X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=266690eecee2ef9d49e5d5f92e3fc8d2fa0e40f4;hb=06e3a52df5af8243cdb67c023c8ddd834711ad36;hp=f28ef68fbe84a9edf53015b80d0d4da36c4a6061;hpb=fd235cc7542d6e308e054a8a76580a6c511ae631;p=jalview.git

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index f28ef68..266690e 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -1,4 +1,5 @@
 /*
+
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
@@ -26,6 +27,7 @@ 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;
@@ -37,12 +39,14 @@ import java.awt.event.ItemEvent;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
+import java.util.LinkedHashSet;
 import java.util.List;
-import java.util.Vector;
 
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
-import javax.swing.ListSelectionModel;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.table.AbstractTableModel;
 
 /**
  * Provides the behaviors for the Structure chooser Panel
@@ -61,9 +65,9 @@ public class StructureChooser extends GStructureChooser
 
   private IProgressIndicator progressIndicator;
 
-  private Collection<PDBResponseSummary> discoveredStructuresSet = new HashSet<PDBResponseSummary>();
+  private Collection<PDBResponseSummary> discoveredStructuresSet;
 
-  private PDBRestRequest pdbRequest;
+  private PDBRestRequest lastPdbRequest;
 
   private PDBRestClient pdbRestCleint;
 
@@ -71,6 +75,7 @@ public class StructureChooser extends GStructureChooser
 
   private boolean isValidPBDEntry;
 
+
   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
           AlignmentPanel ap)
   {
@@ -92,8 +97,13 @@ public class StructureChooser extends GStructureChooser
       public void run()
       {
         long startTime = System.currentTimeMillis();
-        String msg = MessageManager.getString("status.fetching_db_refs");
-        updateProgressIndicator(msg, startTime);
+        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);
@@ -130,61 +140,88 @@ public class StructureChooser extends GStructureChooser
     Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
             .getStructureSummaryFields();
 
-    pdbRequest = new PDBRestRequest();
-    pdbRequest.setAllowEmptySeq(false);
-    pdbRequest.setResponseSize(500);
-    pdbRequest.setFieldToSearchBy("(text:");
-    pdbRequest.setWantedFields(wantedFields);
+    discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+    HashSet<String> errors = new HashSet<String>();
     for (SequenceI seq : selectedSequences)
     {
+      PDBRestRequest pdbRequest = new PDBRestRequest();
+      pdbRequest.setAllowEmptySeq(false);
+      pdbRequest.setResponseSize(500);
+      pdbRequest.setFieldToSearchBy("(text:");
+      pdbRequest.setWantedFields(wantedFields);
       pdbRequest.setSearchTerm(buildQuery(seq) + ")");
-      pdbRequest.setAssociatedSequence(seq.getName());
+      pdbRequest.setAssociatedSequence(seq);
       pdbRestCleint = new PDBRestClient();
-      PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+      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());
-        updateSequenceDbRef(seq, resultList.getSearchSummary());
       }
     }
 
     int noOfStructuresFound = 0;
+    String totalTime = (System.currentTimeMillis() - startTime)
+            + " milli secs";
     if (discoveredStructuresSet != null
             && !discoveredStructuresSet.isEmpty())
     {
-      tbl_summary.setModel(PDBRestResponse.getTableModel(pdbRequest,
+      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();
+        for (String error : errors)
+        {
+          errorMsg.append(error).append("\n");
+        }
+        JOptionPane.showMessageDialog(this, errorMsg.toString(),
+                "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+      }
     }
-    String totalTime = (System.currentTimeMillis() - startTime)
-            + " milli secs";
-    mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
-            + " Found (" + totalTime + ")");
   }
 
