X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=976b77b9c89227e3995c2a4cd095e2802729cfef;hb=7a1a7eea9501cd9e3841e996f4926cf1686be76a;hp=07e36ec7b4f3bd3d8c9986725d28a767490513ea;hpb=7d76e402efd4e04e179bc9bb264551bc2d3df936;p=jalview.git

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 07e36ec..976b77b 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -1,273 +1,915 @@
+/*
+
+ * 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.uimodel.PDBSearchRequest;
-import jalview.ws.uimodel.PDBSearchResponse;
-import jalview.ws.uimodel.PDBSummaryListModel;
-import jalview.ws.uimodel.PDBSummaryListModel.PDBDocField;
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+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.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
 import javax.swing.JOptionPane;
-import javax.swing.SwingUtilities;
+import javax.swing.table.DefaultTableModel;
+
 
+/**
+ * Provides the behaviors for the Structure chooser Panel
+ * 
+ * @author tcnofoegbu
+ *
+ */
 @SuppressWarnings("serial")
 public class StructureChooser extends GStructureChooser
 {
+  private boolean structuresDiscovered = false;
+
+  private SequenceI selectedSequence;
+
+  private SequenceI[] selectedSequences;
+
+  private IProgressIndicator progressIndicator;
+
+  private Collection<PDBResponseSummary> discoveredStructuresSet;
+
+  private PDBRestRequest lastPdbRequest;
+
+  private PDBRestClient pdbRestCleint;
 
+  private String selectedPdbFileName;
 
-  private SequenceI sequence;
+  private boolean isValidPBDEntry;
 
+  private static Hashtable<String, PDBEntry> cachedEntryMap;
 
-  public StructureChooser(AlignmentPanel ap, final SequenceI sequence)
+  public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
+          AlignmentPanel ap)
   {
     this.ap = ap;
-    this.sequence = sequence;
-    fetchStructures();
+    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()
   {
-    jListFoundStructures.setSelectedValue("op1x", true);
+    Thread discoverPDBStructuresThread = new Thread(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        long startTime = System.currentTimeMillis();
+        updateProgressIndicator(MessageManager
+                .getString("status.loading_cached_pdb_entries"), startTime);
+        loadLocalCachedPDBEntries();
+        updateProgressIndicator(null, startTime);
+        updateProgressIndicator(MessageManager
+                .getString("status.searching_for_pdb_structures"),
+                startTime);
+        fetchStructuresMetaData();
+        populateFilterComboBox();
+        updateProgressIndicator(null, startTime);
+        mainFrame.setVisible(true);
+        updateCurrentView();
+      }
+    });
+    discoverPDBStructuresThread.start();
   }
 
-  public void pdbFromFile_actionPerformed()
+  /**
+   * 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)
   {
-    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[]
-            { sequence.getDisplayId(false) }));
-    chooser.setToolTipText(MessageManager.formatMessage(
-            "label.load_pdb_file_associate_with_sequence", new String[]
-            { sequence.getDisplayId(false) }));
+    if (progressIndicator != null)
+    {
+      progressIndicator.setProgressBar(message, id);
+    }
+  }
 
-    int value = chooser.showOpenDialog(null);
+  /**
+   * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
+   * selection group
+   */
+  public void fetchStructuresMetaData()
+  {
+    long startTime = System.currentTimeMillis();
+    Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+            .getStructureSummaryFields();
 
-    if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+    discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+    HashSet<String> errors = new HashSet<String>();
+    for (SequenceI seq : selectedSequences)
     {
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-      new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
-              jalview.io.AppletFormatAdapter.FILE, sequence, true,
-              Desktop.instance);
+      PDBRestRequest pdbRequest = new PDBRestRequest();
+      pdbRequest.setAllowEmptySeq(false);
+      pdbRequest.setResponseSize(500);
+      pdbRequest.setFieldToSearchBy("(text:");
+      pdbRequest.setWantedFields(wantedFields);
+      pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+      pdbRequest.setAssociatedSequence(seq);
+      pdbRestCleint = new PDBRestClient();
+      PDBRestResponse resultList;
+      try
+      {
+        resultList = pdbRestCleint.executeRequest(pdbRequest);
+      } catch (Exception e)
+      {
+        e.printStackTrace();
+        errors.add(e.getMessage());
+        continue;
+      }
+      lastPdbRequest = pdbRequest;
+      if (resultList.getSearchSummary() != null
+              && !resultList.getSearchSummary().isEmpty())
+      {
+        discoveredStructuresSet.addAll(resultList.getSearchSummary());
+        updateSequencePDBEntries(seq, resultList.getSearchSummary());
+      }
     }
 
