X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=5c86ce26e6fcaded633fe0b8d24aebfc1be452a5;hb=bc98852ff1a926cf7b11a92db96ff8fe308ceae0;hp=11fb9433703b4444d0fdf962924a7344d9cf3796;hpb=e4a49e444d89dc2d8d35913813bddc3a0dabcad6;p=jalview.git

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 11fb943..5c86ce2 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -1,142 +1,255 @@
+/*
+
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
 package jalview.gui;
 
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.jbgui.GStructureChooser;
+import jalview.jbgui.PDBDocFieldPreferences;
+import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.ws.dbsources.PDBRestClient;
 import jalview.ws.dbsources.PDBRestClient.PDBDocField;
-import jalview.ws.uimodel.PDBSearchRequest;
-import jalview.ws.uimodel.PDBSearchResponse;
-import jalview.ws.uimodel.PDBSearchResponse.PDBResponseSummary;
+import jalview.ws.uimodel.PDBRestRequest;
+import jalview.ws.uimodel.PDBRestResponse;
+import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
 
+import java.awt.event.ItemEvent;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.LinkedHashSet;
 import java.util.List;
 
-import javax.swing.JOptionPane;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.table.DefaultTableModel;
+
 
+/**
+ * Provides the behaviors for the Structure chooser Panel
+ * 
+ * @author tcnofoegbu
+ *
+ */
 @SuppressWarnings("serial")
 public class StructureChooser extends GStructureChooser
 {
-
-  private boolean structuresWereFound = false;
+  private boolean structuresDiscovered = false;
 
   private SequenceI selectedSequence;
 
   private SequenceI[] selectedSequences;
 
-  public StructureChooser(AlignmentPanel ap, final SequenceI sequence)
+  private IProgressIndicator progressIndicator;
+
+  private Collection<PDBResponseSummary> discoveredStructuresSet;
+
+  private PDBRestRequest lastPdbRequest;
+
+  private PDBRestClient pdbRestCleint;
+
+  private String selectedPdbFileName;
+
+  private boolean isValidPBDEntry;
+
+  private static Hashtable<String, PDBEntry> cachedEntryMap;
+
+  public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
+          AlignmentPanel ap)
   {
     this.ap = ap;
-    this.selectedSequence = sequence;
-    selectedSequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
-    { sequence } : ap.av.getSequenceSelection());
-    fetchStructures();
-    populateFilterOptions();
-    updateCurrentView();
+    this.selectedSequence = selectedSeq;
+    this.selectedSequences = selectedSeqs;
+    this.progressIndicator = (ap == null) ? null : ap.alignFrame;
+    init();
   }
 
-  @Override
-  public void ok_ActionPerformed()
+  /**
+   * Initializes parameters used by the Structure Chooser Panel
+   */
+  public void init()
   {
-    // TODO code to load selected structures to jmol or chimera
+    Thread discoverPDBStructuresThread = new Thread(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        long startTime = System.currentTimeMillis();
+        String msg = MessageManager.getString("status.fetching_db_refs");
+        updateProgressIndicator(msg, startTime);
+        loadLocalCachedPDBEntries();
+        fetchStructuresMetaData();
+        populateFilterComboBox();
+        updateProgressIndicator(null, startTime);
+        mainFrame.setVisible(true);
+        updateCurrentView();
+      }
+    });
+    discoverPDBStructuresThread.start();
   }
 
