned())
\r
1818 JOptionPane.showMessageDialog(Desktop.desktop,
\r
1819 "The sequences must be aligned before creating a tree.\n" +
\r
1820 "Try using the Pad function in the edit menu,\n" +
\r
1821 "or one of the multiple sequence alignment web services.",
\r
1822 "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
\r
1827 tp = new TreePanel(viewport,
\r
1828 viewport.getAlignment().getSequences(), type, pwType, 0,
\r
1829 viewport.alignment.getWidth());
\r
1832 addTreeMenuItem(tp, title);
\r
1833 viewport.setCurrentTree(tp.getTree());
\r
1835 Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
1841 * @param title DOCUMENT ME!
\r
1842 * @param order DOCUMENT ME!
\r
1844 public void addSortByOrderMenuItem(String title, final AlignmentOrder order)
\r
1846 final JMenuItem item = new JMenuItem("by " + title);
\r
1848 item.addActionListener(new java.awt.event.ActionListener()
\r
1850 public void actionPerformed(ActionEvent e)
\r
1852 addHistoryItem(new HistoryItem("Sort", viewport.alignment,
\r
1853 HistoryItem.SORT));
\r
1855 // TODO: JBPNote - have to map order entries to curent SequenceI pointers
\r
1856 AlignmentSorter.sortBy(viewport.getAlignment(), order);
\r
1857 alignPanel.repaint();
\r
1865 * @param treePanel DOCUMENT ME!
\r
1866 * @param title DOCUMENT ME!
\r
1868 void addTreeMenuItem(final TreePanel treePanel, String title)
\r
1870 final JMenuItem item = new JMenuItem(title);
\r
1874 if (treeCount == 1)
\r
1876 sort.add(sortByTreeMenu);
\r
1879 sortByTreeMenu.add(item);
\r
1880 item.addActionListener(new java.awt.event.ActionListener()
\r
1882 public void actionPerformed(ActionEvent e)
\r
1884 addHistoryItem(new HistoryItem("Tree Sort",
\r
1885 viewport.alignment, HistoryItem.SORT));
\r
1886 AlignmentSorter.sortByTree(viewport.getAlignment(),
\r
1887 treePanel.getTree());
\r
1888 alignPanel.repaint();
\r
1892 treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
1894 public void internalFrameClosed(
\r
1895 javax.swing.event.InternalFrameEvent evt)
\r
1898 sortByTreeMenu.remove(item);
\r
1900 if (treeCount == 0)
\r
1902 sort.remove(sortByTreeMenu);
\r
1907 viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()
\r
1909 public void propertyChange(PropertyChangeEvent evt)
\r
1911 if (evt.getPropertyName().equals("alignment"))
\r
1913 treePanel.getTree().UpdatePlaceHolders((Vector) evt.getNewValue());
\r
1914 treePanel.repaint();
\r
1923 * @param e DOCUMENT ME!
\r
1925 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
\r
1927 // TODO:resolve which menu item was actually selected
\r
1928 // Now, check we have enough sequences
\r
1929 SequenceI[] msa = null;
\r
1931 if ((viewport.getSelectionGroup() != null) &&
\r
1932 (viewport.getSelectionGroup().getSize() > 1))
\r
1934 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1935 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1937 msa = new SequenceI[sz = seqs.getSize()];
\r
1939 for (int i = 0; i < sz; i++)
\r
1941 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1946 Vector seqs = viewport.getAlignment().getSequences();
\r
1948 if (seqs.size() > 1)
\r
1950 msa = new SequenceI[seqs.size()];
\r
1952 for (int i = 0; i < seqs.size(); i++)
\r
1954 msa[i] = (SequenceI) seqs.elementAt(i);
\r
1961 jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
\r
1962 title, msa, false, true);
\r
1969 * @param e DOCUMENT ME!
\r
1971 public void ClustalRealign_actionPerformed(ActionEvent e)
\r
1973 // TODO:resolve which menu item was actually selected
\r
1974 // Now, check we have enough sequences
\r
1975 SequenceI[] msa = null;
\r
1977 if ((viewport.getSelectionGroup() != null) &&
\r
1978 (viewport.getSelectionGroup().getSize() > 1))
\r
1980 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
1981 SequenceGroup seqs = viewport.getSelectionGroup();
\r
1983 msa = new SequenceI[sz = seqs.getSize()];
\r
1985 for (int i = 0; i < sz; i++)
\r
1987 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
1992 Vector seqs = viewport.getAlignment().getSequences();
\r
1994 if (seqs.size() > 1)
\r
1996 msa = new SequenceI[seqs.size()];
\r
1998 for (int i = 0; i < seqs.size(); i++)
\r
2000 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2007 jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",
\r
2008 title, msa, true, true);
\r
2015 * @param e DOCUMENT ME!
