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