-  protected void populateFilterOptions()
+  /**
+   * Updates the progress indicator with the specified message
+   * 
+   * @param message
+   *          displayed message for the operation
+   * @param id
+   *          unique handle for this indicator
+   */
+  public void updateProgressIndicator(String message, long id)
   {
-    if (structuresWereFound)
-    {
-      filterOptionsComboBox.addItem(new FilterOptions(
-              "- Filter Criteria -", "",
-              VIEWS_FILTER));
-      filterOptionsComboBox.addItem(new FilterOptions("All", "all",
-              VIEWS_FILTER));
-      filterOptionsComboBox.addItem(new FilterOptions("Best Coverage",
-              "coverage",
-              VIEWS_FILTER));
-      filterOptionsComboBox.addItem(new FilterOptions("Best Resolution",
-              PDBDocField.RESOLUTION.getCode(),
-              VIEWS_FILTER));
-      filterOptionsComboBox.addItem(new FilterOptions("Best Quality",
-              PDBDocField.OVERALL_QUALITY.getCode(),
-              VIEWS_FILTER));
-
-      // "number_of_polymers"), PROTEIN_CHAIN_COUNT(
-      // "Protein Chain Count", "number_of_protein_chains"),
-      // BOUND_MOLECULE_COUNT(
-      // "Bound Molecule Count", "number_of_bound_molecules"),
-      // POLYMER_RESIDUE_COUNT(
-      // "Polymer Residue Count", "number_of_polymer_residues"),
-      // UNIPROT_COVERAGE(
+    if (progressIndicator != null)
+    {
+      progressIndicator.setProgressBar(message, id);
     }
-    filterOptionsComboBox.addItem(new FilterOptions("Enter PDB Id", "-",
-            VIEWS_ENTER_ID));
-    filterOptionsComboBox.addItem(new FilterOptions("From File", "-",
-            VIEWS_FROM_FILE));
   }
 
-  private void fetchStructures()
+  /**
+   * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
+   * selection group
+   */
+  public void fetchStructuresMetaData()
   {
     long startTime = System.currentTimeMillis();
-    // final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new
-    // SequenceI[]
-    // { sequence }
-    // : ap.av.getSequenceSelection());
-
-    int foundStructures = 0;
-    List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
-    wantedFields.add(PDBDocField.MOLECULE_TYPE);
-    wantedFields.add(PDBDocField.PDB_ID);
-    wantedFields.add(PDBDocField.GENUS);
-    wantedFields.add(PDBDocField.GENE_NAME);
-    wantedFields.add(PDBDocField.TITLE);
-
-    PDBSearchRequest request = new PDBSearchRequest();
-    request.setAllowEmptySeq(false);
-    request.setResponseSize(500);
-    request.setSearchTarget("(text:");
-    request.setWantedFields(wantedFields);
-    
-    Collection<PDBResponseSummary> searchSummaries = new HashSet<PDBResponseSummary>();
+    Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+            .getStructureSummaryFields();
+
+    discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
     for (SequenceI seq : selectedSequences)
     {
-      request.setSearchTerm(buildQuery(seq) + ")");
-      PDBRestClient pdbRestCleint = new PDBRestClient();
-      PDBSearchResponse resultList = pdbRestCleint
-              .executeRequest(request);
+      PDBRestRequest pdbRequest = new PDBRestRequest();
+      pdbRequest.setAllowEmptySeq(false);
+      pdbRequest.setResponseSize(500);
+      pdbRequest.setFieldToSearchBy("(text:");
+      pdbRequest.setWantedFields(wantedFields);
+      pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+      pdbRequest.setAssociatedSequence(seq.getName());
+      pdbRestCleint = new PDBRestClient();
+      PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+      lastPdbRequest = pdbRequest;
       if (resultList.getSearchSummary() != null
               && !resultList.getSearchSummary().isEmpty())
       {
-        searchSummaries.addAll(resultList.getSearchSummary());
+        discoveredStructuresSet.addAll(resultList.getSearchSummary());
+        updateSequenceDbRef(seq, resultList.getSearchSummary());
       }
     }
 
-    foundStructures = searchSummaries.size();
-    if (searchSummaries != null)
+    int noOfStructuresFound = 0;
+    if (discoveredStructuresSet != null
+            && !discoveredStructuresSet.isEmpty())
     {
-      jListFoundStructures.setModel(PDBSearchResponse
-              .getListModel(searchSummaries));
-      structuresWereFound = true;
+      tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest,
+              discoveredStructuresSet));
+      structuresDiscovered = true;
+      noOfStructuresFound = discoveredStructuresSet.size();
     }
     String totalTime = (System.currentTimeMillis() - startTime)
             + " milli secs";
-    mainFrame.setTitle("Structure Chooser - " + foundStructures
+    mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
             + " Found (" + totalTime + ")");
   }
 
