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.List;
38 import javax.swing.table.DefaultTableModel;
40 @SuppressWarnings("serial")
41 public class PDBSearchPanel extends GPDBSearchPanel
43 private SequenceFetcher seqFetcher;
45 private IProgressIndicator progressIdicator;
47 private Collection<PDBDocField> wantedFields;
49 public PDBSearchPanel(SequenceFetcher seqFetcher)
51 this.seqFetcher = seqFetcher;
52 this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
53 .getProgressIndicator();
58 * Action performed when an input is detected on txt_search field.
61 public void txt_search_ActionPerformed()
63 boolean allowEmptySequence = false;
64 mainFrame.setTitle(MessageManager
65 .getString("label.pdb_sequence_getcher"));
66 tbl_summary.setModel(new DefaultTableModel());
67 if (txt_search.getText().trim().length() > 0)
69 long startTime = System.currentTimeMillis();
71 String searchTarget = ((PDBDocField) cmb_searchTarget
72 .getSelectedItem()).getCode();
74 wantedFields = PDBDocFieldPreferences
75 .getSearchSummaryFields();
77 String searchTerm = decodeSearchTerm(txt_search.getText(),
80 PDBRestRequest request = new PDBRestRequest();
81 request.setAllowEmptySeq(allowEmptySequence);
82 request.setResponseSize(100);
83 request.setFieldToSearchBy("(" + searchTarget + ":");
84 request.setSearchTerm(searchTerm + ")");
85 request.setWantedFields(wantedFields);
86 // System.out.println(">>>>>>>>>>>>>> " + request.getQuery());
87 PDBRestClient pdbRestCleint = new PDBRestClient();
88 PDBRestResponse resultList = pdbRestCleint.executeRequest(request);
89 if (resultList.getSearchSummary() != null)
91 tbl_summary.setModel(PDBRestResponse.getTableModel(request,
92 resultList.getSearchSummary()));
95 long endTime = System.currentTimeMillis();
96 int resultSetCount = resultList.getNumberOfItemsFound();
97 String result = (resultSetCount > 1) ? MessageManager
98 .getString("label.results") : MessageManager
99 .getString("label.result");
100 mainFrame.setTitle(frameTitle + " - " + resultSetCount + " " + result
101 + " (" + (endTime - startTime) + " milli secs)");
105 public static String decodeSearchTerm(String enteredText,
108 String foundSearchTerms = enteredText;
109 StringBuilder foundSearchTermsBuilder = new StringBuilder();
110 if (enteredText.contains(";"))
112 String[] searchTerms = enteredText.split(";");
113 for (String searchTerm : searchTerms)
115 if (searchTerm.contains(":"))
117 foundSearchTermsBuilder.append(targetField).append(":")
118 .append(searchTerm.split(":")[0]).append(" OR ");
122 foundSearchTermsBuilder.append(targetField).append(":")
123 .append(searchTerm).append(" OR ");
126 int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
127 foundSearchTerms = foundSearchTermsBuilder.toString();
128 if (foundSearchTerms.contains(" OR "))
130 foundSearchTerms = foundSearchTerms.substring(
131 targetField.length() + 1, endIndex);
134 else if (enteredText.contains(":"))
136 foundSearchTerms = foundSearchTerms.split(":")[0];
138 return foundSearchTerms;
143 public void btn_ok_ActionPerformed()
145 loadSelectedPDBSequencesToAlignment();
149 public void btn_back_ActionPerformed()
152 new SequenceFetcher(progressIdicator);
156 public void btn_cancel_ActionPerformed()
162 * Add the discovered/selected sequences to a target alignment window
164 public void loadSelectedPDBSequencesToAlignment()
167 StringBuilder selectedIds = new StringBuilder();
168 int pdbIdCol = PDBRestClient.getPDBIdColumIndex(wantedFields, false);
169 int[] selectedRows = tbl_summary.getSelectedRows();
170 for (int summaryRow : selectedRows)
172 String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
175 String searchTerm = txt_search.getText();
176 selectedIds.append(getPDBIdwithSpecifiedChain(pdbIdStr, searchTerm))
180 String ids = selectedIds.toString();
181 // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
182 seqFetcher.textArea.setText(ids);
183 Thread worker = new Thread(seqFetcher);
187 public static String getPDBIdwithSpecifiedChain(String pdbId,
190 String pdbIdWithChainCode = "";
191 if (searchTerm.contains(";"))
193 String[] foundTerms = searchTerm.split(";");
194 for (String foundTerm : foundTerms)
196 if (foundTerm.contains(pdbId))
198 pdbIdWithChainCode = foundTerm;
202 else if (searchTerm.contains(pdbId))
204 pdbIdWithChainCode = searchTerm;
208 pdbIdWithChainCode = pdbId;
210 return pdbIdWithChainCode;
214 * Populates search target combo-box options
216 public void populateCmbSearchTargetOptions()
218 List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();
219 searchableTargets.add(PDBDocField.PDB_ID);
220 searchableTargets.add(PDBDocField.PFAM_ACCESSION);
221 searchableTargets.add(PDBDocField.MOLECULE_TYPE);
222 searchableTargets.add(PDBDocField.MOLECULE_NAME);
223 searchableTargets.add(PDBDocField.UNIPROT_ACCESSION);
224 searchableTargets.add(PDBDocField.GENE_NAME);
225 searchableTargets.add(PDBDocField.GENUS);
226 searchableTargets.add(PDBDocField.ALL);
228 Collections.sort(searchableTargets, new Comparator<PDBDocField>()
231 public int compare(PDBDocField o1, PDBDocField o2)
233 return o1.getName().compareTo(o2.getName());
237 for (PDBDocField searchTarget : searchableTargets)
239 cmb_searchTarget.addItem(searchTarget);