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 public UniprotFTSPanel(SequenceFetcher seqFetcher)
50 pageLimit = UniProtFTSRestClient.getInstance()
51 .getDefaultResponsePageSize();
52 this.seqFetcher = seqFetcher;
53 this.progressIndicator = (seqFetcher == null) ? null
54 : seqFetcher.getProgressIndicator();
58 public void searchAction(boolean isFreshSearch)
60 mainFrame.requestFocusInWindow();
71 String searchInput = getTypedText();
72 if (searchInput.length() > 0)
74 setSearchInProgress(true);
75 long startTime = System.currentTimeMillis();
76 searchInput = getTypedText();
77 String searchTarget = ((FTSDataColumnI) cmb_searchTarget
78 .getSelectedItem()).getAltCode();
79 wantedFields = UniProtFTSRestClient.getInstance()
80 .getAllDefaultDisplayedFTSDataColumns();
81 String searchTerm = decodeSearchTerm(searchInput, searchTarget);
83 FTSRestRequest request = new FTSRestRequest();
84 request.setFieldToSearchBy(searchTarget);
85 request.setSearchTerm(searchTerm);
86 request.setOffSet(offSet);
87 request.setWantedFields(wantedFields);
88 FTSRestClientI uniProtRestCleint = UniProtFTSRestClient
90 FTSRestResponse resultList;
93 resultList = uniProtRestCleint.executeRequest(request);
97 setErrorMessage(e.getMessage());
99 setSearchInProgress(false);
103 if (resultList.getSearchSummary() != null
104 && resultList.getSearchSummary().size() > 0)
106 getResultTable().setModel(FTSRestResponse.getTableModel(request,
107 resultList.getSearchSummary()));
108 FTSRestResponse.configureTableColumn(getResultTable(),
109 wantedFields, tempUserPrefs);
110 getResultTable().setVisible(true);
113 long endTime = System.currentTimeMillis();
114 totalResultSetCount = resultList.getNumberOfItemsFound();
115 resultSetCount = resultList.getSearchSummary() == null ? 0
116 : resultList.getSearchSummary().size();
117 String result = (resultSetCount > 0)
118 ? MessageManager.getString("label.results")
119 : MessageManager.getString("label.result");
120 if (isPaginationEnabled() && resultSetCount > 0)
122 updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
124 + totalNumberformatter.format((Number) (offSet + 1))
126 + totalNumberformatter
127 .format((Number) (offSet + resultSetCount))
129 + totalNumberformatter
130 .format((Number) totalResultSetCount)
131 + " " + " (" + (endTime - startTime) + " milli secs)");
135 updateSearchFrameTitle(defaultFTSFrameTitle + " - "
136 + resultSetCount + " " + result + " ("
137 + (endTime - startTime) + " milli secs)");
139 setSearchInProgress(false);
140 refreshPaginatorState();
141 updateSummaryTableSelections();
143 txt_search.updateCache();
149 public String decodeSearchTerm(String enteredText, String targetField)
151 int searchTargetLength = targetField.equalsIgnoreCase("Search All") ? 0
152 : targetField.length() + 1;
153 String searchTarget = targetField.equalsIgnoreCase("Search All") ? ""
155 String foundSearchTerms = enteredText;
156 StringBuilder foundSearchTermsBuilder = new StringBuilder();
157 if (enteredText.contains(";"))
159 String[] searchTerms = enteredText.split(";");
160 for (String searchTerm : searchTerms)
162 foundSearchTermsBuilder.append(searchTarget).append(searchTerm)
165 int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
166 foundSearchTerms = foundSearchTermsBuilder.toString();
167 if (foundSearchTerms.contains(" OR "))
169 foundSearchTerms = foundSearchTerms.substring(searchTargetLength,
173 return foundSearchTerms;
177 public boolean isPaginationEnabled()
183 public void okAction()
185 disableActionButtons();
186 StringBuilder selectedIds = new StringBuilder();
187 HashSet<String> selectedIdsSet = new HashSet<>();
188 int primaryKeyColIndex = 0;
191 primaryKeyColIndex = getFTSRestClient()
192 .getPrimaryKeyColumIndex(wantedFields, false);
193 } catch (Exception e)
197 int[] selectedRows = getResultTable().getSelectedRows();
198 for (int summaryRow : selectedRows)
200 String idStr = getResultTable()
201 .getValueAt(summaryRow, primaryKeyColIndex).toString();
202 selectedIdsSet.add(idStr);
204 selectedIdsSet.addAll(paginatorCart);
205 for (String selectedId : selectedIdsSet)
207 selectedIds.append(selectedId).append(";");
210 String ids = selectedIds.toString();
211 // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
212 seqFetcher.getTextArea().setText(ids);
213 Thread worker = new Thread(seqFetcher);
215 delayAndEnableActionButtons();
219 public FTSRestClientI getFTSRestClient()
221 return UniProtFTSRestClient.getInstance();
225 public String getFTSFrameTitle()
227 return defaultFTSFrameTitle;
231 public Map<String, Integer> getTempUserPrefs()
233 return tempUserPrefs;
237 public String getCacheKey()
239 return UNIPROT_FTS_CACHE_KEY;