-  private String buildQuery(SequenceI seq)
+  public void loadLocalCachedPDBEntries()
+  {
+    DefaultTableModel tableModel = new DefaultTableModel();
+    tableModel.addColumn("Sequence");
+    tableModel.addColumn("PDB Id");
+    tableModel.addColumn("Type");
+    tableModel.addColumn("File");
+    cachedEntryMap = new Hashtable<String, PDBEntry>();
+    for (SequenceI seq : selectedSequences)
+    {
+      if (seq.getDatasetSequence() != null
+              && seq.getDatasetSequence().getPDBId() != null)
+      {
+        for (PDBEntry pdbEntry : seq.getDatasetSequence().getPDBId())
+        {
+          String[] pdbEntryRowData = new String[]
+          { seq.getDisplayId(false), pdbEntry.getId(), pdbEntry.getType(),
+              pdbEntry.getFile() };
+          tableModel.addRow(pdbEntryRowData);
+          cachedEntryMap.put(seq.getDisplayId(false) + pdbEntry.getId(),
+                  pdbEntry);
+        }
+      }
+    }
+    tbl_local_pdb.setModel(tableModel);
+  }
+
+  /**
+   * Update the DBRef entry for a given sequence with values retrieved from
+   * PDBResponseSummary
+   * 
+   * @param seq
+   *          the Sequence to update its DBRef entry
+   * @param responseSummaries
+   *          a collection of PDBResponseSummary
+   */
+  public void updateSequenceDbRef(SequenceI seq,
+          Collection<PDBResponseSummary> responseSummaries)
+  {
+    for (PDBResponseSummary response : responseSummaries)
+    {
+      PDBEntry newEntry = new PDBEntry();
+      newEntry.setId(response.getPdbId());
+      newEntry.setType("PDB");
+      seq.getDatasetSequence().addPDBId(newEntry);
+    }
+  }
+
+  /**
+   * Builds a query string for a given sequences using its DBRef entries
+   * 
+   * @param seq
+   *          the sequences to build a query for
+   * @return the built query string
+   */
+
+  public static String buildQuery(SequenceI seq)
   {
     String query = seq.getName();
     StringBuilder queryBuilder = new StringBuilder();
     int count = 0;
+
+    if (seq.getPDBId() != null)
+    {
+      for (PDBEntry entry : seq.getPDBId())
+      {
+        queryBuilder.append("text:").append(entry.getId()).append(" OR ");
+      }
+    }
+
     if (seq.getDBRef() != null && seq.getDBRef().length != 0)
     {
       for (DBRefEntry dbRef : seq.getDBRef())
       {
-        queryBuilder.append("text:").append(dbRef.getAccessionId())
+        queryBuilder.append("text:")
+                .append(dbRef.getAccessionId().replaceAll("GO:", ""))
                 .append(" OR ");
         ++count;
         if (count > 10)
@@ -150,129 +263,458 @@ public class StructureChooser extends GStructureChooser
     return query;
   }
 
