2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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.
24 import jalview.jbgui.GPDBSearchPanel;
25 import jalview.jbgui.PDBDocFieldPreferences;
26 import jalview.util.MessageManager;
27 import jalview.ws.dbsources.PDBRestClient;
28 import jalview.ws.dbsources.PDBRestClient.PDBDocField;
29 import jalview.ws.uimodel.PDBRestRequest;
30 import jalview.ws.uimodel.PDBRestResponse;
32 import java.util.ArrayList;
33 import java.util.Collection;
34 import java.util.Collections;
35 import java.util.Comparator;
36 import java.util.HashSet;
37 import java.util.List;
39 import javax.swing.table.DefaultTableModel;
41 @SuppressWarnings("serial")
42 public class PDBSearchPanel extends GPDBSearchPanel
44 private SequenceFetcher seqFetcher;
46 private IProgressIndicator progressIdicator;
48 private Collection<PDBDocField> wantedFields;
50 public PDBSearchPanel(SequenceFetcher seqFetcher)
52 this.seqFetcher = seqFetcher;
53 this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
54 .getProgressIndicator();
58 * Action performed when an input is detected on txt_search field.
61 public void txt_search_ActionPerformed()
67 lbl_loading.setVisible(false);
68 errorWarning.setLength(0);
69 lbl_warning.setVisible(false);
70 btn_ok.setEnabled(false);
71 boolean allowEmptySequence = false;
72 mainFrame.setTitle(MessageManager
73 .getString("label.pdb_sequence_getcher"));
74 tbl_summary.setModel(new DefaultTableModel());
75 if (txt_search.getText().trim().length() > 0)
77 lbl_loading.setVisible(true);
78 long startTime = System.currentTimeMillis();
80 String searchTarget = ((PDBDocField) cmb_searchTarget
81 .getSelectedItem()).getCode();
83 wantedFields = PDBDocFieldPreferences.getSearchSummaryFields();
85 String searchTerm = decodeSearchTerm(txt_search.getText(),
88 PDBRestRequest request = new PDBRestRequest();
89 request.setAllowEmptySeq(allowEmptySequence);
90 request.setResponseSize(100);
91 request.setFieldToSearchBy("(" + searchTarget + ":");
92 request.setSearchTerm(searchTerm + ")");
93 request.setWantedFields(wantedFields);
94 // System.out.println(">>>>>>>>>>>>>> " + request.getQuery());
95 PDBRestClient pdbRestCleint = new PDBRestClient();
96 PDBRestResponse resultList;
99 resultList = pdbRestCleint.executeRequest(request);
100 } catch (Exception e)
102 // e.printStackTrace();
103 errorWarning.append(e.getMessage());
108 if (resultList.getSearchSummary() != null)
110 tbl_summary.setModel(PDBRestResponse.getTableModel(request,
111 resultList.getSearchSummary()));
114 long endTime = System.currentTimeMillis();
115 int resultSetCount = resultList.getNumberOfItemsFound();
116 String result = (resultSetCount > 1) ? MessageManager
117 .getString("label.results") : MessageManager
118 .getString("label.result");
119 mainFrame.setTitle(frameTitle + " - " + resultSetCount + " "
120 + result + " (" + (endTime - startTime) + " milli secs)");
121 lbl_loading.setVisible(false);
127 public static String decodeSearchTerm(String enteredText,
130 String foundSearchTerms = enteredText;
131 StringBuilder foundSearchTermsBuilder = new StringBuilder();
132 if (enteredText.contains(";"))
134 String[] searchTerms = enteredText.split(";");
135 for (String searchTerm : searchTerms)
137 if (searchTerm.contains(":"))
139 foundSearchTermsBuilder.append(targetField).append(":")
140 .append(searchTerm.split(":")[0]).append(" OR ");
144 foundSearchTermsBuilder.append(targetField).append(":")
145 .append(searchTerm).append(" OR ");
148 int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
