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.pdb;
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 PDBFTSPanel extends GFTSPanel
37 private static String defaultFTSFrameTitle = MessageManager
38 .getString("label.pdb_sequence_fetcher");
40 private String ftsFrameTitle = defaultFTSFrameTitle;
42 public PDBFTSPanel(SequenceFetcher seqFetcher)
44 pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize();
45 this.seqFetcher = seqFetcher;
46 this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
47 .getProgressIndicator();
52 public void searchAction(boolean isFreshSearch)
63 ftsFrameTitle = defaultFTSFrameTitle;
65 boolean allowEmptySequence = false;
66 if (getTypedText().length() > 0)
68 setSearchInProgress(true);
69 long startTime = System.currentTimeMillis();
71 String searchTarget = ((FTSDataColumnI) cmb_searchTarget
72 .getSelectedItem()).getCode();
73 wantedFields = PDBFTSRestClient.getInstance()
74 .getAllDefaulDisplayedDataColumns();
75 String searchTerm = decodeSearchTerm(txt_search.getText(),
78 FTSRestRequest request = new FTSRestRequest();
79 request.setAllowEmptySeq(allowEmptySequence);
80 request.setResponseSize(100);
81 request.setFieldToSearchBy("(" + searchTarget + ":");
82 request.setSearchTerm(searchTerm + ")");
83 request.setOffSet(offSet);
84 request.setWantedFields(wantedFields);
85 FTSRestClientI pdbRestCleint = PDBFTSRestClient.getInstance();
86 FTSRestResponse resultList;
89 resultList = pdbRestCleint.executeRequest(request);
92 setErrorMessage(e.getMessage());
97 if (resultList.getSearchSummary() != null
98 && resultList.getSearchSummary().size() > 0)
100 getResultTable().setModel(
101 FTSRestResponse.getTableModel(request,
102 resultList.getSearchSummary()));
103 FTSRestResponse.configureTableColumn(getResultTable(),
105 getResultTable().setVisible(true);
108 long endTime = System.currentTimeMillis();
109 totalResultSetCount = resultList.getNumberOfItemsFound();
110 resultSetCount = resultList.getSearchSummary().size();
111 String result = (resultSetCount > 0) ? MessageManager
112 .getString("label.results") : MessageManager
113 .getString("label.result");
115 if (isPaginationEnabled() && resultSetCount > 0)
117 updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
118 + " " + (offSet + 1) + " to "
119 + (offSet + resultSetCount) + " of "
120 + totalResultSetCount
121 + " " + " (" + (endTime - startTime) + " milli secs)");
125 updateSearchFrameTitle(defaultFTSFrameTitle + " - "
126 + resultSetCount + " " + result + " ("
127 + (endTime - startTime) + " milli secs)");
130 setSearchInProgress(false);
131 refreshPaginatorState();
137 public static String decodeSearchTerm(String enteredText,
140 String foundSearchTerms = enteredText;
141 StringBuilder foundSearchTermsBuilder = new StringBuilder();
142 if (enteredText.contains(";"))
144 String[] searchTerms = enteredText.split(";");
145 for (String searchTerm : searchTerms)
147 if (searchTerm.contains(":"))
149 foundSearchTermsBuilder.append(targetField).append(":")
150 .append(searchTerm.split(":")[0]).append(" OR ");
154 foundSearchTermsBuilder.append(targetField).append(":")
155 .append(searchTerm).append(" OR ");
158 int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
159 foundSearchTerms = foundSearchTermsBuilder.toString();
160 if (foundSearchTerms.contains(" OR "))
162 foundSearchTerms = foundSearchTerms.substring(
163 targetField.length() + 1, endIndex);
166 else if (enteredText.contains(":"))
168 foundSearchTerms = foundSearchTerms.split(":")[0];
170 return foundSearchTerms;
174 public void okAction()
176 // mainFrame.dispose();
177 disableActionButtons();
178 StringBuilder selectedIds = new StringBuilder();
179 HashSet<String> selectedIdsSet = new HashSet<String>();
180 int primaryKeyColIndex = 0;
183 primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
186 } catch (Exception e)
190 int[] selectedRows = getResultTable().getSelectedRows();
191 for (int summaryRow : selectedRows)
193 String idStr = getResultTable().getValueAt(summaryRow,
196 String searchTerm = txt_search.getText();
197 selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
200 for (String selectedId : selectedIdsSet)
202 selectedIds.append(selectedId).append(";");
205 String ids = selectedIds.toString();
206 // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
207 seqFetcher.getTextArea().setText(ids);
208 Thread worker = new Thread(seqFetcher);
210 delayAndEnableActionButtons();
214 public static String getPDBIdwithSpecifiedChain(String pdbId,
217 String pdbIdWithChainCode = "";
218 if (searchTerm.contains(";"))
220 String[] foundTerms = searchTerm.split(";");
221 for (String foundTerm : foundTerms)
223 if (foundTerm.contains(pdbId))
225 pdbIdWithChainCode = foundTerm;
229 else if (searchTerm.contains(pdbId))
231 pdbIdWithChainCode = searchTerm;
235 pdbIdWithChainCode = pdbId;
237 return pdbIdWithChainCode;
241 public FTSRestClientI getFTSRestClient()
243 return PDBFTSRestClient.getInstance();
247 public String getFTSFrameTitle()
249 return ftsFrameTitle;
253 public boolean isPaginationEnabled()