-  @Override
-  protected void stateChanged()
+  /**
+   * Filters a given list of discovered structures based on supplied argument
+   * 
+   * @param fieldToFilterBy
+   *          the field to filter by
+   */
+  public void filterResultSet(final String fieldToFilterBy)
+  {
+    Thread filterThread = new Thread(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        long startTime = System.currentTimeMillis();
+        try
+        {
+          lbl_loading.setVisible(true);
+
+          Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+                  .getStructureSummaryFields();
+          Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
+          for (SequenceI seq : selectedSequences)
+          {
+            PDBRestRequest pdbRequest = new PDBRestRequest();
+            pdbRequest.setAllowEmptySeq(false);
+            pdbRequest.setResponseSize(1);
+            pdbRequest.setFieldToSearchBy("(text:");
+            pdbRequest.setFieldToSortBy(fieldToFilterBy,
+                    !chk_invertFilter.isSelected());
+            pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+            pdbRequest.setWantedFields(wantedFields);
+            pdbRequest.setAssociatedSequence(seq.getName());
+            pdbRestCleint = new PDBRestClient();
+            PDBRestResponse resultList = pdbRestCleint
+                    .executeRequest(pdbRequest);
+            lastPdbRequest = pdbRequest;
+            if (resultList.getSearchSummary() != null
+                    && !resultList.getSearchSummary().isEmpty())
+            {
+              filteredResponse.addAll(resultList.getSearchSummary());
+            }
+          }
+
+          if (!filteredResponse.isEmpty())
+          {
+            final int filterResponseCount = filteredResponse.size();
+            Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+            reorderedStructuresSet.addAll(filteredResponse);
+            reorderedStructuresSet.addAll(discoveredStructuresSet);
+            tbl_summary.setModel(PDBRestResponse.getTableModel(
+                    lastPdbRequest, reorderedStructuresSet));
+
+            // Update table selection model here
+            tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
+
+          }
+
+          lbl_loading.setVisible(false);
+          String totalTime = (System.currentTimeMillis() - startTime)
+                  + " milli secs";
+          mainFrame.setTitle("Structure Chooser - Filter time ("
+                  + totalTime + ")");
+
+          validateSelections();
+        } catch (Exception e)
+        {
+          e.printStackTrace();
+        }
+      }
+    });
+    filterThread.start();
+  }
+
+
+  /**
+   * Handles action event for btn_pdbFromFile
+   */
+  public void pdbFromFile_actionPerformed()
   {
-    updateCurrentView();
+    jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+    chooser.setFileView(new jalview.io.JalviewFileView());
+    chooser.setDialogTitle(MessageManager.formatMessage(
+            "label.select_pdb_file_for", new String[]
+            { selectedSequence.getDisplayId(false) }));
+    chooser.setToolTipText(MessageManager.formatMessage(
+            "label.load_pdb_file_associate_with_sequence", new String[]
+            { selectedSequence.getDisplayId(false) }));
+
+    int value = chooser.showOpenDialog(null);
+    if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+    {
+      selectedPdbFileName = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+      validateSelections();
+    }
   }
 
-  int debounceCount = 0;
+  /**
+   * Populates the filter combo-box options dynamically depending on discovered
+   * structures
+   */
+  protected void populateFilterComboBox()
+  {
+    if (isStructuresDiscovered())
+    {
+      cmb_filterOption.addItem(new FilterOption("Best Quality",
+              PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER));
+      cmb_filterOption.addItem(new FilterOption("Best UniProt Coverage",
+              PDBDocField.UNIPROT_COVERAGE.getCode(), VIEWS_FILTER));
+      cmb_filterOption.addItem(new FilterOption("Highest Resolution",
+              PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER));
+      cmb_filterOption.addItem(new FilterOption("Highest Protein Chain",
+              PDBDocField.PROTEIN_CHAIN_COUNT.getCode(), VIEWS_FILTER));
+      cmb_filterOption.addItem(new FilterOption("Highest Bound Molecules",
+              PDBDocField.BOUND_MOLECULE_COUNT.getCode(), VIEWS_FILTER));
+      cmb_filterOption.addItem(new FilterOption("Highest Polymer Residues",
+              PDBDocField.POLYMER_RESIDUE_COUNT.getCode(), VIEWS_FILTER));
+    }
+    cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
+            VIEWS_ENTER_ID));
+    cmb_filterOption.addItem(new FilterOption("From File", "-",
+            VIEWS_FROM_FILE));
+    cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-",
+            VIEWS_LOCAL_PDB));
+  }
+
+  /**
+   * Updates the displayed view based on the selected filter option
+   */
   protected void updateCurrentView()
   {
-    FilterOptions currentOption = ((FilterOptions) filterOptionsComboBox
+    FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+            .getSelectedItem());
+    layout_switchableViews.show(pnl_switchableViews,
+            selectedFilterOpt.getView());
+    String filterTitle = mainFrame.getTitle();
+    mainFrame.setTitle(frameTitle);
+    chk_invertFilter.setVisible(false);
+    if (selectedFilterOpt.getView() == VIEWS_FILTER)
+    {
+      mainFrame.setTitle(filterTitle);
+      chk_invertFilter.setVisible(true);
+      filterResultSet(selectedFilterOpt.getValue());
+    }
+    else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
+            || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
+    {
+      idInputAssSeqPanel.loadCmbAssSeq();
+      fileChooserAssSeqPanel.loadCmbAssSeq();
+    }
+    validateSelections();
+  }
+
+  /**
+   * Validates user selection and activates the view button if all parameters
+   * are correct
+   */
+  public void validateSelections()
+  {
+    FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
             .getSelectedItem());
-    switchableViewsLayout.show(switchableViewsPanel,
-            currentOption.getView());
-    ++debounceCount;
-    if (currentOption.getView() == VIEWS_FILTER && debounceCount % 2 == 0)
+    btn_view.setEnabled(false);
+    String currentView = selectedFilterOpt.getView();
+    if (currentView == VIEWS_FILTER)
+    {
+      if (tbl_summary.getSelectedRows().length > 0)
+      {
+        btn_view.setEnabled(true);
+      }
+    }
+    else if (currentView == VIEWS_LOCAL_PDB)
+    {
+      if (tbl_local_pdb.getSelectedRows().length > 0)
+      {
+        btn_view.setEnabled(true);
+      }
+    }
+    else if (currentView == VIEWS_ENTER_ID)
     {
-      filterResultSet(currentOption.getValue());
+      validateAssociationEnterPdb();
+    }
+    else if (currentView == VIEWS_FROM_FILE)
+    {
+      validateAssociationFromFile();
     }
   }
 