+    int noOfStructuresFound = 0;
+    String totalTime = (System.currentTimeMillis() - startTime)
+            + " milli secs";
+    if (discoveredStructuresSet != null
+            && !discoveredStructuresSet.isEmpty())
+    {
+      tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest,
+              discoveredStructuresSet));
+      structuresDiscovered = true;
+      noOfStructuresFound = discoveredStructuresSet.size();
+      mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
+              + " Found (" + totalTime + ")");
+    }
+    else
+    {
+      mainFrame
+.setTitle("Structure Chooser - Manual association");
+      if (errors.size() > 0)
+      {
+        StringBuilder errorMsg = new StringBuilder();
+        // "Operation was unsuccessful due to the following: \n");
+        for (String error : errors)
+        {
+          errorMsg.append(error).append("\n");
+        }
+        JOptionPane.showMessageDialog(this, errorMsg.toString(),
+                "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+      }
+    }
   }
 
-  public void discoverPDB_actionPerformed()
+  public void loadLocalCachedPDBEntries()
   {
-
-    final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
-    { sequence }
-            : ap.av.getSequenceSelection());
-    Thread discpdb = new Thread(new Runnable()
+    DefaultTableModel tableModel = new DefaultTableModel()
     {
       @Override
-      public void run()
+      public boolean isCellEditable(int row, int column)
       {
+        return false;
+      }
+    };
+    tableModel.addColumn("Ref Sequence");
+    tableModel.addColumn("PDB Id");
+    tableModel.addColumn("Chain");
+    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())
+        {
 
-        new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
-                .fetchDBRefs(false);
+          String chain = pdbEntry.getChainCode() == null ? "_" : pdbEntry
+                  .getChainCode();
+          Object[] pdbEntryRowData = new Object[]
+          { seq, pdbEntry.getId(),
+ chain,
+              pdbEntry.getType(),
+              pdbEntry.getFile() };
+          if (pdbEntry.getFile() != null)
+          {
+            tableModel.addRow(pdbEntryRowData);
+          }
+          cachedEntryMap.put(pdbEntry.getId().toLowerCase(),
+                  pdbEntry);
+        }
       }
+    }
+    tbl_local_pdb.setModel(tableModel);
+  }
 
-    });
-    discpdb.start();
+  /**
+   * Update the PDBEntry 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 updateSequencePDBEntries(SequenceI seq,
+          Collection<PDBResponseSummary> responseSummaries)
+  {
+    for (PDBResponseSummary response : responseSummaries)
+    {
+      String pdbIdStr = response.getPdbId();
+      PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
+      if (pdbEntry == null)
+      {
+        pdbEntry = new PDBEntry();
+        pdbEntry.setId(pdbIdStr);
+        pdbEntry.setType(PDBEntry.Type.PDB);
+      }
+      seq.getDatasetSequence().addPDBId(pdbEntry);
+    }
+  }
+
+  /**
+   * 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)
+  {
+    HashSet<String> seqRefs = new LinkedHashSet<String>();
+    String seqName = seq.getName();
+    String[] names = seqName.toLowerCase().split("\\|");
+    for (String name : names)
+    {
+      // System.out.println("Found name : " + name);
+      name.trim();
+      if (isValidSeqName(name))
+      {
+        seqRefs.add(name);
+      }
+    }
+
+    if (seq.getPDBId() != null)
+    {
+      for (PDBEntry entry : seq.getPDBId())
+      {
+        if (isValidSeqName(entry.getId()))
+        {
+          seqRefs.add(entry.getId());
+        }
+      }
+    }
+
+    if (seq.getDBRef() != null && seq.getDBRef().length != 0)
+    {
+      int count = 0;
+      for (DBRefEntry dbRef : seq.getDBRef())
+      {
+        if (isValidSeqName(getDBRefId(dbRef)))
+        {
+          seqRefs.add(getDBRefId(dbRef));
+        }
+        ++count;
+        if (count > 10)
+        {
+          break;
+        }
+      }
+    }
+
+    StringBuilder queryBuilder = new StringBuilder();
+    for (String seqRef : seqRefs)
+    {
+      queryBuilder.append("text:").append(seqRef).append(" OR ");
+    }
+    int endIndex = queryBuilder.lastIndexOf(" OR ");
+    String query = queryBuilder.toString().substring(5, endIndex);
+    return query;
   }
 
