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.uimodel.PDBSearchRequest;
   6 import jalview.ws.uimodel.PDBSearchResponse;
   7 import jalview.ws.uimodel.PDBSummaryListModel;
   8 import jalview.ws.uimodel.PDBSummaryListModel.PDBDocField;
   9
  10 import java.util.ArrayList;
  11 import java.util.List;
  12
  13 import javax.swing.DefaultListModel;
  14 import javax.swing.SwingUtilities;
  15
  16 @SuppressWarnings("serial")
  17 public class PDBFetchPanel extends GPDBFetchPanel
  18 {
  19   private SequenceFetcher seqFetcher;
  20
  21   public enum FieldType
  22   {
  23     INT, STRING, BOOLEAN;
  24   }
  25
  26   public PDBFetchPanel()
  27   {
  28   }
  29
  30   public PDBFetchPanel(SequenceFetcher seqFetcher)
  31   {
  32     this();
  33     this.seqFetcher = seqFetcher;
  34   }
  35
  36   public static void main(String[] args)
  37   {
  38     SwingUtilities.invokeLater(new Runnable()
  39     {
  40       public void run()
  41       {
  42         new PDBFetchPanel();
  43       }
  44     });
  45   }
  46
  47   @Override
  48   public void searchStringAction()
  49   {
  50     boolean allowEmptySequence = false;
  51     jListSearchResult.setModel(new DefaultListModel<PDBSummaryListModel>());
  52     mainFrame.setTitle("PDB Sequence Fetcher");
  53     if (search.getText().trim().length() > 0)
  54     {
  55       long startTime = System.currentTimeMillis();
  56       PDBRestClient pdbRestCleint = new PDBRestClient();
  57       String searchTarget = ((PDBSearchOptionList) searchTargetOptions
  58               .getSelectedItem()).getCode();
  59
  60       PDBSearchRequest request = new PDBSearchRequest();
  61       request.setAllowEmptySeq(allowEmptySequence);
  62       request.setResponseSize(100);
  63       request.setSearchTarget(searchTarget + ":");
  64       request.setSearchTerm(search.getText());
  65       List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
  66       wantedFields.add(PDBDocField.MOLECULE_TYPE);
  67       wantedFields.add(PDBDocField.PDB_ID);
  68       wantedFields.add(PDBDocField.GENUS);
  69       wantedFields.add(PDBDocField.GENE_NAME);
  70       wantedFields.add(PDBDocField.TITLE);
  71       request.setWantedFields(wantedFields);
  72
  73       PDBSearchResponse resultList = pdbRestCleint.executeRequest(request);
  74
  75       if (resultList.getSearchSummary() != null)
  76       {
  77         jListSearchResult.setModel(PDBSearchResponse
  78                 .getListModel(resultList.getSearchSummary()));
  79       }
  80       long endTime = System.currentTimeMillis();
  81       mainFrame.setTitle("PDB Sequence Fetcher - "
  82               + resultList.getItemsFound() + " results ("
  83               + (endTime - startTime) + " milli secs)");
  84     }
  85
  86   }
  87
  88   @Override
  89   public void okActionPerformed()
  90   {
  91     processPDBResponseData();
  92   }
  93
  94
  95   @Override
  96   public void backActionPerformed()
  97   {
  98     System.out.println("back! pressed!");
  99   }
 100
 101   @Override
 102   public void cancelActionPerformed()
 103   {
 104     mainFrame.dispose();
 105   }
 106
 107   private void processPDBResponseData()
 108   {
 109     mainFrame.dispose();
 110     StringBuilder selectedIds = new StringBuilder();
 111     for (PDBSummaryListModel dataSelected : jListSearchResult
 112             .getSelectedValuesList())
 113     {
 114       selectedIds.append(";").append(dataSelected.getPdbId());
 115     }
 116     String ids = selectedIds.deleteCharAt(0).toString();
 117     seqFetcher.textArea.setText(ids);
 118     Thread worker = new Thread(seqFetcher);
 119     worker.start();
 120   }
 121
 122   @SuppressWarnings("unchecked")
 123   public void populateSearchOptionCombo()
 124
 125   {
 126     List<PDBSearchOptionList> searchOptions = new ArrayList<PDBSearchOptionList>();
 127     searchOptions.add(new PDBSearchOptionList("PDB ID", "pdb_id",
 128             FieldType.STRING));
 129     searchOptions.add(new PDBSearchOptionList("PFAM Name", "pfam_name",
 130             FieldType.STRING));
 131     searchOptions.add(new PDBSearchOptionList("ALL", "text",
 132             FieldType.STRING));
 133     searchOptions.add(new PDBSearchOptionList("Molecule Type",
 134             "molecule_type", FieldType.STRING));
 135     searchOptions.add(new PDBSearchOptionList("Title", "title",
 136             FieldType.STRING));
 137     searchOptions.add(new PDBSearchOptionList("Molecule Name",
 138             "molecule_name", FieldType.STRING));
 139     searchOptions.add(new PDBSearchOptionList("Tax ID", "tax_id",
 140             FieldType.STRING));
 141     searchOptions.add(new PDBSearchOptionList("UniProt Accession",
 142             "uniprot_accession", FieldType.STRING));
 143     searchOptions.add(new PDBSearchOptionList("Gene Name", "gene_name",
 144             FieldType.STRING));
 145     searchOptions.add(new PDBSearchOptionList("Genus", "genus",
 146             FieldType.STRING));
 147
 148     java.util.Collections.sort(searchOptions);
 149
 150     for (PDBSearchOptionList pdbSO : searchOptions)
 151     {
 152       searchTargetOptions.addItem(pdbSO);
 153     }
 154   }
 155
 156   @SuppressWarnings("rawtypes")
 157   public class PDBSearchOptionList implements Comparable
 158   {
 159     private String name;
 160
 161     private String code;
 162
 163     private boolean showInSummary;
 164
 165     private boolean searchFilter;
 166
 167     private FieldType type;
 168
 169     public PDBSearchOptionList(String name, String code, FieldType type)
 170     {
 171       this.name = name;
 172       this.code = code;
 173       this.type = type;
 174     }
 175
 176     public String getName()
 177     {
 178       return name;
 179     }
 180
 181     public void setName(String name)
 182     {
 183       this.name = name;
 184     }
 185
 186     public String getCode()
 187     {
 188       return code;
 189     }
 190
 191     public void setCode(String code)
 192     {
 193       this.code = code;
 194     }
 195
 196     public boolean isShowInSummary()
 197     {
 198       return showInSummary;
 199     }
 200
 201     public void setShowInSummary(boolean showInSummary)
 202     {
 203       this.showInSummary = showInSummary;
 204     }
 205
 206     public boolean isSearchFilter()
 207     {
 208       return searchFilter;
 209     }
 210
 211     public void setSearchFilter(boolean searchFilter)
 212     {
 213       this.searchFilter = searchFilter;
 214     }
 215
 216     public FieldType getFieldType()
 217     {
 218       return type;
 219     }
 220
 221     public void setFieldType(FieldType type)
 222     {
 223       this.type = type;
 224     }
 225
 226     public String toString()
 227     {
 228       return name;
 229     }
 230
 231     public PDBSearchOptionList()
 232     {
 233
 234     }
 235
 236     @Override
 237     public int compareTo(Object o)
 238     {
 239       return this.name.compareTo(((PDBSearchOptionList) o).getName());
 240     }
 241
 242   }
 243 }