-  public void filterResultSet(String filterTarget)
+  /**
+   * Validates inputs from the Manual PDB entry panel
+   */
+  public void validateAssociationEnterPdb()
   {
-    System.out.println("-----------------> Filter by : " + filterTarget);
+    AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
+            .getCmb_assSeq().getSelectedItem();
+    lbl_pdbManualFetchStatus.setIcon(errorImage);
+    if (selectedSequences.length == 1
+            || !assSeqOpt.getName().equalsIgnoreCase(
+                    "-Select Associated Seq-"))
+    {
+      txt_search.setEnabled(true);
+      if (isValidPBDEntry)
+      {
+        btn_view.setEnabled(true);
+        lbl_pdbManualFetchStatus.setIcon(goodImage);
+      }
+    }
+    else
+    {
+      txt_search.setEnabled(false);
+      lbl_pdbManualFetchStatus.setIcon(errorImage);
+    }
+  }
 
-    List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
-    wantedFields.add(PDBDocField.MOLECULE_TYPE);
-    wantedFields.add(PDBDocField.PDB_ID);
-    wantedFields.add(PDBDocField.GENUS);
-    wantedFields.add(PDBDocField.GENE_NAME);
-    wantedFields.add(PDBDocField.TITLE);
+  /**
+   * Validates inputs for the manual PDB file selection options
+   */
+  public void validateAssociationFromFile()
+  {
+    AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
+            .getCmb_assSeq().getSelectedItem();
+    lbl_fromFileStatus.setIcon(errorImage);
+    if (selectedSequences.length == 1
+            || (assSeqOpt != null
+            && !assSeqOpt.getName().equalsIgnoreCase(
+                    "-Select Associated Seq-")))
+    {
+      btn_pdbFromFile.setEnabled(true);
+      if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
+      {
+        btn_view.setEnabled(true);
+        lbl_fromFileStatus.setIcon(goodImage);
+      }
+    }
+    else
+    {
+      btn_pdbFromFile.setEnabled(false);
+      lbl_fromFileStatus.setIcon(errorImage);
+    }
+  }
 
-    PDBSearchRequest request = new PDBSearchRequest();
-    request.setAllowEmptySeq(false);
-    request.setResponseSize(1);
-    request.setSearchTarget("(text:");
-    request.setSortTarget(filterTarget, true);
+  @Override
+  public void cmbAssSeqStateChanged()
+  {
+    validateSelections();
+  }
 
-    request.setWantedFields(wantedFields);
+  /**
+   * Handles the state change event for the 'filter' combo-box and 'invert'
+   * check-box
+   */
+  @Override
+  protected void stateChanged(ItemEvent e)
+  {
+    if (e.getSource() instanceof JCheckBox)
+    {
+      updateCurrentView();
+    }
+    else
+    {
+      if (e.getStateChange() == ItemEvent.SELECTED)
+      {
+        updateCurrentView();
+      }
+    }
 