-  // rpdbview.addActionListener(new ActionListener()
-  // {
-  //
-  // @Override
-  // public void actionPerformed(ActionEvent e)
-  // {
-  // new StructureViewer(ap.getStructureSelectionManager())
-  // .viewStructures(ap, pr, ap.av.collateForPDB(pr));
-  // }
-  // });
-
-  public void enterPDB_actionPerformed()
+  /**
+   * Ensures sequence ref names are not less than 3 characters and does not
+   * contain a database name
+   * 
+   * @param seqName
+   * @return
+   */
+  public static boolean isValidSeqName(String seqName)
   {
-    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)
+    // System.out.println("seqName : " + seqName);
+    String ignoreList = "pdb,uniprot,swiss-prot";
+    if (seqName.length() < 3)
+    {
+      return false;
+    }
+    if (seqName.contains(":"))
     {
-      PDBEntry entry = new PDBEntry();
-      entry.setId(id.toUpperCase());
-      sequence.getDatasetSequence().addPDBId(entry);
+      return false;
     }
+    seqName = seqName.toLowerCase();
+    for (String ignoredEntry : ignoreList.split(","))
+    {
+      if (seqName.contains(ignoredEntry))
+      {
+        return false;
+      }
+    }
+    return true;
+  }
+
+  public static String getDBRefId(DBRefEntry dbRef)
+  {
+    String ref = dbRef.getAccessionId().replaceAll("GO:", "");
+    return ref;
   }
 
-  public static void main(String[] args)
+  /**
+   * Filters a given list of discovered structures based on supplied argument
+   * 
+   * @param fieldToFilterBy
+   *          the field to filter by
+   */
+  public void filterResultSet(final String fieldToFilterBy)
   {
-    SwingUtilities.invokeLater(new Runnable()
+    Thread filterThread = new Thread(new Runnable()
     {
+      @Override
       public void run()
       {
-        new StructureChooser(null, null);
+        long startTime = System.currentTimeMillis();
+        lbl_loading.setVisible(true);
+        Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+                .getStructureSummaryFields();
+        Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
+        HashSet<String> errors = new HashSet<String>();
+        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);
+          pdbRestCleint = new PDBRestClient();
+          PDBRestResponse resultList;
+          try
+          {
+            resultList = pdbRestCleint.executeRequest(pdbRequest);
+          } catch (Exception e)
+          {
+            e.printStackTrace();
+            errors.add(e.getMessage());
+            continue;
+          }
+          lastPdbRequest = pdbRequest;
+          if (resultList.getSearchSummary() != null
+                  && !resultList.getSearchSummary().isEmpty())
+          {
+            filteredResponse.addAll(resultList.getSearchSummary());
+          }
+        }
+
+        String totalTime = (System.currentTimeMillis() - startTime)
+                + " milli secs";
+        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);
+
+          mainFrame.setTitle("Structure Chooser - Filter time ("
+                  + totalTime + ")");
+        }
+        else
+        {
+          mainFrame.setTitle("Structure Chooser - Filter time ("
+                  + totalTime + ")");
+          if (errors.size() > 0)
+          {
+            StringBuilder errorMsg = new StringBuilder();
+            for (String error : errors)
+            {
+              errorMsg.append(error).append("\n");
+            }
+            JOptionPane.showMessageDialog(null, errorMsg.toString(),
+                    "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+          }
+        }
+
+        lbl_loading.setVisible(false);
+
+        validateSelections();
       }
     });
+    filterThread.start();
+  }
+
+
+  /**
+   * Handles action event for btn_pdbFromFile
+   */
+  public void pdbFromFile_actionPerformed()
+  {
+    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();
+    }
   }
 
