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");
44 private static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
46 private static final String UNIPROT_FTS_CACHE_KEY = "CACHE.UNIPROT_FTS";
48 public UniprotFTSPanel(SequenceFetcher seqFetcher)
51 pageLimit = UniProtFTSRestClient.getInstance()
52 .getDefaultResponsePageSize();
53 this.seqFetcher = seqFetcher;
54 this.progressIndicator = (seqFetcher == null) ? null : seqFetcher
55 .getProgressIndicator();
60 public void searchAction(boolean isFreshSearch)
72 String searchInput = getTypedText();
73 if (searchInput.length() > 0)
75 setSearchInProgress(true);
76 long startTime = System.currentTimeMillis();
77 searchInput = getTypedText();
78 String searchTarget = ((FTSDataColumnI) cmb_searchTarget
79 .getSelectedItem()).getAltCode();
80 wantedFields = UniProtFTSRestClient.getInstance()
81 .getAllDefaultDisplayedFTSDataColumns();
82 String searchTerm = decodeSearchTerm(searchInput, searchTarget);
84 FTSRestRequest request = new FTSRestRequest();
85 request.setFieldToSearchBy(searchTarget);
86 request.setSearchTerm(searchTerm);
87 request.setOffSet(offSet);
88 request.setWantedFields(wantedFields);
89 FTSRestClientI uniProtRestCleint = UniProtFTSRestClient
91 FTSRestResponse resultList;
94 resultList = uniProtRestCleint.executeRequest(request);
98 setErrorMessage(e.getMessage());
103 if (resultList.getSearchSummary() != null
104 && resultList.getSearchSummary().size() > 0)
106 getResultTable().setModel(
107 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) ? MessageManager
119 .getString("label.results") : MessageManager
120 .getString("label.result");
121 if (isPaginationEnabled() && resultSetCount > 0)
123 updateSearchFrameTitle(defaultFTSFrameTitle
127 + totalNumberformatter.format((Number) (offSet + 1))
129 + totalNumberformatter
130 .format((Number) (offSet + resultSetCount))
132 + totalNumberformatter
133 .format((Number) totalResultSetCount) + " "
134 + " (" + (endTime - startTime) + " milli secs)");
138 updateSearchFrameTitle(defaultFTSFrameTitle + " - "
139 + resultSetCount + " " + result + " ("
140 + (endTime - startTime) + " milli secs)");
142 setSearchInProgress(false);
143 refreshPaginatorState();
144 updateSummaryTableSelections();
152 public String decodeSearchTerm(String enteredText, String targetField)
154 int searchTargetLength = targetField.equalsIgnoreCase("Search All") ? 0
155 : targetField.length() + 1;
156 String searchTarget = targetField.equalsIgnoreCase("Search All") ? ""
158 String foundSearchTerms = enteredText;
159 StringBuilder foundSearchTermsBuilder = new StringBuilder();
160 if (enteredText.contains(";"))
162 String[] searchTerms = enteredText.split(";");
163 for (String searchTerm : searchTerms)
165 foundSearchTermsBuilder.append(searchTarget).append(searchTerm)
168 int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
169 foundSearchTerms = foundSearchTermsBuilder.toString();
170 if (foundSearchTerms.contains(" OR "))
172 foundSearchTerms = foundSearchTerms.substring(searchTargetLength,
176 return foundSearchTerms;
180 public boolean isPaginationEnabled()
186 public void okAction()
188 disableActionButtons();
189 StringBuilder selectedIds = new StringBuilder();
190 HashSet<String> selectedIdsSet = new HashSet<String>();
191 int primaryKeyColIndex = 0;
194 primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
195 wantedFields, false);
196 } catch (Exception e)
200 int[] selectedRows = getResultTable().getSelectedRows();
201 for (int summaryRow : selectedRows)
203 String idStr = getResultTable().getValueAt(summaryRow,
204 primaryKeyColIndex).toString();
205 selectedIdsSet.add(idStr);
207 selectedIdsSet.addAll(paginatorCart);
208 for (String selectedId : selectedIdsSet)
210 selectedIds.append(selectedId).append(";");
213 String ids = selectedIds.toString();
214 // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
215 seqFetcher.getTextArea().setText(ids);
216 Thread worker = new Thread(seqFetcher);
218 delayAndEnableActionButtons();
222 public FTSRestClientI getFTSRestClient()
224 return UniProtFTSRestClient.getInstance();
228 public String getFTSFrameTitle()
230 return defaultFTSFrameTitle;
234 public Map<String, Integer> getTempUserPrefs()
236 return tempUserPrefs;
240 public String getCacheKey()
242 return UNIPROT_FTS_CACHE_KEY;