src/jalview/gui/PDBSearchPanel.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   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.
  11  *
  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.
  16  *
  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.
  20  */
  21
  22 package jalview.gui;
  23
  24 import jalview.jbgui.GPDBSearchPanel;
  25 import jalview.util.MessageManager;
  26 import jalview.ws.dbsources.PDBRestClient;
  27 import jalview.ws.dbsources.PDBRestClient.PDBDocField;
  28 import jalview.ws.uimodel.PDBRestRequest;
  29 import jalview.ws.uimodel.PDBRestResponse;
  30 import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
  31
  32 import java.util.ArrayList;
  33 import java.util.Collections;
  34 import java.util.Comparator;
  35 import java.util.List;
  36
  37 import javax.swing.DefaultListModel;
  38 import javax.swing.SwingUtilities;
  39
  40 @SuppressWarnings("serial")
  41 public class PDBSearchPanel extends GPDBSearchPanel
  42 {
  43   private SequenceFetcher seqFetcher;
  44
  45   private IProgressIndicator progressIdicator;
  46
  47   public PDBSearchPanel(SequenceFetcher seqFetcher)
  48   {
  49     this.seqFetcher = seqFetcher;
  50     this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
  51             .getProgressIndicator();
  52   }
  53
  54   public static void main(String[] args)
  55   {
  56     SwingUtilities.invokeLater(new Runnable()
  57     {
  58       public void run()
  59       {
  60         new PDBSearchPanel(null);
  61       }
  62     });
  63   }
  64
  65   @Override
  66   public void txt_search_ActionPerformed()
  67   {
  68     boolean allowEmptySequence = false;
  69     lst_searchResult.setModel(new DefaultListModel<PDBResponseSummary>());
  70     mainFrame.setTitle(MessageManager
  71             .getString("label.pdb_sequence_getcher"));
  72     if (txt_search.getText().trim().length() > 0)
  73     {
  74       long startTime = System.currentTimeMillis();
  75       PDBRestClient pdbRestCleint = new PDBRestClient();
  76       String searchTarget = ((PDBDocField) cmb_searchTarget
  77               .getSelectedItem()).getCode();
  78
  79       PDBRestRequest request = new PDBRestRequest();
  80       request.setAllowEmptySeq(allowEmptySequence);
  81       request.setResponseSize(100);
  82       request.setFieldToSearchBy(searchTarget + ":");
  83       request.setSearchTerm(txt_search.getText());
  84       List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
  85       wantedFields.add(PDBDocField.MOLECULE_TYPE);
  86       wantedFields.add(PDBDocField.PDB_ID);
  87       // wantedFields.add(PDBDocField.GENUS);
  88       wantedFields.add(PDBDocField.GENE_NAME);
  89       wantedFields.add(PDBDocField.TITLE);
  90       // wantedFields.add(PDBDocField.RESOLUTION);
  91       // wantedFields.add(PDBDocField.EXPERIMENTAL_METHOD);
  92       request.setWantedFields(wantedFields);
  93       PDBRestResponse resultList = pdbRestCleint.executeRequest(request);
  94       if (resultList.getSearchSummary() != null)
  95       {
  96         lst_searchResult.setModel(PDBRestResponse
  97                 .getListModel(resultList.getSearchSummary()));
  98       }
  99
 100       long endTime = System.currentTimeMillis();
 101       int resultSetCount = resultList.getNumberOfItemsFound();
 102       String result = (resultSetCount > 1) ? MessageManager
 103               .getString("label.results") : MessageManager
 104               .getString("label.result");
 105       mainFrame.setTitle(frameTitle + " - " + resultSetCount + " " + result
 106               + " (" + (endTime - startTime) + " milli secs)");
 107     }
 108   }
 109
 110   @Override
 111   public void btn_ok_ActionPerformed()
 112   {
 113     loadSelectedPDBSequencesToAlignment();
 114   }
 115
 116   @Override
 117   public void btn_back_ActionPerformed()
 118   {
 119     mainFrame.dispose();
 120     new SequenceFetcher(progressIdicator);
 121   }
 122
 123   @Override
 124   public void btn_cancel_ActionPerformed()
 125   {
 126     mainFrame.dispose();
 127   }
 128
 129   public void loadSelectedPDBSequencesToAlignment()
 130   {
 131     mainFrame.dispose();
 132     StringBuilder selectedIds = new StringBuilder();
 133     for (PDBResponseSummary dataSelected : lst_searchResult
 134             .getSelectedValuesList())
 135     {
 136       selectedIds.append(";").append(dataSelected.getPdbId());
 137     }
 138     String ids = selectedIds.deleteCharAt(0).toString();
 139     seqFetcher.textArea.setText(ids);
 140     Thread worker = new Thread(seqFetcher);
 141     worker.start();
 142   }
 143
 144   public void populateCmbSearchTargetOptions()
 145   {
 146     List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();
 147     searchableTargets.add(PDBDocField.PDB_ID);
 148     searchableTargets.add(PDBDocField.PFAM_ACCESSION);
 149     searchableTargets.add(PDBDocField.MOLECULE_TYPE);
 150     searchableTargets.add(PDBDocField.MOLECULE_NAME);
 151     searchableTargets.add(PDBDocField.UNIPROT_ACCESSION);
 152     searchableTargets.add(PDBDocField.GENE_NAME);
 153     searchableTargets.add(PDBDocField.GENUS);
 154     searchableTargets.add(PDBDocField.ALL);
 155
 156     Collections.sort(searchableTargets, new Comparator<PDBDocField>()
 157     {
 158       @Override
 159       public int compare(PDBDocField o1, PDBDocField o2)
 160       {
 161         return o1.getName().compareTo(o2.getName());
 162       }
 163     });
 164
 165     for (PDBDocField searchTarget : searchableTargets)
 166     {
 167       cmb_searchTarget.addItem(searchTarget);
 168     }
 169   }
 170
 171 }