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.HashMap;
33 import java.util.HashSet;
36 @SuppressWarnings("serial")
37 public class PDBFTSPanel extends GFTSPanel
39 private static String defaultFTSFrameTitle = MessageManager
40 .getString("label.pdb_sequence_fetcher");
42 private String ftsFrameTitle = defaultFTSFrameTitle;
44 private static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
46 public PDBFTSPanel(SequenceFetcher seqFetcher)
48 pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize();
49 this.seqFetcher = seqFetcher;
50 this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
51 .getProgressIndicator();
56 public void searchAction(boolean isFreshSearch)
67 ftsFrameTitle = defaultFTSFrameTitle;
69 boolean allowEmptySequence = false;
70 if (getTypedText().length() > 0)
72 setSearchInProgress(true);
73 long startTime = System.currentTimeMillis();
75 String searchTarget = ((FTSDataColumnI) cmb_searchTarget
76 .getSelectedItem()).getCode();
77 wantedFields = PDBFTSRestClient.getInstance()
78 .getAllDefaultDisplayedFTSDataColumns();
79 String searchTerm = decodeSearchTerm(txt_search.getText(),
82 FTSRestRequest request = new FTSRestRequest();
83 request.setAllowEmptySeq(allowEmptySequence);
84 request.setResponseSize(100);
85 request.setFieldToSearchBy("(" + searchTarget + ":");
86 request.setSearchTerm(searchTerm + ")");
87 request.setOffSet(offSet);
88 request.setWantedFields(wantedFields);
89 FTSRestClientI pdbRestCleint = PDBFTSRestClient.getInstance();
90 FTSRestResponse resultList;
93 resultList = pdbRestCleint.executeRequest(request);
96 setErrorMessage(e.getMessage());
101 if (resultList.getSearchSummary() != null
102 && resultList.getSearchSummary().size() > 0)
104 getResultTable().setModel(
105 FTSRestResponse.getTableModel(request,
106 resultList.getSearchSummary()));
107 FTSRestResponse.configureTableColumn(getResultTable(),
108 wantedFields, tempUserPrefs);
109 getResultTable().setVisible(true);
112 long endTime = System.currentTimeMillis();
113 totalResultSetCount = resultList.getNumberOfItemsFound();
114 resultSetCount = resultList.getSearchSummary() == null ? 0
115 : resultList.getSearchSummary().size();
116 String result = (resultSetCount > 0) ? MessageManager
117 .getString("label.results") : MessageManager
118 .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)");
140 setSearchInProgress(false);
141 refreshPaginatorState();
142 updateSummaryTableSelections();
148 public static String decodeSearchTerm(String enteredText,
151 String foundSearchTerms = enteredText;
152 StringBuilder foundSearchTermsBuilder = new StringBuilder();
153 if (enteredText.contains(";"))
155 String[] searchTerms = enteredText.split(";");
156 for (String searchTerm : searchTerms)
158 if (searchTerm.contains(":"))
160 foundSearchTermsBuilder.append(targetField).append(":")
161 .append(searchTerm.split(":")[0]).append(" OR ");
165 foundSearchTermsBuilder.append(targetField).append(":")
166 .append(searchTerm).append(" OR ");
169 int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
170 foundSearchTerms = foundSearchTermsBuilder.toString();
171 if (foundSearchTerms.contains(" OR "))
173 foundSearchTerms = foundSearchTerms.substring(
174 targetField.length() + 1, endIndex);
177 else if (enteredText.contains(":"))
179 foundSearchTerms = foundSearchTerms.split(":")[0];
181 return foundSearchTerms;
185 public void okAction()
187 // mainFrame.dispose();
188 disableActionButtons();
189 StringBuilder selectedIds = new StringBuilder();
190 HashSet<String> selectedIdsSet = new HashSet<String>();
191 int primaryKeyColIndex = 0;
194 primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
197 } catch (Exception e)
201 int[] selectedRows = getResultTable().getSelectedRows();
202 String searchTerm = txt_search.getText();
203 for (int summaryRow : selectedRows)
205 String idStr = getResultTable().getValueAt(summaryRow,
208 selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
211 for (String idStr : paginatorCart)
213 selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
216 for (String selectedId : selectedIdsSet)
218 selectedIds.append(selectedId).append(";");
221 String ids = selectedIds.toString();
222 // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
223 seqFetcher.getTextArea().setText(ids);
224 Thread worker = new Thread(seqFetcher);
226 delayAndEnableActionButtons();
230 public static String getPDBIdwithSpecifiedChain(String pdbId,
233 String pdbIdWithChainCode = "";
234 if (searchTerm.contains(";"))
236 String[] foundTerms = searchTerm.split(";");
237 for (String foundTerm : foundTerms)
239 if (foundTerm.contains(pdbId))
241 pdbIdWithChainCode = foundTerm;
245 else if (searchTerm.contains(pdbId))
247 pdbIdWithChainCode = searchTerm;
251 pdbIdWithChainCode = pdbId;
253 return pdbIdWithChainCode;
257 public FTSRestClientI getFTSRestClient()
259 return PDBFTSRestClient.getInstance();
263 public String getFTSFrameTitle()
265 return ftsFrameTitle;
269 public boolean isPaginationEnabled()
275 public Map<String, Integer> getTempUserPrefs()
277 return tempUserPrefs;