Check for all gapped seqs
[jalview.git] / src / jalview / gui / Finder.java
1 /*\r
2  * Jalview - A Sequence Alignment Editor and Viewer\r
3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
4  *\r
5  * This program is free software; you can redistribute it and/or\r
6  * modify it under the terms of the GNU General Public License\r
7  * as published by the Free Software Foundation; either version 2\r
8  * of the License, or (at your option) any later version.\r
9  *\r
10  * This program is distributed in the hope that it will be useful,\r
11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
13  * GNU General Public License for more details.\r
14  *\r
15  * You should have received a copy of the GNU General Public License\r
16  * along with this program; if not, write to the Free Software\r
17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
18  */\r
19 package jalview.gui;\r
20 \r
21 import jalview.datamodel.*;\r
22 \r
23 import jalview.jbgui.*;\r
24 \r
25 import java.awt.*;\r
26 import java.awt.event.*;\r
27 \r
28 import java.util.*;\r
29 \r
30 import javax.swing.*;\r
31 import javax.swing.event.*;\r
32 \r
33 \r
34 /**\r
35  * DOCUMENT ME!\r
36  *\r
37  * @author $author$\r
38  * @version $Revision$\r
39  */\r
40 public class Finder extends GFinder\r
41 {\r
42     AlignViewport av;\r
43     AlignmentPanel ap;\r
44     JInternalFrame frame;\r
45     int seqIndex = 0;\r
46     int resIndex = 0;\r
47 \r
48     SearchResults searchResults;\r
49 \r
50     /**\r
51      * Creates a new Finder object.\r
52      *\r
53      * @param av DOCUMENT ME!\r
54      * @param ap DOCUMENT ME!\r
55      * @param f DOCUMENT ME!\r
56      */\r
57     public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)\r
58     {\r
59         this.av = av;\r
60         this.ap = ap;\r
61         frame = f;\r
62 \r
63         // all a big pain, but we need to wait until the frame is visible before the textfield can\r
64         // obtain the focus/////////////////////////\r
65         frame.addInternalFrameListener(new InternalFrameAdapter()\r
66             {\r
67                 public void internalFrameOpened(InternalFrameEvent evt)\r
68                 {\r
69                     SwingUtilities.invokeLater(new Runnable()\r
70                         {\r
71                             public void run()\r
72                             {\r
73                                 textfield.requestFocus();\r
74                             }\r
75                         });\r
76                 }\r
77             });\r
78     }\r
79 \r
80 \r
81     /**\r
82      * DOCUMENT ME!\r
83      *\r
84      * @param e DOCUMENT ME!\r
85      */\r
86     public void findNext_actionPerformed(ActionEvent e)\r
87     {\r
88         doSearch(false);\r
89     }\r
90 \r
91     /**\r
92      * DOCUMENT ME!\r
93      *\r
94      * @param e DOCUMENT ME!\r
95      */\r
96     public void findAll_actionPerformed(ActionEvent e)\r
97     {\r
98         resIndex = 0;\r
99         seqIndex = 0;\r
100         doSearch(true);\r
101     }\r
102 \r
103 \r
104     /**\r
105      * DOCUMENT ME!\r
106      *\r
107      * @param e DOCUMENT ME!\r
108      */\r
109     public void createNewGroup_actionPerformed(ActionEvent e)\r
110     {\r
111         JLabel label = new JLabel("Enter name of new sequence feature");\r
112         JTextField textinput = new JTextField(textfield.getText());\r
113         JPanel panel = new JPanel(new BorderLayout());\r
114         panel.add(label, BorderLayout.NORTH);\r
115         panel.add(textinput, BorderLayout.SOUTH);\r
116 \r
117          int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
118             panel, "New Sequence Feature Name",\r
119           JOptionPane.OK_CANCEL_OPTION );\r
120 \r
121          if(reply != JOptionPane.OK_OPTION)\r
122            return;\r
123 \r
124         for (int i = 0; i < searchResults.getSize(); i ++ )\r
125         {\r
126             SequenceI seq = searchResults.getResultSequence(i);\r
127 \r
128             SequenceFeature sf = new SequenceFeature(textinput.getText(),\r
129                 "Search Results", null,\r
130                 searchResults.getResultStart(i),\r
131                searchResults.getResultEnd(i),\r
132                "Search Results");\r
133 \r
134             ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(\r
135                 textinput.getText(), new Color(60,160,115),\r
136                     "Search Results");\r
137 \r
138             seq.getDatasetSequence().addSequenceFeature(sf);\r
139         }\r
140 \r
141         ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();\r
142         ap.alignFrame.showSeqFeatures.setSelected(true);\r
143         av.setShowSequenceFeatures(true);\r
144         ap.highlightSearchResults(null);\r
145     }\r
146 \r
147     /**\r
148      * DOCUMENT ME!\r
149      *\r
150      * @param findAll DOCUMENT ME!\r
151      */\r
152     void doSearch(boolean findAll)\r
153     {\r
154         createNewGroup.setEnabled(false);\r
155 \r
156         String searchString = textfield.getText().trim();\r
157         if(!caseSensitive.isSelected())\r
158           searchString = searchString.toUpperCase();\r
159 \r
160         if(searchString.length()<1)\r
161           return;\r
162 \r
163         com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
164 \r
165         searchResults = new SearchResults();\r
166 \r
167         Sequence seq;\r
168         String item = null;\r
169         boolean found = false;\r
170 \r
171         ////// is the searchString a residue number?\r
172         try\r
173         {\r
174             int res = Integer.parseInt(searchString);\r
175             found = true;\r
