src/jalview/gui/PDBFetchPanel.java

   1 package jalview.gui;
   2
   3 import jalview.jbgui.GPDBFetchPanel;
   4 import jalview.ws.dbsources.PDBRestClient;
   5 import jalview.ws.dbsources.PDBRestClient.PDBDocField;
   6 import jalview.ws.uimodel.PDBSearchRequest;
   7 import jalview.ws.uimodel.PDBSearchResponse;
   8 import jalview.ws.uimodel.PDBSearchResponse.PDBResponseSummary;
   9
  10 import java.util.ArrayList;
  11 import java.util.Collections;
  12 import java.util.Comparator;
  13 import java.util.List;
  14
  15 import javax.swing.DefaultListModel;
  16 import javax.swing.SwingUtilities;
  17
  18 @SuppressWarnings("serial")
  19 public class PDBFetchPanel extends GPDBFetchPanel
  20 {
  21   private SequenceFetcher seqFetcher;
  22
  23   public enum FieldType
  24   {
  25     INT, STRING, BOOLEAN;
  26   }
  27
  28   public PDBFetchPanel()
  29   {
  30   }
  31
  32   public PDBFetchPanel(SequenceFetcher seqFetcher)
  33   {
  34     this();
  35     this.seqFetcher = seqFetcher;
  36   }
  37
  38   public static void main(String[] args)
  39   {
  40     SwingUtilities.invokeLater(new Runnable()
  41     {
  42       public void run()
  43       {
  44         new PDBFetchPanel();
  45       }
  46     });
  47   }
  48
  49   @Override
  50   public void searchStringAction()
  51   {
  52     boolean allowEmptySequence = false;
  53     jListSearchResult.setModel(new DefaultListModel<PDBResponseSummary>());
  54     mainFrame.setTitle("PDB Sequence Fetcher");
  55     if (search.getText().trim().length() > 0)
  56     {
  57       long startTime = System.currentTimeMillis();
  58       PDBRestClient pdbRestCleint = new PDBRestClient();
  59       String searchTarget = ((PDBDocField) searchTargetOptions
  60               .getSelectedItem()).getCode();
  61
  62       PDBSearchRequest request = new PDBSearchRequest();
  63       request.setAllowEmptySeq(allowEmptySequence);
  64       request.setResponseSize(100);
  65       request.setSearchTarget(searchTarget + ":");
  66       request.setSearchTerm(search.getText());
  67       List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
  68       wantedFields.add(PDBDocField.MOLECULE_TYPE);
  69       wantedFields.add(PDBDocField.PDB_ID);
  70       wantedFields.add(PDBDocField.GENUS);
  71       wantedFields.add(PDBDocField.GENE_NAME);
  72       wantedFields.add(PDBDocField.TITLE);
  73       request.setWantedFields(wantedFields);
  74
  75       PDBSearchResponse resultList = pdbRestCleint.executeRequest(request);
  76
  77       if (resultList.getSearchSummary() != null)
  78       {
  79         jListSearchResult.setModel(PDBSearchResponse
  80                 .getListModel(resultList.getSearchSummary()));
  81       }
  82       long endTime = System.currentTimeMillis();
  83       mainFrame.setTitle("PDB Sequence Fetcher - "
  84               + resultList.getItemsFound() + " results ("
  85               + (endTime - startTime) + " milli secs)");
  86     }
  87
  88   }
  89
  90   @Override
  91   public void okActionPerformed()
  92   {
  93     importSelectedPDBSequencesToAlignment();
  94   }
  95
  96
  97   @Override
  98   public void backActionPerformed()
  99   {
 100     System.out.println("back! pressed!");
 101   }
 102
 103   @Override
 104   public void cancelActionPerformed()
 105   {
 106     mainFrame.dispose();
 107   }
 108
 109   private void importSelectedPDBSequencesToAlignment()
 110   {
 111     mainFrame.dispose();
 112     StringBuilder selectedIds = new StringBuilder();
 113     for (PDBResponseSummary dataSelected : jListSearchResult
 114             .getSelectedValuesList())
 115     {
 116       selectedIds.append(";").append(dataSelected.getPdbId());
 117     }
 118     String ids = selectedIds.deleteCharAt(0).toString();
 119     seqFetcher.textArea.setText(ids);
 120     Thread worker = new Thread(seqFetcher);
 121     worker.start();
 122   }
 123
 124   public void populateSearchOptionComboBox()
 125   {
 126     List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();
 127     searchableTargets.add(PDBDocField.PDB_ID);
 128     searchableTargets.add(PDBDocField.PFAM_ACCESSION);
 129     searchableTargets.add(PDBDocField.MOLECULE_TYPE);
 130     searchableTargets.add(PDBDocField.MOLECULE_NAME);
 131     searchableTargets.add(PDBDocField.UNIPROT_ACCESSION);
 132     searchableTargets.add(PDBDocField.GENE_NAME);
 133     searchableTargets.add(PDBDocField.GENUS);
 134     searchableTargets.add(PDBDocField.ALL);
 135
 136     Collections.sort(searchableTargets, new Comparator<PDBDocField>()
 137     {
 138       @Override
 139       public int compare(PDBDocField o1, PDBDocField o2)
 140       {
 141         return o1.getName().compareTo(o2.getName());
 142       }
 143     });
 144
 145     for (PDBDocField searchTarget : searchableTargets)
 146     {
 147       searchTargetOptions.addItem(searchTarget);
 148     }
 149   }
 150
 151 }