-  /**
-   * 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)
+  public void loadLocalCachedPDBEntries()
   {
-    for (PDBResponseSummary response : responseSummaries)
+    ArrayList<CachedPDB> entries = new ArrayList<CachedPDB>();
+    for (SequenceI seq : selectedSequences)
     {
-      PDBEntry newEntry = new PDBEntry();
-      newEntry.setId(response.getPdbId());
-      newEntry.setType("PDB");
-      seq.getDatasetSequence().addPDBId(newEntry);
+      if (seq.getDatasetSequence() != null
+              && seq.getDatasetSequence().getAllPDBEntries() != null)
+      {
+        for (PDBEntry pdbEntry : seq.getDatasetSequence().getAllPDBEntries())
+        {
+          if (pdbEntry.getFile() != null)
+          {
+            entries.add(new CachedPDB(seq, pdbEntry));
+          }
+        }
+      }
     }
+
+    PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
+    tbl_local_pdb.setModel(tableModelx);
   }
 
+
   /**
    * Builds a query string for a given sequences using its DBRef entries
    * 
@@ -192,41 +229,97 @@ public class StructureChooser extends GStructureChooser
    *          the sequences to build a query for
    * @return the built query string
    */
-  @SuppressWarnings("unchecked")
+
   public static String buildQuery(SequenceI seq)
   {
-    String query = seq.getName();
-    StringBuilder queryBuilder = new StringBuilder();
-    int count = 0;
+    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)
+    if (seq.getAllPDBEntries() != null)
     {
-      for (PDBEntry entry : (Vector<PDBEntry>) seq.getPDBId())
+      for (PDBEntry entry : seq.getAllPDBEntries())
       {
-        queryBuilder.append("text:").append(entry.getId()).append(" OR ");
+        if (isValidSeqName(entry.getId()))
+        {
+          seqRefs.add(entry.getId());
+        }
       }
     }
 
     if (seq.getDBRef() != null && seq.getDBRef().length != 0)
     {
+      int count = 0;
       for (DBRefEntry dbRef : seq.getDBRef())
       {
-        queryBuilder.append("text:")
-                .append(dbRef.getAccessionId().replaceAll("GO:", ""))
-                .append(" OR ");
+        if (isValidSeqName(getDBRefId(dbRef)))
+        {
+          seqRefs.add(getDBRefId(dbRef));
+        }
         ++count;
         if (count > 10)
         {
           break;
         }
       }
-      int endIndex = queryBuilder.lastIndexOf(" OR ");
-      query = queryBuilder.toString().substring(5, endIndex);
     }
+
+    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;
   }
 
   /**
+   * 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)
+  {
+    // System.out.println("seqName : " + seqName);
+    String ignoreList = "pdb,uniprot,swiss-prot";
+    if (seqName.length() < 3)
+    {
+      return false;
+    }
+    if (seqName.contains(":"))
+    {
+      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;
+  }
+
+  /**
    * Filters a given list of discovered structures based on supplied argument
    * 
    * @param fieldToFilterBy
@@ -240,64 +333,75 @@ public class StructureChooser extends GStructureChooser
       public void run()
       {
         long startTime = System.currentTimeMillis();
-        try
+        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)
         {
-          lbl_loading.setVisible(true);
+          PDBRestRequest pdbRequest = new PDBRestRequest();
+          pdbRequest.setAllowEmptySeq(false);
           pdbRequest.setResponseSize(1);
           pdbRequest.setFieldToSearchBy("(text:");
           pdbRequest.setFieldToSortBy(fieldToFilterBy,
                   !chk_invertFilter.isSelected());
-
-          Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
-          for (SequenceI seq : selectedSequences)
+          pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+          pdbRequest.setWantedFields(wantedFields);
+          pdbRequest.setAssociatedSequence(seq);
+          pdbRestCleint = new PDBRestClient();
+          PDBRestResponse resultList;
+          try
           {
-            pdbRequest.setSearchTerm(buildQuery(seq) + ")");
-            pdbRequest.setAssociatedSequence(seq.getName());
-            pdbRestCleint = new PDBRestClient();
-            PDBRestResponse resultList = pdbRestCleint
-                    .executeRequest(pdbRequest);
-            if (resultList.getSearchSummary() != null
-                    && !resultList.getSearchSummary().isEmpty())
-            {
-              filteredResponse.addAll(resultList.getSearchSummary());
-            }
+            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());
           }
+        }
 