-  @SuppressWarnings("unchecked")
-  protected void populateFilterOptions()
+  /**
+   * Populates the filter combo-box options dynamically depending on discovered
+   * structures
+   */
+  protected void populateFilterComboBox()
   {
-    filterOptions.addItem(new FilterOptions("- Filter Criteria -", "",
-            VIEWS_AUTO));
-    filterOptions.addItem(new FilterOptions("All", "all", VIEWS_AUTO));
-    filterOptions
-            .addItem(new FilterOptions("Best Coverage", "", VIEWS_AUTO));
-    filterOptions.addItem(new FilterOptions("Best Resolution", "",
-            VIEWS_AUTO));
-    filterOptions
-            .addItem(new FilterOptions("Best Quality", "", VIEWS_AUTO));
-    filterOptions.addItem(new FilterOptions("Enter PDB Id", "", VIEWS_ID));
-    filterOptions.addItem(new FilterOptions("From File", "", VIEWS_FILE));
+    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()
   {
-    String currentView = ((FilterOptions) filterOptions.getSelectedItem())
-            .getView();
-    switchableViewsLayout.show(switchableViewsPanel, currentView);
+    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)
+    {
+      mainFrame.setTitle(filterTitle);
+      idInputAssSeqPanel.loadCmbAssSeq();
+      fileChooserAssSeqPanel.loadCmbAssSeq();
+    }
+    validateSelections();
   }
 
-  private void fetchStructures()
+  /**
+   * Validates user selection and activates the view button if all parameters
+   * are correct
+   */
+  public void validateSelections()
   {
-    long startTime = System.currentTimeMillis();
-    final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
-    { sequence }
-            : ap.av.getSequenceSelection());
-    int foundStructures = 0;
-    PDBSearchRequest request = new PDBSearchRequest();
-    request.setAllowEmptySeq(false);
-    request.setResponseSize(500);
-    request.setSearchTarget("(text:");
-    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);
-    request.setWantedFields(wantedFields);
-    
-    Collection<PDBSummaryListModel> searchSummaries = new HashSet<PDBSummaryListModel>();
-    // searchSummaries.
-    for (SequenceI seq : sequences)
-    {
-      // System.out.println("Selected : " + seq.getName());
-      request.setSearchTerm(buildQuery(seq) + ")");
-
-      PDBRestClient pdbRestCleint = new PDBRestClient();
-
-      PDBSearchResponse resultList = pdbRestCleint
-              .executeRequest(request);
-      if (resultList.getSearchSummary() != null
-              && !resultList.getSearchSummary().isEmpty())
+    FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+            .getSelectedItem());
+    btn_view.setEnabled(false);
+    String currentView = selectedFilterOpt.getView();
+    if (currentView == VIEWS_FILTER)
+    {
+      if (tbl_summary.getSelectedRows().length > 0)
       {
-        searchSummaries.addAll(resultList.getSearchSummary());
+        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)
+    {
+      validateAssociationEnterPdb();
+    }
+    else if (currentView == VIEWS_FROM_FILE)
+    {
+      validateAssociationFromFile();
+    }
+  }
 
-    foundStructures = searchSummaries.size();
-    if (searchSummaries != null)
+  /**
+   * Validates inputs from the Manual PDB entry panel
+   */
+  public void validateAssociationEnterPdb()
+  {
+    AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
+            .getCmb_assSeq().getSelectedItem();
+    lbl_pdbManualFetchStatus.setIcon(errorImage);
+    lbl_pdbManualFetchStatus.setToolTipText("");
+    if (txt_search.getText().length() > 0)
     {
-      jListFoundStructures.setModel(PDBSearchResponse
-              .getListModel(searchSummaries));
+      lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
+              true, "No PDB entry found for \'" + txt_search.getText()
+                      + "\'"));
     }
 