149 foundSearchTerms = foundSearchTermsBuilder.toString();
150 if (foundSearchTerms.contains(" OR "))
152 foundSearchTerms = foundSearchTerms.substring(
153 targetField.length() + 1, endIndex);
156 else if (enteredText.contains(":"))
158 foundSearchTerms = foundSearchTerms.split(":")[0];
160 return foundSearchTerms;
164 public void btn_ok_ActionPerformed()
166 loadSelectedPDBSequencesToAlignment();
170 public void btn_back_ActionPerformed()
173 new SequenceFetcher(progressIdicator);
177 public void btn_cancel_ActionPerformed()
182 public void transferToSequenceFetcher(String ids)
184 // mainFrame.dispose();
185 seqFetcher.textArea.setText(ids);
186 Thread worker = new Thread(seqFetcher);
191 * Add the discovered/selected sequences to a target alignment window
193 public void loadSelectedPDBSequencesToAlignment()
195 // mainFrame.dispose();
196 disableActionButtons();
197 StringBuilder selectedIds = new StringBuilder();
198 HashSet<String> selectedIdsSet = new HashSet<String>();
199 int pdbIdCol = PDBRestClient.getPDBIdColumIndex(wantedFields, false);
200 int[] selectedRows = tbl_summary.getSelectedRows();
201 for (int summaryRow : selectedRows)
203 String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
205 String searchTerm = txt_search.getText();
206 selectedIdsSet.add(getPDBIdwithSpecifiedChain(pdbIdStr, searchTerm));
209 for (String selectedId : selectedIdsSet)
211 selectedIds.append(selectedId).append(";");
214 String ids = selectedIds.toString();
215 // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
216 seqFetcher.textArea.setText(ids);
217 Thread worker = new Thread(seqFetcher);
219 delayAndEnableActionButtons();
223 private void disableActionButtons()
225 btn_ok.setEnabled(false);
226 btn_back.setEnabled(false);
227 btn_cancel.setEnabled(false);
230 private void delayAndEnableActionButtons()
239 } catch (InterruptedException e)
243 btn_ok.setEnabled(true);
244 btn_back.setEnabled(true);
245 btn_cancel.setEnabled(true);
250 public static String getPDBIdwithSpecifiedChain(String pdbId,
253 String pdbIdWithChainCode = "";
254 if (searchTerm.contains(";"))
256 String[] foundTerms = searchTerm.split(";");
257 for (String foundTerm : foundTerms)
259 if (foundTerm.contains(pdbId))
261 pdbIdWithChainCode = foundTerm;
265 else if (searchTerm.contains(pdbId))
267 pdbIdWithChainCode = searchTerm;
271 pdbIdWithChainCode = pdbId;
273 return pdbIdWithChainCode;
277 * Populates search target combo-box options
279 public void populateCmbSearchTargetOptions()
281 List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();
282 searchableTargets.add(PDBDocField.PDB_ID);
283 searchableTargets.add(PDBDocField.PFAM_ACCESSION);
284 searchableTargets.add(PDBDocField.MOLECULE_TYPE);
285 searchableTargets.add(PDBDocField.MOLECULE_NAME);
286 searchableTargets.add(PDBDocField.UNIPROT_ACCESSION);
287 searchableTargets.add(PDBDocField.GENE_NAME);
288 searchableTargets.add(PDBDocField.GENUS);
289 searchableTargets.add(PDBDocField.ALL);
291 Collections.sort(searchableTargets, new Comparator<PDBDocField>()
294 public int compare(PDBDocField o1, PDBDocField o2)
296 return o1.getName().compareTo(o2.getName());
300 for (PDBDocField searchTarget : searchableTargets)
302 cmb_searchTarget.addItem(searchTarget);
306 public void checkForErrors()
308 lbl_warning.setVisible(false);
309 if (errorWarning.length() > 0)
311 lbl_loading.setVisible(false);
312 lbl_warning.setToolTipText(JvSwingUtils.wrapTooltip(true,
313 errorWarning.toString()));
314 lbl_warning.setVisible(true);