-    Collection<PDBResponseSummary> searchSummaries = new HashSet<PDBResponseSummary>();
-    for (SequenceI seq : selectedSequences)
+  }
+
+  /**
+   * Handles action event for btn_ok
+   */
+  @Override
+  public void ok_ActionPerformed()
+  {
+    FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+            .getSelectedItem());
+    String currentView = selectedFilterOpt.getView();
+    if (currentView == VIEWS_FILTER)
     {
-      request.setSearchTerm(buildQuery(seq) + ")");
-      PDBRestClient pdbRestCleint = new PDBRestClient();
-      PDBSearchResponse resultList = pdbRestCleint.executeRequest(request);
-      if (resultList.getSearchSummary() != null
-              && !resultList.getSearchSummary().isEmpty())
+      int pdbIdCol = PDBRestClient.getPDBIdColumIndex(
+              lastPdbRequest.getWantedFields(), true);
+      int[] selectedRows = tbl_summary.getSelectedRows();
+      PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+      int count = 0;
+      for (int summaryRow : selectedRows)
       {
-        searchSummaries.addAll(resultList.getSearchSummary());
+        String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
+                .toString();
+        PDBEntry pdbEntry = new PDBEntry();
+        pdbEntry.setId(pdbIdStr);
+        pdbEntry.setType("PDB");
+        pdbEntriesToView[count++] = pdbEntry;
+      }
 
+      launchStructureViewer(ap.getStructureSelectionManager(),
+              pdbEntriesToView, ap, selectedSequences);
+    }
+    else if(currentView == VIEWS_LOCAL_PDB){
+      int[] selectedRows = tbl_local_pdb.getSelectedRows();
+      PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+      int count = 0;
+      for (int row : selectedRows)
+      {
+         String entryKey = tbl_local_pdb.getValueAt(row, 0).toString() + tbl_local_pdb.getValueAt(row, 1).toString();
+        pdbEntriesToView[count++] = cachedEntryMap.get(entryKey);
       }
+      launchStructureViewer(ap.getStructureSelectionManager(),
+              pdbEntriesToView, ap, selectedSequences);
     }
-
-    for (PDBResponseSummary summary : searchSummaries)
+    else if (currentView == VIEWS_ENTER_ID)
+    {
+      SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
+              .getCmb_assSeq().getSelectedItem()).getSequence();
+      if (userSelectedSeq != null)
+      {
+        selectedSequence = userSelectedSeq;
+      }
+      PDBEntry pdbEntry = new PDBEntry();
+      pdbEntry.setId(txt_search.getText());
+      pdbEntry.setType("PDB");
+      selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
+      PDBEntry[] pdbEntriesToView = new PDBEntry[]
+      { pdbEntry };
+      launchStructureViewer(ap.getStructureSelectionManager(),
+              pdbEntriesToView, ap, new SequenceI[]
+              { selectedSequence });
+    }
+    else if (currentView == VIEWS_FROM_FILE)
     {
-      jListFoundStructures.setSelectedValue(summary, true);
-      // jListFoundStructures.
-      break;
+      SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
+              .getCmb_assSeq().getSelectedItem()).getSequence();
+      if (userSelectedSeq != null)
+      {
+        selectedSequence = userSelectedSeq;
+      }
+      PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+              .associatePdbWithSeq(
+              selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
+              selectedSequence, true, Desktop.instance);
+
+      launchStructureViewer(ap.getStructureSelectionManager(),
+              new PDBEntry[]
+              { fileEntry }, ap, new SequenceI[]
+              { selectedSequence });
     }
-    System.out.println("Found item count : " + searchSummaries.size());
+    mainFrame.dispose();
   }
 
-  public void pdbFromFile_actionPerformed()
+  private void launchStructureViewer(StructureSelectionManager ssm,
+          PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel,
+          SequenceI[] selectedSequences)
   {
-    jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-    chooser.setFileView(new jalview.io.JalviewFileView());
-    chooser.setDialogTitle(MessageManager.formatMessage(
-            "label.select_pdb_file_for", new String[]
-            { selectedSequence.getDisplayId(false) }));
-    chooser.setToolTipText(MessageManager.formatMessage(
-            "label.load_pdb_file_associate_with_sequence", new String[]
-            { selectedSequence.getDisplayId(false) }));
-
-    int value = chooser.showOpenDialog(null);
+    StructureViewer sViewer = new StructureViewer(ssm);
+    if (pdbEntriesToView.length > 1)
+    {
+      sViewer.viewStructures(alignPanel, pdbEntriesToView,
+              alignPanel.av.collateForPDB(pdbEntriesToView));
+    }
+    else
+    {
+      sViewer.viewStructures(pdbEntriesToView[0], selectedSequences, null,
+              alignPanel);
+    }
+  }
 
