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PDBFTSPanel | 41 | 105 | 33 |
1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
7 | * Jalview is free software: you can redistribute it and/or | |
8 | * modify it under the terms of the GNU General Public License | |
9 | * as published by the Free Software Foundation, either version 3 | |
10 | * of the License, or (at your option) any later version. | |
11 | * | |
12 | * Jalview is distributed in the hope that it will be useful, but | |
13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
15 | * PURPOSE. See the GNU General Public License for more details. | |
16 | * | |
17 | * You should have received a copy of the GNU General Public License | |
18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
20 | */ | |
21 | ||
22 | package jalview.fts.service.pdb; | |
23 | ||
24 | import java.util.HashMap; | |
25 | import java.util.HashSet; | |
26 | import java.util.Map; | |
27 | ||
28 | import javax.help.HelpSetException; | |
29 | ||
30 | import jalview.fts.api.FTSDataColumnI; | |
31 | import jalview.fts.api.FTSRestClientI; | |
32 | import jalview.fts.core.FTSRestRequest; | |
33 | import jalview.fts.core.FTSRestResponse; | |
34 | import jalview.fts.core.GFTSPanel; | |
35 | import jalview.gui.Help; | |
36 | import jalview.gui.Help.HelpId; | |
37 | import jalview.gui.SequenceFetcher; | |
38 | import jalview.util.MessageManager; | |
39 | ||
40 | @SuppressWarnings("serial") | |
41 | public class PDBFTSPanel extends GFTSPanel | |
42 | { | |
43 | private static String defaultFTSFrameTitle = MessageManager | |
44 | .getString("label.pdb_sequence_fetcher"); | |
45 | ||
46 | private static Map<String, Integer> tempUserPrefs = new HashMap<>(); | |
47 | ||
48 | private static final String PDB_FTS_CACHE_KEY = "CACHE.PDB_FTS"; | |
49 | ||
50 | private static final String PDB_AUTOSEARCH = "FTS.PDB.AUTOSEARCH"; | |
51 | ||
52 | 1 | public PDBFTSPanel(SequenceFetcher fetcher) |
53 | { | |
54 | 1 | super(fetcher); |
55 | 1 | pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize(); |
56 | 1 | this.seqFetcher = fetcher; |
57 | 1 | this.progressIndicator = (fetcher == null) ? null |
58 | : fetcher.getProgressIndicator(); | |
59 | } | |
60 | ||
61 | 0 | @Override |
62 | public void searchAction(boolean isFreshSearch) | |
63 | { | |
64 | 0 | mainFrame.requestFocusInWindow(); |
65 | 0 | if (isFreshSearch) |
66 | { | |
67 | 0 | offSet = 0; |
68 | } | |
69 | 0 | new Thread() |
70 | { | |
71 | 0 | @Override |
72 | public void run() | |
73 | { | |
74 | 0 | reset(); |
75 | 0 | boolean allowEmptySequence = false; |
76 | 0 | if (getTypedText().length() > 0) |
77 | { | |
78 | 0 | setSearchInProgress(true); |
79 | 0 | long startTime = System.currentTimeMillis(); |
80 | ||
81 | 0 | String searchTarget = ((FTSDataColumnI) cmb_searchTarget |
82 | .getSelectedItem()).getCode(); | |
83 | 0 | wantedFields = PDBFTSRestClient.getInstance() |
84 | .getAllDefaultDisplayedFTSDataColumns(); | |
85 | 0 | String searchTerm = decodeSearchTerm(getTypedText(), |
86 | searchTarget); | |
87 | ||
88 | 0 | FTSRestRequest request = new FTSRestRequest(); |
89 | 0 | request.setAllowEmptySeq(allowEmptySequence); |
90 | 0 | request.setResponseSize(100); |
91 | 0 | request.setFieldToSearchBy("(" + searchTarget + ":"); |
92 | 0 | request.setSearchTerm(searchTerm + ")"); |
93 | 0 | request.setOffSet(offSet); |
94 | 0 | request.setWantedFields(wantedFields); |