176             if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)\r
177             {\r
178               seq = (Sequence) av.getAlignment().getSequenceAt(0);\r
179             }\r
180             else\r
181             {\r
182               seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));\r
183             }\r
184 \r
185             searchResults.addResult(seq, res, res);\r
186         }\r
187         catch (NumberFormatException ex)\r
188         {\r
189         }\r
190 \r
191         ///////////////////////////////////////////////\r
192 \r
193         int end = av.alignment.getHeight();\r
194 \r
195         SequenceGroup selection = av.getSelectionGroup();\r
196 \r
197         if (selection != null)\r
198         {\r
199             if ((selection.getSize(false) < 1) ||\r
200                     ((selection.getEndRes() - selection.getStartRes()) < 2))\r
201             {\r
202                 selection = null;\r
203             }\r
204         }\r
205 \r
206         while (!found && (seqIndex < end))\r
207         {\r
208             seq = (Sequence) av.alignment.getSequenceAt(seqIndex);\r
209 \r
210             if ((selection != null) && !selection.getSequences(false).contains(seq))\r
211             {\r
212                 seqIndex++;\r
213                 resIndex = 0;\r
214 \r
215                 continue;\r
216             }\r
217 \r
218             item = seq.getSequence();\r
219             if(!caseSensitive.isSelected())\r
220               item = item.toUpperCase();\r
221 \r
222             if ((selection != null) &&\r
223                     (selection.getEndRes() < av.alignment.getWidth()-1))\r
224             {\r
225                 item = item.substring(0, selection.getEndRes() + 1);\r
226             }\r
227 \r
228             ///Shall we ignore gaps????\r
229             StringBuffer noGapsSB = new StringBuffer();\r
230             int insertCount = 0;\r
231             Vector spaces = new Vector();\r
232 \r
233             for (int j = 0; j < item.length(); j++)\r
234             {\r
235                 if (!jalview.util.Comparison.isGap(item.charAt(j)))\r
236                 {\r
237                     noGapsSB.append(item.charAt(j));\r
238                     spaces.add(new Integer(insertCount));\r
239                 }\r
240                 else\r
241                 {\r
242                     insertCount++;\r
243                 }\r
244             }\r
245 \r
246             String noGaps = noGapsSB.toString();\r
247 \r
248             for (int r = resIndex; r < noGaps.length(); r++)\r
249             {\r
250 \r
251                 if (regex.searchFrom(noGaps, r))\r
252                 {\r
253                     resIndex = regex.matchedFrom();\r
254 \r
255                     if ((selection != null) &&\r
256                             ((resIndex +\r
257                             Integer.parseInt(spaces.get(resIndex).toString())) < selection.getStartRes()))\r
258                     {\r
259                         continue;\r
260                     }\r
261 \r
262 \r
263                     int sres = seq.findPosition(resIndex +\r
264                             Integer.parseInt(spaces.elementAt(resIndex)\r
265                                                    .toString()));\r
266                     int eres = seq.findPosition(regex.matchedTo() - 1 +\r
267                             Integer.parseInt(spaces.elementAt(regex.matchedTo() -\r
268                                     1).toString()));\r
269 \r
270                     searchResults.addResult(seq, sres, eres);\r
271 \r
272                     if (!findAll)\r
273                     {\r
274                         // thats enough, break and display the result\r
275                         found = true;\r
276                         resIndex++;\r
277 \r
278                         break;\r
279                     }\r
280 \r
281                     r = resIndex;\r
282                 }\r
283                 else\r
284                 {\r
285                   break;\r
286                 }\r
287             }\r
288 \r
289             if (!found)\r
290             {\r
291                 seqIndex++;\r
292                 resIndex = 0;\r
293             }\r
294         }\r
295 \r
296         Vector idMatch = new Vector();\r
297 \r
298         for (int id = 0; id < av.alignment.getHeight(); id++)\r
299         {\r
300             if (regex.search(av.alignment.getSequenceAt(id).getName()))\r
301             {\r
302                 idMatch.add(av.alignment.getSequenceAt(id));\r
303             }\r
304         }\r
305 \r
306         if ((searchResults.getSize() == 0) && (idMatch.size() > 0))\r
307         {\r
308             ap.idPanel.highlightSearchResults(idMatch);\r
309         }\r
310 \r
311 \r
312         int resultSize = searchResults.getSize();\r
313 \r
314         if (searchResults.getSize() > 0)\r
315           createNewGroup.setEnabled(true);\r
316         else\r
317           searchResults = null;\r
318 \r
319         // if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
320         ap.highlightSearchResults(searchResults);\r
321 \r
322         if(!findAll && resultSize==0)\r
323         {\r
324             JOptionPane.showInternalMessageDialog(this, "Finished searching",\r
325                 null, JOptionPane.INFORMATION_MESSAGE);\r
326             resIndex = 0;\r
327             seqIndex = 0;\r
328         }\r
329 \r
330         if (findAll)\r
331         {\r
332           String message = resultSize + " matches found.";\r
333           JOptionPane.showInternalMessageDialog(this, message, null,\r
334                                                 JOptionPane.INFORMATION_MESSAGE);\r
335         }\r
336 \r
337     }\r
338 }\r