-    if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+  /**
+   * Populates the combo-box used in associating manually fetched structures to
+   * a unique sequence when more than one sequence selection is made.
+   */
+  public void populateCmbAssociateSeqOptions(
+          JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq)
+  {
+    cmb_assSeq.removeAllItems();
+    cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-",
+            null));
+    // cmb_assSeq.addItem(new AssociateSeqOptions("Auto Detect", null));
+    lbl_associateSeq.setVisible(false);
+    if (selectedSequences.length > 1)
     {
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-      new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
-              jalview.io.AppletFormatAdapter.FILE, selectedSequence, true,
-              Desktop.instance);
+      for (SequenceI seq : selectedSequences)
+      {
+        cmb_assSeq.addItem(new AssociateSeqOptions(seq));
+      }
     }
+    else
+    {
+      String seqName = selectedSequence.getDisplayId(false);
+      seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
+      lbl_associateSeq.setText(seqName);
+      lbl_associateSeq.setVisible(true);
+      cmb_assSeq.setVisible(false);
+    }
+  }
 
+  public boolean isStructuresDiscovered()
+  {
+    return structuresDiscovered;
   }
 
+  public void setStructuresDiscovered(boolean structuresDiscovered)
+  {
+    this.structuresDiscovered = structuresDiscovered;
+  }
 
-  // rpdbview.addActionListener(new ActionListener()
-  // {
-  //
-  // @Override
-  // public void actionPerformed(ActionEvent e)
-  // {
-  // new StructureViewer(ap.getStructureSelectionManager())
-  // .viewStructures(ap, pr, ap.av.collateForPDB(pr));
-  // }
-  // });
+  public Collection<PDBResponseSummary> getDiscoveredStructuresSet()
+  {
+    return discoveredStructuresSet;
+  }
 
-  public void enterPDB_actionPerformed()
+  @Override
+  protected void txt_search_ActionPerformed()
   {
-    String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
-            MessageManager.getString("label.enter_pdb_id"),
-            MessageManager.getString("label.enter_pdb_id"),
-            JOptionPane.QUESTION_MESSAGE);
-    if (id != null && id.length() > 0)
-    {
-      PDBEntry entry = new PDBEntry();
-      entry.setId(id.toUpperCase());
-      selectedSequence.getDatasetSequence().addPDBId(entry);
+    isValidPBDEntry = false;
+    if (txt_search.getText().length() > 0)
+    {
+      List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+      wantedFields.add(PDBDocField.PDB_ID);
+      PDBRestRequest pdbRequest = new PDBRestRequest();
+      pdbRequest.setAllowEmptySeq(false);
+      pdbRequest.setResponseSize(1);
+      pdbRequest.setFieldToSearchBy("(pdb_id:");
+      pdbRequest.setWantedFields(wantedFields);
+      pdbRequest.setSearchTerm(txt_search.getText() + ")");
+      pdbRequest.setAssociatedSequence(selectedSequence.getName());
+      pdbRestCleint = new PDBRestClient();
+      PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+      if (resultList.getSearchSummary() != null
+              && resultList.getSearchSummary().size() > 0)
+      {
+        isValidPBDEntry = true;
+      }
     }
+    validateSelections();
   }
 
-  // public static void main(String[] args)
-  // {
-  // SwingUtilities.invokeLater(new Runnable()
-  // {
-  // public void run()
-  // {
-  // new StructureChooser(null, null);
-  // }
-  // });
-  // }
-
+  @Override
+  public void tabRefresh()
+  {
+    if (selectedSequences != null)
+    {
+      Thread refreshThread = new Thread(new Runnable()
+      {
+        @Override
+        public void run()
+        {
+          fetchStructuresMetaData();
+          filterResultSet(((FilterOption) cmb_filterOption
+                  .getSelectedItem()).getValue());
+        }
+      });
+      refreshThread.start();
+    }
+  }
 
 }