-          if (filteredResponse != null)
+        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)
           {
-            int filterResponseCount = filteredResponse.size();
-            List<PDBResponseSummary> originalDiscoveredStructuresList = new ArrayList<PDBResponseSummary>(
-                    discoveredStructuresSet);
-            originalDiscoveredStructuresList.removeAll(filteredResponse);
-            Collection<PDBResponseSummary> reorderedStructuresSet = new ArrayList<PDBResponseSummary>();
-            reorderedStructuresSet.addAll(filteredResponse);
-            reorderedStructuresSet.addAll(originalDiscoveredStructuresList);
-
-            tbl_summary.setModel(PDBRestResponse.getTableModel(pdbRequest,
-                    reorderedStructuresSet));
-
-            ListSelectionModel model = tbl_summary.getSelectionModel();
-            model.clearSelection();
-            for (int x = 0; x < filterResponseCount; x++)
+            StringBuilder errorMsg = new StringBuilder();
+            for (String error : errors)
             {
-              model.addSelectionInterval(x, x);
+              errorMsg.append(error).append("\n");
             }
-
-            // Discard unwanted objects to make them eligible for garbage
-            // collection
-            originalDiscoveredStructuresList = null;
-            reorderedStructuresSet = null;
+            JOptionPane.showMessageDialog(null, errorMsg.toString(),
+                    "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
           }
-
-          lbl_loading.setVisible(false);
-        } catch (Exception e)
-        {
-          e.printStackTrace();
         }
-        String totalTime = (System.currentTimeMillis() - startTime)
-                + " milli secs";
-        mainFrame.setTitle("Structure Chooser - Filter time (" + totalTime
-                + ")");
+
+        lbl_loading.setVisible(false);
 
         validateSelections();
       }
@@ -305,8 +409,6 @@ public class StructureChooser extends GStructureChooser
     filterThread.start();
   }
 
-
-
   /**
    * Handles action event for btn_pdbFromFile
    */
@@ -356,6 +458,8 @@ public class StructureChooser extends GStructureChooser
             VIEWS_ENTER_ID));
     cmb_filterOption.addItem(new FilterOption("From File", "-",
             VIEWS_FROM_FILE));
+    cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-",
+            VIEWS_LOCAL_PDB));
   }
 
   /**
@@ -376,8 +480,10 @@ public class StructureChooser extends GStructureChooser
       chk_invertFilter.setVisible(true);
       filterResultSet(selectedFilterOpt.getValue());
     }
-    else
+    else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
+            || selectedFilterOpt.getView() == VIEWS_FROM_FILE)
     {
+      mainFrame.setTitle(filterTitle);
       idInputAssSeqPanel.loadCmbAssSeq();
       fileChooserAssSeqPanel.loadCmbAssSeq();
     }
@@ -401,6 +507,13 @@ public class StructureChooser extends GStructureChooser
         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();
@@ -409,7 +522,6 @@ public class StructureChooser extends GStructureChooser
     {
       validateAssociationFromFile();
     }
-
   }
 