-    String totalTime = (System.currentTimeMillis() - startTime)
-            + " milli secs";
-    mainFrame.setTitle("Structure Chooser - " + foundStructures
-            + " Found (" + totalTime + ")");
+    if (errorWarning.length() > 0)
+    {
+      lbl_pdbManualFetchStatus.setIcon(warningImage);
+      lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
+              true, errorWarning.toString()));
+    }
+
+    if (selectedSequences.length == 1
+            || !assSeqOpt.getName().equalsIgnoreCase(
+                    "-Select Associated Seq-"))
+    {
+      txt_search.setEnabled(true);
+      if (isValidPBDEntry)
+      {
+        btn_view.setEnabled(true);
+        lbl_pdbManualFetchStatus.setToolTipText("");
+        lbl_pdbManualFetchStatus.setIcon(goodImage);
+      }
+    }
+    else
+    {
+      txt_search.setEnabled(false);
+      lbl_pdbManualFetchStatus.setIcon(errorImage);
+    }
   }
 
-  private String buildQuery(SequenceI seq)
+  /**
+   * Validates inputs for the manual PDB file selection options
+   */
+  public void validateAssociationFromFile()
   {
-    String query = seq.getName();
-    StringBuilder queryBuilder = new StringBuilder();
-    int count = 0;
-    if (seq.getDBRef() != null && seq.getDBRef().length != 0)
+    AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
+            .getCmb_assSeq().getSelectedItem();
+    lbl_fromFileStatus.setIcon(errorImage);
+    if (selectedSequences.length == 1
+            || (assSeqOpt != null
+            && !assSeqOpt.getName().equalsIgnoreCase(
+                    "-Select Associated Seq-")))
     {
-      for (DBRefEntry dbRef : seq.getDBRef())
+      btn_pdbFromFile.setEnabled(true);
+      if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
       {
-        System.out.println("dbref : " + dbRef.getAccessionId());
-        queryBuilder.append("text:").append(dbRef.getAccessionId())
-                .append(" OR ");
-        ++count;
-        if (count > 10)
-        {
-          break;
-        }
+        btn_view.setEnabled(true);
+        lbl_fromFileStatus.setIcon(goodImage);
       }
-      // int beginIndex = queryBuilder. firstIndexOf("text");
-      int endIndex = queryBuilder.lastIndexOf(" OR ");
-      query = queryBuilder.toString().substring(5, endIndex);
     }
-    System.out.println("------------> " + query);
-    return query;
+    else
+    {
+      btn_pdbFromFile.setEnabled(false);
+      lbl_fromFileStatus.setIcon(errorImage);
+    }
   }
 
-  public class FilterOptions
+  @Override
+  public void cmbAssSeqStateChanged()
   {
-    private String name;
+    validateSelections();
+  }
 
-    private String value;
+  /**
+   * 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();
+      }
+    }
 
-    private String view;
+  }
 
-    public FilterOptions(String name, String value, String view)
+  /**
+   * 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)
     {
-      this.name = name;
-      this.value = value;
-      this.view = view;
+      int pdbIdColIndex = tbl_summary.getColumn(
+              PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex();
+      int refSeqColIndex = tbl_summary.getColumn("Ref Sequence")
+              .getModelIndex();
+      int[] selectedRows = tbl_summary.getSelectedRows();
+      PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+      int count = 0;
+      ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+      for (int summaryRow : selectedRows)
+      {
+        String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdColIndex)
+                .toString();
+        SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(
+                summaryRow, refSeqColIndex);
+        selectedSeqsToView.add(selectedSeq);
+        PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
+        if (pdbEntry == null)
+        {
+          pdbEntry = new PDBEntry();
+          pdbEntry.setId(pdbIdStr);
+          pdbEntry.setType(PDBEntry.Type.PDB);
+        }
+        pdbEntriesToView[count++] = pdbEntry;
+      }
+      SequenceI[] selectedSeqs = selectedSeqsToView
+              .toArray(new SequenceI[selectedSeqsToView.size()]);
+      launchStructureViewer(ap.getStructureSelectionManager(),
+              pdbEntriesToView, ap, selectedSeqs);
     }
+    else if(currentView == VIEWS_LOCAL_PDB){
+      int[] selectedRows = tbl_local_pdb.getSelectedRows();
+      PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+      int count = 0;
+      int pdbIdColIndex = tbl_local_pdb.getColumn(
+              PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex();
+      int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
+              .getModelIndex();
+      ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+      for (int row : selectedRows)
+      {
+        String entryKey = tbl_local_pdb.getValueAt(row, pdbIdColIndex)
+                .toString()
+                .toLowerCase();
+        pdbEntriesToView[count++] = cachedEntryMap.get(entryKey);
+        SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row,
+                refSeqColIndex);
+        selectedSeqsToView.add(selectedSeq);
 
