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();
59 * Action performed when an input is detected on txt_search field.
62 public void txt_search_ActionPerformed()
64 btn_ok.setEnabled(false);
65 boolean allowEmptySequence = false;
66 mainFrame.setTitle(MessageManager
67 .getString("label.pdb_sequence_getcher"));
68 tbl_summary.setModel(new DefaultTableModel());
69 if (txt_search.getText().trim().length() > 0)
71 long startTime = System.currentTimeMillis();
73 String searchTarget = ((PDBDocField) cmb_searchTarget
74 .getSelectedItem()).getCode();
76 wantedFields = PDBDocFieldPreferences
77 .getSearchSummaryFields();
79 String searchTerm = decodeSearchTerm(txt_search.getText(),
82 PDBRestRequest request = new PDBRestRequest();
83 request.setAllowEmptySeq(allowEmptySequence);
84 request.setResponseSize(100);
85 request.setFieldToSearchBy("(" + searchTarget + ":");
86 request.setSearchTerm(searchTerm + ")");
87 request.setWantedFields(wantedFields);
88 // System.out.println(">>>>>>>>>>>>>> " + request.getQuery());
89 PDBRestClient pdbRestCleint = new PDBRestClient();
90 PDBRestResponse resultList = pdbRestCleint.executeRequest(request);
91 if (resultList.getSearchSummary() != null)
93 tbl_summary.setModel(PDBRestResponse.getTableModel(request,
94 resultList.getSearchSummary()));
97 long endTime = System.currentTimeMillis();
98 int resultSetCount = resultList.getNumberOfItemsFound();
99 String result = (resultSetCount > 1) ? MessageManager
100 .getString("label.results") : MessageManager
101 .getString("label.result");
102 mainFrame.setTitle(frameTitle + " - " + resultSetCount + " " + result
103 + " (" + (endTime - startTime) + " milli secs)");
107 public static String decodeSearchTerm(String enteredText,
110 String foundSearchTerms = enteredText;
111 StringBuilder foundSearchTermsBuilder = new StringBuilder();
112 if (enteredText.contains(";"))
114 String[] searchTerms = enteredText.split(";");
115 for (String searchTerm : searchTerms)
117 if (searchTerm.contains(":"))
119 foundSearchTermsBuilder.append(targetField).append(":")
120 .append(searchTerm.split(":")[0]).append(" OR ");
124 foundSearchTermsBuilder.append(targetField).append(":")
125 .append(searchTerm).append(" OR ");
128 int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
129 foundSearchTerms = foundSearchTermsBuilder.toString();
130 if (foundSearchTerms.contains(" OR "))
132 foundSearchTerms = foundSearchTerms.substring(
133 targetField.length() + 1, endIndex);
136 else if (enteredText.contains(":"))
138 foundSearchTerms = foundSearchTerms.split(":")[0];
140 return foundSearchTerms;
145 public void btn_ok_ActionPerformed()
147 loadSelectedPDBSequencesToAlignment();
151 public void btn_back_ActionPerformed()
154 new SequenceFetcher(progressIdicator);
158 public void btn_cancel_ActionPerformed()
164 * Add the discovered/selected sequences to a target alignment window
166 public void loadSelectedPDBSequencesToAlignment()
169 StringBuilder selectedIds = new StringBuilder();
170 HashSet<String> selectedIdsSet = new HashSet<String>();
171 int pdbIdCol = PDBRestClient.getPDBIdColumIndex(wantedFields, false);
172 int[] selectedRows = tbl_summary.getSelectedRows();
173 for (int summaryRow : selectedRows)
175 String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
177 String searchTerm = txt_search.getText();
178 selectedIdsSet.add(getPDBIdwithSpecifiedChain(pdbIdStr, searchTerm));
181 for (String selectedId : selectedIdsSet)
183 selectedIds.append(selectedId).append(";");
186 String ids = selectedIds.toString();
187 System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
188 seqFetcher.textArea.setText(ids);
189 Thread worker = new Thread(seqFetcher);
193 public static String getPDBIdwithSpecifiedChain(String pdbId,
196 String pdbIdWithChainCode = "";
197 if (searchTerm.contains(";"))
199 String[] foundTerms = searchTerm.split(";");
200 for (String foundTerm : foundTerms)
202 if (foundTerm.contains(pdbId))
204 pdbIdWithChainCode = foundTerm;
208 else if (searchTerm.contains(pdbId))
210 pdbIdWithChainCode = searchTerm;
214 pdbIdWithChainCode = pdbId;
216 return pdbIdWithChainCode;
220 * Populates search target combo-box options
222 public void populateCmbSearchTargetOptions()
224 List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();
225 searchableTargets.add(PDBDocField.PDB_ID);
226 searchableTargets.add(PDBDocField.PFAM_ACCESSION);
227 searchableTargets.add(PDBDocField.MOLECULE_TYPE);
228 searchableTargets.add(PDBDocField.MOLECULE_NAME);
229 searchableTargets.add(PDBDocField.UNIPROT_ACCESSION);
230 searchableTargets.add(PDBDocField.GENE_NAME);
231 searchableTargets.add(PDBDocField.GENUS);
232 searchableTargets.add(PDBDocField.ALL);
234 Collections.sort(searchableTargets, new Comparator<PDBDocField>()
237 public int compare(PDBDocField o1, PDBDocField o2)
239 return o1.getName().compareTo(o2.getName());
243 for (PDBDocField searchTarget : searchableTargets)
245 cmb_searchTarget.addItem(searchTarget);