src/jalview/gui/Finder.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.gui;
  20
  21 import jalview.datamodel.*;
  22
  23 import jalview.jbgui.*;
  24
  25 import java.awt.*;
  26 import java.awt.event.*;
  27
  28 import java.util.*;
  29
  30 import javax.swing.*;
  31 import javax.swing.event.*;
  32
  33
  34 /**
  35  * DOCUMENT ME!
  36  *
  37  * @author $author$
  38  * @version $Revision$
  39  */
  40 public class Finder extends GFinder
  41 {
  42     AlignViewport av;
  43     AlignmentPanel ap;
  44     JInternalFrame frame;
  45     int seqIndex = 0;
  46     int resIndex = 0;
  47
  48     SearchResults searchResults;
  49
  50     /**
  51      * Creates a new Finder object.
  52      *
  53      * @param av DOCUMENT ME!
  54      * @param ap DOCUMENT ME!
  55      * @param f DOCUMENT ME!
  56      */
  57     public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)
  58     {
  59         this.av = av;
  60         this.ap = ap;
  61         frame = f;
  62
  63         // all a big pain, but we need to wait until the frame is visible before the textfield can
  64         // obtain the focus/////////////////////////
  65         frame.addInternalFrameListener(new InternalFrameAdapter()
  66             {
  67                 public void internalFrameOpened(InternalFrameEvent evt)
  68                 {
  69                     SwingUtilities.invokeLater(new Runnable()
  70                         {
  71                             public void run()
  72                             {
  73                                 textfield.requestFocus();
  74                             }
  75                         });
  76                 }
  77             });
  78     }
  79
  80
  81     /**
  82      * DOCUMENT ME!
  83      *
  84      * @param e DOCUMENT ME!
  85      */
  86     public void findNext_actionPerformed(ActionEvent e)
  87     {
  88         doSearch(false);
  89     }
  90
  91     /**
  92      * DOCUMENT ME!
  93      *
  94      * @param e DOCUMENT ME!
  95      */
  96     public void findAll_actionPerformed(ActionEvent e)
  97     {
  98         resIndex = 0;
  99         seqIndex = 0;
 100         doSearch(true);
 101     }
 102
 103
 104     /**
 105      * DOCUMENT ME!
 106      *
 107      * @param e DOCUMENT ME!
 108      */
 109     public void createNewGroup_actionPerformed(ActionEvent e)
 110     {
 111         JLabel label = new JLabel("Enter name of new sequence feature");
 112         JTextField textinput = new JTextField(textfield.getText());
 113         JPanel panel = new JPanel(new BorderLayout());
 114         panel.add(label, BorderLayout.NORTH);
 115         panel.add(textinput, BorderLayout.SOUTH);
 116
 117          int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
 118             panel, "New Sequence Feature Name",
 119           JOptionPane.OK_CANCEL_OPTION );
 120
 121          if(reply != JOptionPane.OK_OPTION)
 122            return;
 123
 124         for (int i = 0; i < searchResults.getSize(); i ++ )
 125         {
 126             SequenceI seq = searchResults.getResultSequence(i);
 127
 128             SequenceFeature sf = new SequenceFeature(textinput.getText(),
 129                 "Search Results", null,
 130                 searchResults.getResultStart(i),
 131                searchResults.getResultEnd(i),
 132                "Search Results");
 133
 134             ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
 135                 textinput.getText(), new Color(60,160,115),
 136                     "Search Results");
 137
 138             seq.getDatasetSequence().addSequenceFeature(sf);
 139         }
 140
 141         ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();
 142         ap.alignFrame.showSeqFeatures.setSelected(true);
 143         av.setShowSequenceFeatures(true);
 144         ap.highlightSearchResults(null);
 145     }
 146
 147     /**
 148      * DOCUMENT ME!
 149      *
 150      * @param findAll DOCUMENT ME!
 151      */
 152     void doSearch(boolean findAll)
 153     {
 154         createNewGroup.setEnabled(false);
 155
 156         String searchString = textfield.getText().trim();
 157         if(!caseSensitive.isSelected())
 158           searchString = searchString.toUpperCase();
 159
 160         if(searchString.length()<1)
 161           return;
 162
 163         com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
 164
 165         searchResults = new SearchResults();
 166
 167         Sequence seq;
 168         String item = null;
 169         boolean found = false;
 170
 171         ////// is the searchString a residue number?
