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.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;
  31
  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;
  37
  38 import javax.swing.table.DefaultTableModel;
  39
  40 @SuppressWarnings("serial")
  41 public class PDBSearchPanel extends GPDBSearchPanel
  42 {
  43   private SequenceFetcher seqFetcher;
  44
  45   private IProgressIndicator progressIdicator;
  46
  47   private Collection<PDBDocField> wantedFields;
  48
  49   public PDBSearchPanel(SequenceFetcher seqFetcher)
  50   {
  51     this.seqFetcher = seqFetcher;
  52     this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
  53             .getProgressIndicator();
  54   }
  55
  56
  57   /**
  58    * Action performed when an input is detected on txt_search field.
  59    */
  60   @Override
  61   public void txt_search_ActionPerformed()
  62   {
  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)
  68     {
  69       long startTime = System.currentTimeMillis();
  70
  71       String searchTarget = ((PDBDocField) cmb_searchTarget
  72               .getSelectedItem()).getCode();
  73
  74       wantedFields = PDBDocFieldPreferences
  75               .getSearchSummaryFields();
  76
  77       String searchTerm = txt_search.getText();
  78       if (searchTerm.contains(":"))
  79       {
  80         searchTerm = searchTerm.split(":")[0];
  81       }
  82
  83       PDBRestRequest request = new PDBRestRequest();
  84       request.setAllowEmptySeq(allowEmptySequence);
  85       request.setResponseSize(100);
  86       request.setFieldToSearchBy(searchTarget + ":");
  87       request.setSearchTerm(searchTerm);
  88       request.setWantedFields(wantedFields);
  89
  90       PDBRestClient pdbRestCleint = new PDBRestClient();
  91       PDBRestResponse resultList = pdbRestCleint.executeRequest(request);
  92       if (resultList.getSearchSummary() != null)
  93       {
  94         tbl_summary.setModel(PDBRestResponse.getTableModel(request,
  95                 resultList.getSearchSummary()));
  96       }
  97
  98       long endTime = System.currentTimeMillis();
  99       int resultSetCount = resultList.getNumberOfItemsFound();
 100       String result = (resultSetCount > 1) ? MessageManager
 101               .getString("label.results") : MessageManager
 102               .getString("label.result");
 103       mainFrame.setTitle(frameTitle + " - " + resultSetCount + " " + result
 104               + " (" + (endTime - startTime) + " milli secs)");
 105     }
 106   }
 107
 108   @Override
 109   public void btn_ok_ActionPerformed()
 110   {
 111     loadSelectedPDBSequencesToAlignment();
 112   }
 113
 114   @Override
 115   public void btn_back_ActionPerformed()
 116   {
 117     mainFrame.dispose();
 118     new SequenceFetcher(progressIdicator);
 119   }
 120
 121   @Override
 122   public void btn_cancel_ActionPerformed()
 123   {
 124     mainFrame.dispose();
 125   }
 126
 127   /**
 128    * Add the discovered/selected sequences to a target alignment window
 129    */
 130   public void loadSelectedPDBSequencesToAlignment()
 131   {
 132     mainFrame.dispose();
 133     StringBuilder selectedIds = new StringBuilder();
 134     int pdbIdCol = PDBRestClient.getPDBIdColumIndex(wantedFields, false);
 135     int[] selectedRows = tbl_summary.getSelectedRows();
 136     for (int summaryRow : selectedRows)
 137     {
 138       String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
 139               .toString();
 140
 141       String searchTerm = txt_search.getText();
 142       if (searchTerm.contains(":"))
 143       {
 144         selectedIds.append(";").append(pdbIdStr).append(":")
 145                 .append(searchTerm.split(":")[1].toUpperCase());
 146       }
 147       else
 148       {
 149         selectedIds.append(";").append(pdbIdStr);
 150       }
 151     }
 152
 153     String ids = selectedIds.deleteCharAt(0).toString();
 154     seqFetcher.textArea.setText(ids);
 155     Thread worker = new Thread(seqFetcher);
 156     worker.start();
 157   }
 158
 159   /**
 160    * Populates search target combo-box options
 161    */
 162   public void populateCmbSearchTargetOptions()
 163   {
 164     List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();
 165     searchableTargets.add(PDBDocField.PDB_ID);
 166     searchableTargets.add(PDBDocField.PFAM_ACCESSION);
 167     searchableTargets.add(PDBDocField.MOLECULE_TYPE);
 168     searchableTargets.add(PDBDocField.MOLECULE_NAME);
 169     searchableTargets.add(PDBDocField.UNIPROT_ACCESSION);
 170     searchableTargets.add(PDBDocField.GENE_NAME);
 171     searchableTargets.add(PDBDocField.GENUS);
 172     searchableTargets.add(PDBDocField.ALL);
 173
 174     Collections.sort(searchableTargets, new Comparator<PDBDocField>()
 175     {
 176       @Override
 177       public int compare(PDBDocField o1, PDBDocField o2)
 178       {
 179         return o1.getName().compareTo(o2.getName());
 180       }
 181     });
 182
 183     for (PDBDocField searchTarget : searchableTargets)
 184     {
 185       cmb_searchTarget.addItem(searchTarget);
 186     }
 187   }
 188
 189 }