1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.fts.service.pdb

File PDBFTSPanel.java

 

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49% of files have more coverage

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28
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0.31
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Classes

Class
Line #
Actions
PDBFTSPanel 41 105 33
0.380952438.1%
 

Contributing tests

This file is covered by 3 tests. .

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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 toggle 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 toggle @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 toggle @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 toggle 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 toggle @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 toggle 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 toggle @Override
259    public FTSRestClientI getFTSRestClient()
260    {
261  3 return PDBFTSRestClient.getInstance();
262    }
263   
 
264  2 toggle @Override
265    public String getFTSFrameTitle()
266    {
267  2 return defaultFTSFrameTitle;
268    }
269   
 
270  1 toggle @Override
271    public boolean isPaginationEnabled()
272    {
273  1 return true;
274    }
275   
 
276  4 toggle @Override
277    public Map<String, Integer> getTempUserPrefs()
278    {
279  4 return tempUserPrefs;
280    }
281   
 
282  1 toggle @Override
283    public String getCacheKey()
284    {
285  1 return PDB_FTS_CACHE_KEY;
286    }
287   
 
288  1 toggle @Override
289    public String getAutosearchPreference()
290    {
291  1 return PDB_AUTOSEARCH;
292    }
293   
 
294  0 toggle @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 toggle public String getDbName()
307    {
308  1 return "PDB";
309    }
310    }