   /**
@@ -420,6 +532,21 @@ public class StructureChooser extends GStructureChooser
     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
             .getCmb_assSeq().getSelectedItem();
     lbl_pdbManualFetchStatus.setIcon(errorImage);
+    lbl_pdbManualFetchStatus.setToolTipText("");
+    if (txt_search.getText().length() > 0)
+    {
+      lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
+              true, "No PDB entry found for \'" + txt_search.getText()
+                      + "\'"));
+    }
+
+    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-"))
@@ -428,6 +555,7 @@ public class StructureChooser extends GStructureChooser
       if (isValidPBDEntry)
       {
         btn_view.setEnabled(true);
+        lbl_pdbManualFetchStatus.setToolTipText("");
         lbl_pdbManualFetchStatus.setIcon(goodImage);
       }
     }
@@ -447,8 +575,7 @@ public class StructureChooser extends GStructureChooser
             .getCmb_assSeq().getSelectedItem();
     lbl_fromFileStatus.setIcon(errorImage);
     if (selectedSequences.length == 1
-            || (assSeqOpt != null
-            && !assSeqOpt.getName().equalsIgnoreCase(
+            || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase(
                     "-Select Associated Seq-")))
     {
       btn_pdbFromFile.setEnabled(true);
@@ -503,60 +630,145 @@ public class StructureChooser extends GStructureChooser
     String currentView = selectedFilterOpt.getView();
     if (currentView == VIEWS_FILTER)
     {
-      int pdbIdCol = PDBRestClient.getPDBIdColumIndex(
-              pdbRequest.getWantedFields(), true);
+      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;
-      for (int summaryRow : selectedRows)
+      ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+      for (int row : selectedRows)
       {
-        String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
+        String pdbIdStr = tbl_summary.getValueAt(row, pdbIdColIndex)
                 .toString();
-        PDBEntry pdbEntry = new PDBEntry();
-        pdbEntry.setId(pdbIdStr);
-        pdbEntry.setType("PDB");
+        SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row,
+                refSeqColIndex);
+        selectedSeqsToView.add(selectedSeq);
+        PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
+        if (pdbEntry == null)
+        {
+          pdbEntry = new PDBEntry();
+          pdbEntry.setId(pdbIdStr);
+          pdbEntry.setType(PDBEntry.Type.PDB);
+          selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
+        }
+        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)
+      {
+        PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
+                pdbIdColIndex);
         pdbEntriesToView[count++] = pdbEntry;
+        SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row,
+                refSeqColIndex);
+        selectedSeqsToView.add(selectedSeq);
       }
-      new StructureViewer(ap.getStructureSelectionManager())
-              .viewStructures(ap, pdbEntriesToView,
-                      ap.av.collateForPDB(pdbEntriesToView));
+      SequenceI[] selectedSeqs = selectedSeqsToView
+              .toArray(new SequenceI[selectedSeqsToView.size()]);
+      launchStructureViewer(ap.getStructureSelectionManager(),
+              pdbEntriesToView, ap, selectedSeqs);
     }
     else if (currentView == VIEWS_ENTER_ID)
     {
-      selectedSequence = ((AssociateSeqOptions) idInputAssSeqPanel
+      SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
               .getCmb_assSeq().getSelectedItem()).getSequence();
-      PDBEntry pdbEntry = new PDBEntry();
-      pdbEntry.setId(txt_search.getText());
-      pdbEntry.setType("PDB");
-      selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
+      if (userSelectedSeq != null)
+      {
+        selectedSequence = userSelectedSeq;
+      }
+
+      String pdbIdStr = txt_search.getText();
+      PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
+      if (pdbEntry == null)
+      {
+        pdbEntry = new PDBEntry();
+        pdbEntry.setId(pdbIdStr);
+        pdbEntry.setType(PDBEntry.Type.PDB);
+        selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
+      }
+
       PDBEntry[] pdbEntriesToView = new PDBEntry[]
       { pdbEntry };
-      new StructureViewer(ap.getStructureSelectionManager())
-              .viewStructures(ap, pdbEntriesToView,
-                      ap.av.collateForPDB(pdbEntriesToView));
+      launchStructureViewer(ap.getStructureSelectionManager(),
+              pdbEntriesToView, ap, new SequenceI[]
+              { selectedSequence });
     }
     else if (currentView == VIEWS_FROM_FILE)
     {
-      selectedSequence = ((AssociateSeqOptions) fileChooserAssSeqPanel
+      SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
               .getCmb_assSeq().getSelectedItem()).getSequence();
-      new AssociatePdbFileWithSeq().associatePdbWithSeq(
-              selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
-              selectedSequence, true, Desktop.instance);
+      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();
   }
 
