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
  39 @SuppressWarnings("serial")
  40 public class PDBSearchPanel extends GPDBSearchPanel
  41 {
  42   private SequenceFetcher seqFetcher;
  43
  44   private IProgressIndicator progressIdicator;
  45
  46   public PDBSearchPanel(SequenceFetcher seqFetcher)
  47   {
  48     this.seqFetcher = seqFetcher;
  49     this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
  50             .getProgressIndicator();
  51   }
  52
  53
  54   @Override
  55   public void txt_search_ActionPerformed()
  56   {
  57     boolean allowEmptySequence = false;
  58     lst_searchResult.setModel(new DefaultListModel<PDBResponseSummary>());
  59     mainFrame.setTitle(MessageManager
  60             .getString("label.pdb_sequence_getcher"));
  61     if (txt_search.getText().trim().length() > 0)
  62     {
  63       long startTime = System.currentTimeMillis();
  64
  65       String searchTarget = ((PDBDocField) cmb_searchTarget
  66               .getSelectedItem()).getCode();
  67
  68       List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
  69       wantedFields.add(PDBDocField.MOLECULE_TYPE);
  70       wantedFields.add(PDBDocField.PDB_ID);
  71       // wantedFields.add(PDBDocField.GENUS);
  72       wantedFields.add(PDBDocField.GENE_NAME);
  73       wantedFields.add(PDBDocField.TITLE);
  74       // wantedFields.add(PDBDocField.RESOLUTION);
  75       // wantedFields.add(PDBDocField.EXPERIMENTAL_METHOD);
  76
  77       PDBRestRequest request = new PDBRestRequest();
  78       request.setAllowEmptySeq(allowEmptySequence);
  79       request.setResponseSize(100);
  80       request.setFieldToSearchBy(searchTarget + ":");
  81       request.setSearchTerm(txt_search.getText());
  82       request.setWantedFields(wantedFields);
  83
  84       PDBRestClient pdbRestCleint = new PDBRestClient();
  85       PDBRestResponse resultList = pdbRestCleint.executeRequest(request);
  86       if (resultList.getSearchSummary() != null)
  87       {
  88         lst_searchResult.setModel(PDBRestResponse
  89                 .getListModel(resultList.getSearchSummary()));
  90       }
  91
  92       long endTime = System.currentTimeMillis();
  93       int resultSetCount = resultList.getNumberOfItemsFound();
  94       String result = (resultSetCount > 1) ? MessageManager
  95               .getString("label.results") : MessageManager
  96               .getString("label.result");
  97       mainFrame.setTitle(frameTitle + " - " + resultSetCount + " " + result
  98               + " (" + (endTime - startTime) + " milli secs)");
  99     }
 100   }
 101
 102   @Override
 103   public void btn_ok_ActionPerformed()
 104   {
 105     loadSelectedPDBSequencesToAlignment();
 106   }
 107
 108   @Override
 109   public void btn_back_ActionPerformed()
 110   {
 111     mainFrame.dispose();
 112     new SequenceFetcher(progressIdicator);
 113   }
 114
 115   @Override
 116   public void btn_cancel_ActionPerformed()
 117   {
 118     mainFrame.dispose();
 119   }
 120
 121   /**
 122    * Add the discovered/selected sequences to a target alignment window
 123    */
 124   public void loadSelectedPDBSequencesToAlignment()
 125   {
 126     mainFrame.dispose();
 127     StringBuilder selectedIds = new StringBuilder();
 128     for (PDBResponseSummary dataSelected : lst_searchResult
 129             .getSelectedValuesList())
 130     {
 131       selectedIds.append(";").append(dataSelected.getPdbId());
 132     }
 133     String ids = selectedIds.deleteCharAt(0).toString();
 134     seqFetcher.textArea.setText(ids);
 135     Thread worker = new Thread(seqFetcher);
 136     worker.start();
 137   }
 138
 139   /**
 140    * Populates search target combo-box options
 141    */
 142   public void populateCmbSearchTargetOptions()
 143   {
 144     List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();
 145     searchableTargets.add(PDBDocField.PDB_ID);
 146     searchableTargets.add(PDBDocField.PFAM_ACCESSION);
 147     searchableTargets.add(PDBDocField.MOLECULE_TYPE);
 148     searchableTargets.add(PDBDocField.MOLECULE_NAME);
 149     searchableTargets.add(PDBDocField.UNIPROT_ACCESSION);
 150     searchableTargets.add(PDBDocField.GENE_NAME);
 151     searchableTargets.add(PDBDocField.GENUS);
 152     searchableTargets.add(PDBDocField.ALL);
 153
 154     Collections.sort(searchableTargets, new Comparator<PDBDocField>()
 155     {
 156       @Override
 157       public int compare(PDBDocField o1, PDBDocField o2)
 158       {
 159         return o1.getName().compareTo(o2.getName());
 160       }
 161     });
 162
 163     for (PDBDocField searchTarget : searchableTargets)
 164     {
 165       cmb_searchTarget.addItem(searchTarget);
 166     }
 167   }
 168
 169 }