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.HashSet;
34 @SuppressWarnings("serial")
35 public class UniprotFTSPanel extends GFTSPanel
38 private static String defaultFTSFrameTitle = MessageManager
39 .getString("label.uniprot_sequence_fetcher");
41 private String ftsFrameTitle = defaultFTSFrameTitle;
43 private int resultSetCount;
47 private static int pageLimit = UniProtFTSRestClient.getInstance()
48 .getDefaultResponsePageSize();
50 public UniprotFTSPanel(SequenceFetcher seqFetcher)
52 this.seqFetcher = seqFetcher;
53 this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
54 .getProgressIndicator();
58 public void searchAction()
64 public void executeSearch()
71 ftsFrameTitle = defaultFTSFrameTitle;
73 if (getTypedText().length() > 0)
75 setSearchInProgress(true);
76 long startTime = System.currentTimeMillis();
78 String searchTarget = ((FTSDataColumnI) cmb_searchTarget
79 .getSelectedItem()).getAltCode();
81 wantedFields = UniProtFTSRestClient.getInstance()
82 .getAllDefaulDisplayedDataColumns();
83 String searchTerm = txt_search.getText();
85 FTSRestRequest request = new FTSRestRequest();
86 request.setFieldToSearchBy(searchTarget);
87 request.setSearchTerm(searchTerm);
88 request.setOffSet(offSet);
89 request.setWantedFields(wantedFields);
90 FTSRestClientI uniProtRestCleint = UniProtFTSRestClient
92 FTSRestResponse resultList;
95 resultList = uniProtRestCleint.executeRequest(request);
99 setErrorMessage(e.getMessage());
104 if (resultList.getSearchSummary() != null
105 && resultList.getSearchSummary().size() > 0)
107 getResultTable().setModel(
108 FTSRestResponse.getTableModel(request,
109 resultList.getSearchSummary()));
110 FTSRestResponse.configureTableColumn(getResultTable(),
112 getResultTable().setVisible(true);
115 long endTime = System.currentTimeMillis();
116 resultSetCount = resultList.getNumberOfItemsFound();
117 String result = (resultSetCount > 0) ? MessageManager
118 .getString("label.results") : MessageManager
119 .getString("label.result");
120 if (isPaginationEnabled() && resultSetCount > 0)
122 updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
123 + " " + (offSet + 1) + " to "
124 + (offSet + resultSetCount)
125 + " " + " (" + (endTime - startTime) + " milli secs)");
129 updateSearchFrameTitle(defaultFTSFrameTitle + " - "
130 + resultSetCount + " " + result + " ("
131 + (endTime - startTime) + " milli secs)");
133 setSearchInProgress(false);
134 refreshPaginatorState();
143 public void refreshPaginatorState()
145 // System.out.println("resultSet count : " + resultSetCount);
146 // System.out.println("offSet : " + offSet);
147 // System.out.println("page limit : " + pageLimit);
148 setPrevPageButtonEnabled(false);
149 setNextPageButtonEnabled(false);
150 if (resultSetCount >= pageLimit)
152 setNextPageButtonEnabled(true);
154 if (offSet >= pageLimit)
156 setPrevPageButtonEnabled(true);
161 public void prevPageAction()
163 if (offSet >= pageLimit)
165 offSet = offSet - pageLimit;
168 refreshPaginatorState();
173 public void nextPageAction()
175 offSet = offSet + pageLimit;
181 public boolean isPaginationEnabled()
187 public void okAction()
189 disableActionButtons();
190 StringBuilder selectedIds = new StringBuilder();
191 HashSet<String> selectedIdsSet = new HashSet<String>();
192 int primaryKeyColIndex = 0;
195 primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
196 wantedFields, false);
197 } catch (Exception e)
201 int[] selectedRows = getResultTable().getSelectedRows();
202 for (int summaryRow : selectedRows)
204 String idStr = getResultTable().getValueAt(summaryRow,
205 primaryKeyColIndex).toString();
206 selectedIdsSet.add(idStr);
209 for (String selectedId : selectedIdsSet)
211 selectedIds.append(selectedId).append(";");
214 String ids = selectedIds.toString();
215 // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
216 seqFetcher.getTextArea().setText(ids);
217 Thread worker = new Thread(seqFetcher);
219 delayAndEnableActionButtons();
223 public FTSRestClientI getFTSRestClient()
225 return UniProtFTSRestClient.getInstance();
229 public String getFTSFrameTitle()
231 return ftsFrameTitle;