95 | 0 | FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance(); |
96 | 0 | FTSRestResponse resultList; |
97 | 0 | try |
98 | { | |
99 | 0 | resultList = pdbRestClient.executeRequest(request); |
100 | } catch (Exception e) | |
101 | { | |
102 | 0 | setErrorMessage(e.getMessage()); |
103 | 0 | checkForErrors(); |
104 | 0 | setSearchInProgress(false); |
105 | 0 | return; |
106 | } | |
107 | ||
108 | 0 | if (resultList.getSearchSummary() != null |
109 | && resultList.getSearchSummary().size() > 0) | |
110 | { | |
111 | 0 | getResultTable().setModel(FTSRestResponse.getTableModel(request, |
112 | resultList.getSearchSummary())); | |
113 | 0 | FTSRestResponse.configureTableColumn(getResultTable(), |
114 | wantedFields, tempUserPrefs); | |
115 | 0 | getResultTable().setVisible(true); |
116 | } | |
117 | ||
118 | 0 | long endTime = System.currentTimeMillis(); |
119 | 0 | totalResultSetCount = resultList.getNumberOfItemsFound(); |
120 | 0 | resultSetCount = resultList.getSearchSummary() == null ? 0 |
121 | : resultList.getSearchSummary().size(); | |
122 | 0 | String result = (resultSetCount > 0) |
123 | ? MessageManager.getString("label.results") | |
124 | : MessageManager.getString("label.result"); | |
125 | ||
126 | 0 | if (isPaginationEnabled() && resultSetCount > 0) |
127 | { | |
128 | 0 | String f1 = totalNumberformatter |
129 | .format(Integer.valueOf(offSet + 1)); | |
130 | 0 | String f2 = totalNumberformatter |
131 | .format(Integer.valueOf(offSet + resultSetCount)); | |
132 | 0 | String f3 = totalNumberformatter |
133 | .format(Integer.valueOf(totalResultSetCount)); | |
134 | 0 | updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result |
135 | + " " + f1 + " to " + f2 + " of " + f3 + " " + " (" | |
136 | + (endTime - startTime) + " milli secs)"); | |
137 | } | |
138 | else | |
139 | { | |
140 | 0 | updateSearchFrameTitle(defaultFTSFrameTitle + " - " |
141 | + resultSetCount + " " + result + " (" | |
142 | + (endTime - startTime) + " milli secs)"); | |
143 | } | |
144 | ||
145 | 0 | setSearchInProgress(false); |
146 | 0 | refreshPaginatorState(); |
147 | 0 | updateSummaryTableSelections(); |
148 | } | |
149 | 0 | txt_search.updateCache(); |
150 | } | |
151 | }.start(); | |
152 | } | |
153 | ||
154 | 2 | public static String decodeSearchTerm(String enteredText, |
155 | String targetField) | |
156 | { | |
157 | 2 | String foundSearchTerms = enteredText; |
158 | 2 | StringBuilder foundSearchTermsBuilder = new StringBuilder(); |
159 | 2 | if (enteredText.contains(";")) |
160 | { | |
161 | 1 | String[] searchTerms = enteredText.split(";"); |
162 | 1 | for (String searchTerm : searchTerms) |
163 | { | |
164 | 3 | if (searchTerm.contains(":")) |
165 | { | |
166 | 1 | foundSearchTermsBuilder.append(targetField).append(":") |
167 | .append(searchTerm.split(":")[0]).append(" OR "); | |
168 | } | |
169 | else | |
170 | { | |
171 | 2 | foundSearchTermsBuilder.append(targetField).append(":") |
172 | .append(searchTerm).append(" OR "); | |
173 | } | |
174 | } | |
175 | 1 | int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR "); |
176 | 1 | foundSearchTerms = foundSearchTermsBuilder.toString(); |
177 | 1 | if (foundSearchTerms.contains(" OR ")) |
178 | { | |
179 | 1 | foundSearchTerms = foundSearchTerms |
180 | .substring(targetField.length() + 1, endIndex); | |
181 | } | |
182 | } | |
183 | 1 | else if (enteredText.contains(":")) |
184 | { | |
185 | 0 | foundSearchTerms = foundSearchTerms.split(":")[0]; |