\r
2017 protected void jpred_actionPerformed(ActionEvent e)
\r
2019 SequenceI seq = null;
\r
2020 SequenceI[] msa = null;
\r
2022 if ((viewport.getSelectionGroup() != null) &&
\r
2023 (viewport.getSelectionGroup().getSize() > 0))
\r
2025 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2026 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2028 if ((seqs.getSize() == 1) || !viewport.alignment.isAligned())
\r
2030 seq = (SequenceI) seqs.getSequenceAt(0);
\r
2035 msa = new SequenceI[sz = seqs.getSize()];
\r
2037 for (int i = 0; i < sz; i++)
\r
2039 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2045 Vector seqs = viewport.getAlignment().getSequences();
\r
2047 if ((seqs.size() == 1) || !viewport.alignment.isAligned())
\r
2049 seq = (SequenceI) seqs.elementAt(0);
\r
2053 msa = new SequenceI[seqs.size()];
\r
2055 for (int i = 0; i < seqs.size(); i++)
\r
2057 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2064 JPredClient ct = new JPredClient(title, msa);
\r
2066 else if (seq != null)
\r
2068 JPredClient ct = new JPredClient(title, seq);
\r
2073 "JALVIEW ERROR! - Unexpected JPred selection state!\n");
\r
2080 * @param e DOCUMENT ME!
\r
2082 protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
\r
2084 // TODO:resolve which menu item was actually selected
\r
2085 // Now, check we have enough sequences
\r
2086 SequenceI[] msa = null;
\r
2088 if ((viewport.getSelectionGroup() != null) &&
\r
2089 (viewport.getSelectionGroup().getSize() > 1))
\r
2091 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
\r
2092 SequenceGroup seqs = viewport.getSelectionGroup();
\r
2094 msa = new SequenceI[sz = seqs.getSize()];
\r
2096 for (int i = 0; i < sz; i++)
\r
2098 msa[i] = (SequenceI) seqs.getSequenceAt(i);
\r
2103 Vector seqs = viewport.getAlignment().getSequences();
\r
2105 if (seqs.size() > 1)
\r
2107 msa = new SequenceI[seqs.size()];
\r
2109 for (int i = 0; i < seqs.size(); i++)
\r
2111 msa[i] = (SequenceI) seqs.elementAt(i);
\r
2118 MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,
\r
2126 * @param e DOCUMENT ME!
\r
2128 protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
\r
2130 // Pick the tree file
\r
2131 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
\r
2132 "LAST_DIRECTORY"));
\r
2133 chooser.setFileView(new JalviewFileView());
\r
2134 chooser.setDialogTitle("Select a newick-like tree file");
\r
2135 chooser.setToolTipText("Load a tree file");
\r
2137 int value = chooser.showOpenDialog(null);
\r
2139 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
2141 String choice = chooser.getSelectedFile().getPath();
\r
2142 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
2146 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,
\r
2148 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
\r
2150 catch (Exception ex)
\r
2152 JOptionPane.showMessageDialog(Desktop.desktop,
\r
2153 "Problem reading tree file", ex.getMessage(),
\r
2154 JOptionPane.WARNING_MESSAGE);
\r
2155 ex.printStackTrace();
\r
2163 * @param nf DOCUMENT ME!
\r
2164 * @param title DOCUMENT ME!
\r
2166 * @return DOCUMENT ME!
\r
2168 public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
2170 TreePanel tp = null;
\r
2176 if (nf.getTree() != null)
\r
2178 tp = new TreePanel(viewport,
\r
2179 viewport.getAlignment().getSequences(), nf, "FromFile",
\r
2181 Desktop.addInternalFrame(tp, title, 600, 500);
\r
2182 addTreeMenuItem(tp, title);
\r
2185 catch (Exception ex)
\r
2187 ex.printStackTrace();
\r
2193 class PrintThread extends Thread
\r
2197 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
2198 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
2199 printJob.setPrintable(alignPanel, pf);
\r
2201 if (printJob.printDialog())
\r
2207 catch (Exception PrintException)
\r
2209 PrintException.printStackTrace();
\r