+  private void launchStructureViewer(final StructureSelectionManager ssm,
+          final PDBEntry[] pdbEntriesToView,
+          final AlignmentPanel alignPanel, final SequenceI[] sequences)
+  {
+    final StructureViewer sViewer = new StructureViewer(ssm);
+    new Thread(new Runnable()
+    {
+      public void run()
+      {
+        if (pdbEntriesToView.length > 1)
+        {
+          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);
+        }
+        else
+        {
+          sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
+        }
+      }
+    }).start();
+  }
+
   /**
    * 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)
+          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)
     {
       for (SequenceI seq : selectedSequences)
@@ -566,6 +778,10 @@ public class StructureChooser extends GStructureChooser
     }
     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);
     }
   }
@@ -588,20 +804,32 @@ public class StructureChooser extends GStructureChooser
   @Override
   protected void txt_search_ActionPerformed()
   {
+    errorWarning.setLength(0);
     isValidPBDEntry = false;
     if (txt_search.getText().length() > 0)
     {
       List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
       wantedFields.add(PDBDocField.PDB_ID);
-      pdbRequest = new PDBRestRequest();
+      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());
+      pdbRequest.setAssociatedSequence(selectedSequence);
       pdbRestCleint = new PDBRestClient();
-      PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+      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)
       {
@@ -611,4 +839,122 @@ public class StructureChooser extends GStructureChooser
     validateSelections();
   }
 
+  @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();
+    }
+  }
+
+  public class PDBEntryTableModel extends AbstractTableModel
+  {
+    String[] columns =
+    { "Ref Sequence", "PDB Id", "Chain", "Type", "File" };
+
+    private List<CachedPDB> pdbEntries;
+
+    public PDBEntryTableModel(List<CachedPDB> pdbEntries)
+    {
+      this.pdbEntries = new ArrayList<CachedPDB>(pdbEntries);
+    }
+
+    @Override
+    public String getColumnName(int columnIndex)
+    {
+      return columns[columnIndex];
+    }
+
+    @Override
+    public int getRowCount()
+    {
+      return pdbEntries.size();
+    }
+
+    @Override
+    public int getColumnCount()
+    {
+      return columns.length;
+    }
+
+    @Override
+    public boolean isCellEditable(int row, int column)
+    {
+      return false;
+    }
+
+    @Override
+    public Object getValueAt(int rowIndex, int columnIndex)
+    {
+      Object value = "??";
+      CachedPDB entry = pdbEntries.get(rowIndex);
+      switch (columnIndex)
+      {
+      case 0:
+        value = entry.getSequence();
+        break;
+      case 1:
+        value = entry.getPdbEntry();
+        break;
+      case 2:
+        value = entry.getPdbEntry().getChainCode() == null ? "_" : entry
+                .getPdbEntry().getChainCode();
+        break;
+      case 3:
+        value = entry.getPdbEntry().getType();
+        break;
+      case 4:
+        value = entry.getPdbEntry().getFile();
+        break;
+      }
+      return value;
+    }
+
+    @Override
+    public Class<?> getColumnClass(int columnIndex)
+    {
+      return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
+    }
+
+    public CachedPDB getPDBEntryAt(int row)
+    {
+      return pdbEntries.get(row);
+    }
+
+  }
+
+  private class CachedPDB
+  {
+    private SequenceI sequence;
+
+    private PDBEntry pdbEntry;
+
+    public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
+    {
+      this.sequence = sequence;
+      this.pdbEntry = pdbEntry;
+    }
+
+    public SequenceI getSequence()
+    {
+      return sequence;
+    }
+
+    public PDBEntry getPdbEntry()
+    {
+      return pdbEntry;
+    }
+
+  }
 }