-    public String getName()
-    {
-      return name;
+      }
+      SequenceI[] selectedSeqs = selectedSeqsToView
+              .toArray(new SequenceI[selectedSeqsToView.size()]);
+      launchStructureViewer(ap.getStructureSelectionManager(),
+              pdbEntriesToView, ap, selectedSeqs);
     }
+    else if (currentView == VIEWS_ENTER_ID)
+    {
+      SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
+              .getCmb_assSeq().getSelectedItem()).getSequence();
+      if (userSelectedSeq != null)
+      {
+        selectedSequence = userSelectedSeq;
+      }
+
+      String pdbIdStr = txt_search.getText();
+      PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
+      if (pdbEntry == null)
+      {
+        pdbEntry = new PDBEntry();
+        pdbEntry.setId(txt_search.getText());
+        pdbEntry.setType(PDBEntry.Type.PDB);
+      }
 
-    public void setName(String name)
+      selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
+      PDBEntry[] pdbEntriesToView = new PDBEntry[]
+      { pdbEntry };
+      launchStructureViewer(ap.getStructureSelectionManager(),
+              pdbEntriesToView, ap, new SequenceI[]
+              { selectedSequence });
+    }
+    else if (currentView == VIEWS_FROM_FILE)
     {
-      this.name = name;
+      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 });
     }
+    mainFrame.dispose();
+  }
 
-    public String getValue()
+  private void launchStructureViewer(StructureSelectionManager ssm,
+          PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel,
+          SequenceI[] sequences)
+  {
+    StructureViewer sViewer = new StructureViewer(ssm);
+    if (pdbEntriesToView.length > 1)
     {
-      return value;
+      ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
+      for (SequenceI seq : sequences)
+      {
+        seqsMap.add(new SequenceI[]
+        { seq });
+      }
+      SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
+      sViewer.viewStructures(pdbEntriesToView, collatedSeqs,
+              alignPanel);
+      // sViewer.viewStructures(pdbEntriesToView,
+      // alignPanel.av.collateForPDB(pdbEntriesToView),
+      // alignPanel);
     }
-
-    public void setValue(String value)
+    else
     {
-      this.value = value;
+      sViewer.viewStructures(pdbEntriesToView[0], sequences,
+              alignPanel);
     }
+  }
 
-    public String getView()
+  /**
+   * 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)
     {
-      return view;
+      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 setView(String view)
+  public void setStructuresDiscovered(boolean structuresDiscovered)
+  {
+    this.structuresDiscovered = structuresDiscovered;
+  }
+
+  public Collection<PDBResponseSummary> getDiscoveredStructuresSet()
+  {
+    return discoveredStructuresSet;
+  }
+
+  @Override
+  protected void txt_search_ActionPerformed()
+  {
+    errorWarning.setLength(0);
+    isValidPBDEntry = false;
+    if (txt_search.getText().length() > 0)
     {
-      this.view = view;
+      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);
+      pdbRestCleint = new PDBRestClient();
+      PDBRestResponse resultList;
+      try
+      {
+        resultList = pdbRestCleint.executeRequest(pdbRequest);
+      } catch (Exception e)
+      {
+        errorWarning.append(e.getMessage());
+        return;
+      } finally
+      {
+        validateSelections();
+      }
+      if (resultList.getSearchSummary() != null
+              && resultList.getSearchSummary().size() > 0)
+      {
+        isValidPBDEntry = true;
+      }
     }
+    validateSelections();
+  }
 
-    public String toString()
+  @Override
+  public void tabRefresh()
+  {
+    if (selectedSequences != null)
     {
-      return this.name;
+      Thread refreshThread = new Thread(new Runnable()
+      {
+        @Override
+        public void run()
+        {
+          fetchStructuresMetaData();
+          filterResultSet(((FilterOption) cmb_filterOption
+                  .getSelectedItem()).getValue());
+        }
+      });
+      refreshThread.start();
     }
   }
+
 }