186 | } | |
187 | 2 | return foundSearchTerms; |
188 | } | |
189 | ||
190 | 0 | @Override |
191 | public void okAction() | |
192 | { | |
193 | // mainFrame.dispose(); | |
194 | 0 | disableActionButtons(); |
195 | 0 | StringBuilder selectedIds = new StringBuilder(); |
196 | 0 | HashSet<String> selectedIdsSet = new HashSet<>(); |
197 | 0 | int primaryKeyColIndex = 0; |
198 | 0 | try |
199 | { | |
200 | 0 | primaryKeyColIndex = getFTSRestClient() |
201 | .getPrimaryKeyColumIndex(wantedFields, false); | |
202 | } catch (Exception e) | |
203 | { | |
204 | 0 | e.printStackTrace(); |
205 | } | |
206 | 0 | int[] selectedRows = getResultTable().getSelectedRows(); |
207 | 0 | String searchTerm = getTypedText(); |
208 | 0 | for (int summaryRow : selectedRows) |
209 | { | |
210 | 0 | String idStr = getResultTable() |
211 | .getValueAt(summaryRow, primaryKeyColIndex).toString(); | |
212 | 0 | selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm)); |
213 | } | |
214 | ||
215 | 0 | for (String idStr : paginatorCart) |
216 | { | |
217 | 0 | selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm)); |
218 | } | |
219 | ||
220 | 0 | for (String selectedId : selectedIdsSet) |
221 | { | |
222 | 0 | selectedIds.append(selectedId).append(";"); |
223 | } | |
224 | ||
225 | 0 | String ids = selectedIds.toString(); |
226 | 0 | seqFetcher.setQuery(ids); |
227 | 0 | Thread worker = new Thread(seqFetcher); |
228 | 0 | worker.start(); |
229 | 0 | delayAndEnableActionButtons(); |
230 | } | |
231 | ||
232 | 3 | public static String getPDBIdwithSpecifiedChain(String pdbId, |
233 | String searchTerm) | |
234 | { | |
235 | 3 | String pdbIdWithChainCode = ""; |
236 | 3 | if (searchTerm.contains(";")) |
237 | { | |
238 | 2 | String[] foundTerms = searchTerm.split(";"); |
239 | 2 | for (String foundTerm : foundTerms) |
240 | { | |
241 | 6 | if (foundTerm.contains(pdbId)) |
242 | { | |
243 | 2 | pdbIdWithChainCode = foundTerm; |
244 | } | |
245 | } | |
246 | } | |
247 | 1 | else if (searchTerm.contains(pdbId)) |
248 | { | |
249 | 1 | pdbIdWithChainCode = searchTerm; |
250 | } | |
251 | else | |
252 | { | |
253 | 0 | pdbIdWithChainCode = pdbId; |
254 | } | |
255 | 3 | return pdbIdWithChainCode; |
256 | } | |
257 | ||
258 | 3 | @Override |
259 | public FTSRestClientI getFTSRestClient() | |
260 | { | |
261 | 3 | return PDBFTSRestClient.getInstance(); |
262 | } | |
263 | ||
264 | 2 | @Override |
265 | public String getFTSFrameTitle() | |
266 | { | |
267 | 2 | return defaultFTSFrameTitle; |
268 | } | |
269 | ||
270 | 1 | @Override |
271 | public boolean isPaginationEnabled() | |
272 | { | |
273 | 1 | return true; |
274 | } | |
275 | ||
276 | 4 | @Override |
277 | public Map<String, Integer> getTempUserPrefs() | |
278 | { | |
279 | 4 | return tempUserPrefs; |
280 | } | |
281 | ||
282 | 1 | @Override |
283 | public String getCacheKey() | |
284 | { | |
285 | 1 | return PDB_FTS_CACHE_KEY; |
286 | } | |
287 | ||
288 | 1 | @Override |
289 | public String getAutosearchPreference() | |
290 | { | |
291 | 1 | return PDB_AUTOSEARCH; |
292 | } | |
293 | ||
294 | 0 | @Override |
295 | protected void showHelp() | |
296 | { | |
297 | 0 | try |
298 | { | |
299 | 0 | Help.showHelpWindow(HelpId.PdbFts); |
300 | } catch (HelpSetException e1) | |
301 | { | |
302 | 0 | e1.printStackTrace(); |
303 | } | |
304 | } | |
305 | ||
306 | 1 | public String getDbName() |
307 | { | |
308 | 1 | return "PDB"; |
309 | } | |
310 | } |