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.
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()
68 lbl_loading.setVisible(false);
69 errorWarning.setLength(0);
70 lbl_warning.setVisible(false);
71 btn_ok.setEnabled(false);
72 boolean allowEmptySequence = false;
73 mainFrame.setTitle(MessageManager
74 .getString("label.pdb_sequence_getcher"));
75 tbl_summary.setModel(new DefaultTableModel());
76 if (txt_search.getText().trim().length() > 0)
78 lbl_loading.setVisible(true);
79 long startTime = System.currentTimeMillis();
81 String searchTarget = ((PDBDocField) cmb_searchTarget
82 .getSelectedItem()).getCode();
84 wantedFields = PDBDocFieldPreferences.getSearchSummaryFields();
86 String searchTerm = decodeSearchTerm(txt_search.getText(),
89 PDBRestRequest request = new PDBRestRequest();
90 request.setAllowEmptySeq(allowEmptySequence);
91 request.setResponseSize(100);
92 request.setFieldToSearchBy("(" + searchTarget + ":");
93 request.setSearchTerm(searchTerm + ")");
94 request.setWantedFields(wantedFields);
95 // System.out.println(">>>>>>>>>>>>>> " + request.getQuery());
96 PDBRestClient pdbRestCleint = new PDBRestClient();
97 PDBRestResponse resultList;
100 resultList = pdbRestCleint.executeRequest(request);
101 } catch (Exception e)
103 // e.printStackTrace();
104 errorWarning.append(e.getMessage());
109 if (resultList.getSearchSummary() != null)
111 tbl_summary.setModel(PDBRestResponse.getTableModel(request,
112 resultList.getSearchSummary()));
115 PDBRestResponse.configureTableColumn(tbl_summary, wantedFields);
117 long endTime = System.currentTimeMillis();
118 int resultSetCount = resultList.getNumberOfItemsFound();
119 String result = (resultSetCount > 1) ? MessageManager
120 .getString("label.results") : MessageManager
121 .getString("label.result");
122 mainFrame.setTitle(frameTitle + " - " + resultSetCount + " "
123 + result + " (" + (endTime - startTime) + " milli secs)");
124 lbl_loading.setVisible(false);
130 public static String decodeSearchTerm(String enteredText,
133 String foundSearchTerms = enteredText;
134 StringBuilder foundSearchTermsBuilder = new StringBuilder();
135 if (enteredText.contains(";"))
137 String[] searchTerms = enteredText.split(";");
138 for (String searchTerm : searchTerms)
140 if (searchTerm.contains(":"))
142 foundSearchTermsBuilder.append(targetField).append(":")
143 .append(searchTerm.split(":")[0]).append(" OR ");
147 foundSearchTermsBuilder.append(targetField).append(":")
148 .append(searchTerm).append(" OR ");
151 int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
152 foundSearchTerms = foundSearchTermsBuilder.toString();
153 if (foundSearchTerms.contains(" OR "))
155 foundSearchTerms = foundSearchTerms.substring(
156 targetField.length() + 1, endIndex);
159 else if (enteredText.contains(":"))
161 foundSearchTerms = foundSearchTerms.split(":")[0];
163 return foundSearchTerms;
167 public void btn_ok_ActionPerformed()
169 loadSelectedPDBSequencesToAlignment();
173 public void btn_back_ActionPerformed()
176 new SequenceFetcher(progressIdicator);
180 public void btn_cancel_ActionPerformed()
186 public void transferToSequenceFetcher(String ids)
188 // mainFrame.dispose();
189 seqFetcher.textArea.setText(ids);
190 Thread worker = new Thread(seqFetcher);
195 * Add the discovered/selected sequences to a target alignment window
197 public void loadSelectedPDBSequencesToAlignment()
199 // mainFrame.dispose();
200 disableActionButtons();
201 StringBuilder selectedIds = new StringBuilder();
202 HashSet<String> selectedIdsSet = new HashSet<String>();
203 int pdbIdCol = PDBRestClient.getPDBIdColumIndex(wantedFields, false);
204 int[] selectedRows = tbl_summary.getSelectedRows();
205 for (int summaryRow : selectedRows)
207 String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
209 String searchTerm = txt_search.getText();
210 selectedIdsSet.add(getPDBIdwithSpecifiedChain(pdbIdStr, searchTerm));
213 for (String selectedId : selectedIdsSet)
215 selectedIds.append(selectedId).append(";");
218 String ids = selectedIds.toString();
219 // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
220 seqFetcher.textArea.setText(ids);
221 Thread worker = new Thread(seqFetcher);
223 delayAndEnableActionButtons();
227 private void disableActionButtons()
229 btn_ok.setEnabled(false);
230 btn_back.setEnabled(false);
231 btn_cancel.setEnabled(false);
234 private void delayAndEnableActionButtons()
244 } catch (InterruptedException e)
248 btn_ok.setEnabled(true);
249 btn_back.setEnabled(true);
250 btn_cancel.setEnabled(true);
255 public static String getPDBIdwithSpecifiedChain(String pdbId,
258 String pdbIdWithChainCode = "";
259 if (searchTerm.contains(";"))
261 String[] foundTerms = searchTerm.split(";");
262 for (String foundTerm : foundTerms)
264 if (foundTerm.contains(pdbId))
266 pdbIdWithChainCode = foundTerm;
270 else if (searchTerm.contains(pdbId))
272 pdbIdWithChainCode = searchTerm;
276 pdbIdWithChainCode = pdbId;
278 return pdbIdWithChainCode;
282 * Populates search target combo-box options
285 public void populateCmbSearchTargetOptions()
287 List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();
288 searchableTargets.add(PDBDocField.PDB_ID);
289 searchableTargets.add(PDBDocField.PFAM_ACCESSION);
290 searchableTargets.add(PDBDocField.MOLECULE_TYPE);
291 searchableTargets.add(PDBDocField.MOLECULE_NAME);
292 searchableTargets.add(PDBDocField.UNIPROT_ACCESSION);
293 searchableTargets.add(PDBDocField.GENE_NAME);
294 searchableTargets.add(PDBDocField.GENUS);
295 searchableTargets.add(PDBDocField.ALL);
297 Collections.sort(searchableTargets, new Comparator<PDBDocField>()
300 public int compare(PDBDocField o1, PDBDocField o2)
302 return o1.getName().compareTo(o2.getName());
306 for (PDBDocField searchTarget : searchableTargets)
308 cmb_searchTarget.addItem(searchTarget);
312 public void checkForErrors()
314 lbl_warning.setVisible(false);
315 if (errorWarning.length() > 0)
317 lbl_loading.setVisible(false);
318 lbl_warning.setToolTipText(JvSwingUtils.wrapTooltip(true,
319 errorWarning.toString()));
320 lbl_warning.setVisible(true);