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.datamodel.*;
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23 import jalview.jbgui.*;
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26 import java.awt.event.*;
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30 import javax.swing.*;
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31 import javax.swing.event.*;
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38 * @version $Revision$
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40 public class Finder extends GFinder
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44 JInternalFrame frame;
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48 SearchResults searchResults;
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51 * Creates a new Finder object.
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53 * @param av DOCUMENT ME!
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54 * @param ap DOCUMENT ME!
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55 * @param f DOCUMENT ME!
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57 public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)
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63 // all a big pain, but we need to wait until the frame is visible before the textfield can
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64 // obtain the focus/////////////////////////
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65 frame.addInternalFrameListener(new InternalFrameAdapter()
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67 public void internalFrameOpened(InternalFrameEvent evt)
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69 SwingUtilities.invokeLater(new Runnable()
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73 textfield.requestFocus();
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84 * @param e DOCUMENT ME!
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86 public void findNext_actionPerformed(ActionEvent e)
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94 * @param e DOCUMENT ME!
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96 public void findAll_actionPerformed(ActionEvent e)
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107 * @param e DOCUMENT ME!
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109 public void createNewGroup_actionPerformed(ActionEvent e)
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111 JLabel label = new JLabel("Enter name of new sequence feature");
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112 JTextField textinput = new JTextField(textfield.getText());
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113 JPanel panel = new JPanel(new BorderLayout());
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114 panel.add(label, BorderLayout.NORTH);
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115 panel.add(textinput, BorderLayout.SOUTH);
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117 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
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118 panel, "New Sequence Feature Name",
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119 JOptionPane.OK_CANCEL_OPTION );
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121 if(reply != JOptionPane.OK_OPTION)
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124 for (int i = 0; i < searchResults.getSize(); i ++ )
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126 SequenceI seq = searchResults.getResultSequence(i);
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128 SequenceFeature sf = new SequenceFeature(textinput.getText(),
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129 "Search Results", null,
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130 searchResults.getResultStart(i),
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131 searchResults.getResultEnd(i));
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133 ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
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134 textinput.getText(), new Color(60,160,115));
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136 seq.getDatasetSequence().addSequenceFeature(sf);
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139 ap.alignFrame.showSeqFeatures.setSelected(true);
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140 av.setShowSequenceFeatures(true);
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141 ap.highlightSearchResults(null);
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147 * @param findAll DOCUMENT ME!
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149 void doSearch(boolean findAll)
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151 createNewGroup.setEnabled(false);
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153 String searchString = textfield.getText().toUpperCase().trim();
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154 if(searchString.length()<1)
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157 com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
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159 searchResults = new SearchResults();
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162 String item = null;
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163 boolean found = false;
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165 ////// is the searchString a residue number?
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168 int res = Integer.parseInt(searchString);
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170 if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)
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172 seq = (Sequence) av.getAlignment().getSequenceAt(0);
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176 seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
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179 searchResults.addResult(seq, res, res);
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181 catch (NumberFormatException ex)
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185 ///////////////////////////////////////////////
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186 Color[] newColors = new Color[24];
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188 for (int i = 0; i < 24; i++)
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190 newColors[i] = new Color(60, 160, 115);
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193 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
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195 //SG searchGroup = new SuperGroup(searchString, ucs, true, true, false);
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197 int end = av.alignment.getHeight();
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199 SequenceGroup selection = av.getSelectionGroup();
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201 if (selection != null)
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203 if ((selection.getSize() < 1) ||
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204 ((selection.getEndRes() - selection.getStartRes()) < 2))
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210 while (!found && (seqIndex < end))
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212 seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
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214 if ((selection != null) && !selection.sequences.contains(seq))
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222 item = seq.getSequence().toUpperCase();
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224 if ((selection != null) &&
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225 (selection.getEndRes() < av.alignment.getWidth()-1))
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227 item = item.substring(0, selection.getEndRes() + 1);
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230 ///Shall we ignore gaps????
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231 StringBuffer noGapsSB = new StringBuffer();
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232 int insertCount = 0;
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233 Vector spaces = new Vector();
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235 for (int j = 0; j < item.length(); j++)
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237 if (!jalview.util.Comparison.isGap(item.charAt(j)))
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239 noGapsSB.append(item.charAt(j));
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240 spaces.add(new Integer(insertCount));
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248 String noGaps = noGapsSB.toString();
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250 for (int r = resIndex; r < noGaps.length(); r++)
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253 if (regex.searchFrom(noGaps, r))
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255 resIndex = regex.matchedFrom();
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257 if ((selection != null) &&
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259 Integer.parseInt(spaces.get(resIndex).toString())) < selection.getStartRes()))
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265 int sres = seq.findPosition(resIndex +
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266 Integer.parseInt(spaces.elementAt(resIndex)
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268 int eres = seq.findPosition(regex.matchedTo() - 1 +
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269 Integer.parseInt(spaces.elementAt(regex.matchedTo() -
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272 searchResults.addResult(seq, sres, eres);
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276 // thats enough, break and display the result
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298 Vector idMatch = new Vector();
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300 for (int id = 0; id < av.alignment.getHeight(); id++)
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302 if (regex.search(av.alignment.getSequenceAt(id).getName()))
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304 idMatch.add(av.alignment.getSequenceAt(id));
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308 if ((searchResults.getSize() == 0) && (idMatch.size() > 0))
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310 ap.idPanel.highlightSearchResults(idMatch);
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314 int resultSize = searchResults.getSize();
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316 if (searchResults.getSize() > 0)
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317 createNewGroup.setEnabled(true);
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319 searchResults = null;
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321 // if allResults is null, this effectively switches displaySearch flag in seqCanvas
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322 ap.highlightSearchResults(searchResults);
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324 if(!findAll && resultSize==0)
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326 JOptionPane.showInternalMessageDialog(this, "Finished searching",
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327 null, JOptionPane.INFORMATION_MESSAGE);
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334 String message = resultSize + " matches found.";
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335 JOptionPane.showInternalMessageDialog(this, message, null,
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336 JOptionPane.INFORMATION_MESSAGE);
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