 172         try
 173         {
 174             int res = Integer.parseInt(searchString);
 175             found = true;
 176             if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)
 177             {
 178               seq = (Sequence) av.getAlignment().getSequenceAt(0);
 179             }
 180             else
 181             {
 182               seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
 183             }
 184
 185             searchResults.addResult(seq, res, res);
 186         }
 187         catch (NumberFormatException ex)
 188         {
 189         }
 190
 191         ///////////////////////////////////////////////
 192
 193         int end = av.alignment.getHeight();
 194
 195         SequenceGroup selection = av.getSelectionGroup();
 196
 197         if (selection != null)
 198         {
 199             if ((selection.getSize(false) < 1) ||
 200                     ((selection.getEndRes() - selection.getStartRes()) < 2))
 201             {
 202                 selection = null;
 203             }
 204         }
 205
 206         while (!found && (seqIndex < end))
 207         {
 208             seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
 209
 210             if ((selection != null) && !selection.getSequences(false).contains(seq))
 211             {
 212                 seqIndex++;
 213                 resIndex = 0;
 214
 215                 continue;
 216             }
 217
 218             item = seq.getSequence();
 219             if(!caseSensitive.isSelected())
 220               item = item.toUpperCase();
 221
 222             if ((selection != null) &&
 223                     (selection.getEndRes() < av.alignment.getWidth()-1))
 224             {
 225                 item = item.substring(0, selection.getEndRes() + 1);
 226             }
 227
 228             ///Shall we ignore gaps????
 229             StringBuffer noGapsSB = new StringBuffer();
 230             int insertCount = 0;
 231             Vector spaces = new Vector();
 232
 233             for (int j = 0; j < item.length(); j++)
 234             {
 235                 if (!jalview.util.Comparison.isGap(item.charAt(j)))
 236                 {
 237                     noGapsSB.append(item.charAt(j));
 238                     spaces.add(new Integer(insertCount));
 239                 }
 240                 else
 241                 {
 242                     insertCount++;
 243                 }
 244             }
 245
 246             String noGaps = noGapsSB.toString();
 247
 248             for (int r = resIndex; r < noGaps.length(); r++)
 249             {
 250
 251                 if (regex.searchFrom(noGaps, r))
 252                 {
 253                     resIndex = regex.matchedFrom();
 254
 255                     if ((selection != null) &&
 256                             ((resIndex +
 257                             Integer.parseInt(spaces.get(resIndex).toString())) < selection.getStartRes()))
 258                     {
 259                         continue;
 260                     }
 261
 262
 263                     int sres = seq.findPosition(resIndex +
 264                             Integer.parseInt(spaces.elementAt(resIndex)
 265                                                    .toString()));
 266                     int eres = seq.findPosition(regex.matchedTo() - 1 +
 267                             Integer.parseInt(spaces.elementAt(regex.matchedTo() -
 268                                     1).toString()));
 269
 270                     searchResults.addResult(seq, sres, eres);
 271
 272                     if (!findAll)
 273                     {
 274                         // thats enough, break and display the result
 275                         found = true;
 276                         resIndex++;
 277
 278                         break;
 279                     }
 280
 281                     r = resIndex;
 282                 }
 283                 else
 284                 {
 285                   break;
 286                 }
 287             }
 288
 289             if (!found)
 290             {
 291                 seqIndex++;
 292                 resIndex = 0;
 293             }
 294         }
 295
 296         Vector idMatch = new Vector();
 297
 298         for (int id = 0; id < av.alignment.getHeight(); id++)
 299         {
 300             if (regex.search(av.alignment.getSequenceAt(id).getName()))
 301             {
 302                 idMatch.add(av.alignment.getSequenceAt(id));
 303             }
 304         }
 305
 306         if ((searchResults.getSize() == 0) && (idMatch.size() > 0))
 307         {
 308             ap.idPanel.highlightSearchResults(idMatch);
 309         }
 310
 311
 312         int resultSize = searchResults.getSize();
 313
 314         if (searchResults.getSize() > 0)
 315           createNewGroup.setEnabled(true);
 316         else
 317           searchResults = null;
 318
 319         // if allResults is null, this effectively switches displaySearch flag in seqCanvas
 320         ap.highlightSearchResults(searchResults);
 321
 322         if(!findAll && resultSize==0)
 323         {
 324             JOptionPane.showInternalMessageDialog(this, "Finished searching",
 325                 null, JOptionPane.INFORMATION_MESSAGE);
 326             resIndex = 0;
 327             seqIndex = 0;
 328         }
 329
 330         if (findAll)
 331         {
 332           String message = resultSize + " matches found.";
 333           JOptionPane.showInternalMessageDialog(this, message, null,
 334                                                 JOptionPane.INFORMATION_MESSAGE);
 335         }
 336
 337     }
 338 }