2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
22 package jalview.fts.service.uniprot;
24 import jalview.fts.api.FTSDataColumnI;
25 import jalview.fts.api.FTSRestClientI;
26 import jalview.fts.core.FTSRestRequest;
27 import jalview.fts.core.FTSRestResponse;
28 import jalview.fts.core.GFTSPanel;
29 import jalview.gui.SequenceFetcher;
30 import jalview.util.MessageManager;
32 import java.util.HashMap;
33 import java.util.HashSet;
36 @SuppressWarnings("serial")
37 public class UniprotFTSPanel extends GFTSPanel
40 private static String defaultFTSFrameTitle = MessageManager
41 .getString("label.uniprot_sequence_fetcher");
43 private static Map<String, Integer> tempUserPrefs = new HashMap<>();
45 private static final String UNIPROT_FTS_CACHE_KEY = "CACHE.UNIPROT_FTS";
47 private static final String UNIPROT_AUTOSEARCH = "FTS.UNIPROT.AUTOSEARCH";
49 public UniprotFTSPanel(SequenceFetcher fetcher)
52 pageLimit = UniProtFTSRestClient.getInstance()
53 .getDefaultResponsePageSize();
54 this.seqFetcher = fetcher;
55 this.progressIndicator = (fetcher == null) ? null
56 : fetcher.getProgressIndicator();
60 public void searchAction(boolean isFreshSearch)
62 mainFrame.requestFocusInWindow();
73 String searchInput = getTypedText();
74 if (searchInput.length() > 0)
76 setSearchInProgress(true);
77 long startTime = System.currentTimeMillis();
78 searchInput = getTypedText();
79 String searchTarget = ((FTSDataColumnI) cmb_searchTarget
80 .getSelectedItem()).getAltCode();
81 wantedFields = UniProtFTSRestClient.getInstance()
82 .getAllDefaultDisplayedFTSDataColumns();
83 String searchTerm = decodeSearchTerm(searchInput, searchTarget);
85 FTSRestRequest request = new FTSRestRequest();
86 request.setFieldToSearchBy(searchTarget);
87 request.setSearchTerm(searchTerm);
88 request.setOffSet(offSet);
89 request.setWantedFields(wantedFields);
90 FTSRestClientI uniProtRestClient = UniProtFTSRestClient
92 FTSRestResponse resultList;
95 resultList = uniProtRestClient.executeRequest(request);
98 setErrorMessage(e.getMessage());
100 setSearchInProgress(false);
104 if (resultList.getSearchSummary() != null
105 && resultList.getSearchSummary().size() > 0)
107 getResultTable().setModel(FTSRestResponse.getTableModel(request,
108 resultList.getSearchSummary()));
109 FTSRestResponse.configureTableColumn(getResultTable(),
110 wantedFields, tempUserPrefs);
111 getResultTable().setVisible(true);
114 long endTime = System.currentTimeMillis();
115 totalResultSetCount = resultList.getNumberOfItemsFound();
116 resultSetCount = resultList.getSearchSummary() == null ? 0
117 : resultList.getSearchSummary().size();
118 String result = (resultSetCount > 0)
119 ? MessageManager.getString("label.results")
120 : MessageManager.getString("label.result");
121 if (isPaginationEnabled() && resultSetCount > 0)
123 updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
125 + totalNumberformatter.format((Number) (offSet + 1))
127 + totalNumberformatter
128 .format((Number) (offSet + resultSetCount))
130 + totalNumberformatter
131 .format((Number) totalResultSetCount)
132 + " " + " (" + (endTime - startTime) + " milli secs)");
136 updateSearchFrameTitle(defaultFTSFrameTitle + " - "
137 + resultSetCount + " " + result + " ("
138 + (endTime - startTime) + " milli secs)");
140 setSearchInProgress(false);
141 refreshPaginatorState();
142 updateSummaryTableSelections();
144 txt_search.updateCache();
150 public String decodeSearchTerm(String enteredText, String targetField)
152 int searchTargetLength = targetField.equalsIgnoreCase("Search All") ? 0
153 : targetField.length() + 1;
154 String searchTarget = targetField.equalsIgnoreCase("Search All") ? ""
156 String foundSearchTerms = enteredText;
157 StringBuilder foundSearchTermsBuilder = new StringBuilder();
158 if (enteredText.contains(";"))
160 String[] searchTerms = enteredText.split(";");
161 for (String searchTerm : searchTerms)
163 foundSearchTermsBuilder.append(searchTarget).append(searchTerm)
166 int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
167 foundSearchTerms = foundSearchTermsBuilder.toString();
168 if (foundSearchTerms.contains(" OR "))
170 foundSearchTerms = foundSearchTerms.substring(searchTargetLength,
174 return foundSearchTerms;
178 public boolean isPaginationEnabled()
184 public void okAction()
186 disableActionButtons();
187 StringBuilder selectedIds = new StringBuilder();
188 HashSet<String> selectedIdsSet = new HashSet<>();
189 int primaryKeyColIndex = 0;
192 primaryKeyColIndex = getFTSRestClient()
193 .getPrimaryKeyColumIndex(wantedFields, false);
194 } catch (Exception e)
198 int[] selectedRows = getResultTable().getSelectedRows();
199 for (int summaryRow : selectedRows)
201 String idStr = getResultTable()
202 .getValueAt(summaryRow, primaryKeyColIndex).toString();
203 selectedIdsSet.add(idStr);
205 selectedIdsSet.addAll(paginatorCart);
206 for (String selectedId : selectedIdsSet)
208 selectedIds.append(selectedId).append(";");
211 String ids = selectedIds.toString();
212 // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
213 seqFetcher.getTextArea().setText(ids);
214 Thread worker = new Thread(seqFetcher);
216 delayAndEnableActionButtons();
220 public FTSRestClientI getFTSRestClient()
222 return UniProtFTSRestClient.getInstance();
226 public String getFTSFrameTitle()
228 return defaultFTSFrameTitle;
232 public Map<String, Integer> getTempUserPrefs()
234 return tempUserPrefs;
238 public String getCacheKey()
240 return UNIPROT_FTS_CACHE_KEY;
244 public String getAutosearchPreference()
246 return UNIPROT_AUTOSEARCH;