From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Fri, 7 Aug 2015 13:59:50 +0000 (+0100)
Subject: JAL-1824 updated caching procedure for pdb entries. Also refactored getPDBEntry metho... 
X-Git-Tag: Release_2_10_0~548
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=06e3a52df5af8243cdb67c023c8ddd834711ad36;p=jalview.git

JAL-1824 updated caching procedure for pdb entries. Also refactored getPDBEntry method in SequenceI to getAllPDBEntries as it returns a collection of all available PDBEntry
---

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 7b7f4b0..58991f3 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -388,11 +388,11 @@ public class PDBfile extends jalview.io.AlignFile
         {
           if (sq.getDatasetSequence() != null)
           {
-            sq.getDatasetSequence().getPDBId().clear();
+            sq.getDatasetSequence().getAllPDBEntries().clear();
           }
           else
           {
-            sq.getPDBId().clear();
+            sq.getAllPDBEntries().clear();
           }
         }
         replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
@@ -456,16 +456,16 @@ public class PDBfile extends jalview.io.AlignFile
         {
           if (sq.getDatasetSequence() != null)
           {
-            if (sq.getDatasetSequence().getPDBId() != null)
+            if (sq.getDatasetSequence().getAllPDBEntries() != null)
             {
-              sq.getDatasetSequence().getPDBId().clear();
+              sq.getDatasetSequence().getAllPDBEntries().clear();
             }
           }
           else
           {
-            if (sq.getPDBId() != null)
+            if (sq.getAllPDBEntries() != null)
             {
-              sq.getPDBId().clear();
+              sq.getAllPDBEntries().clear();
             }
           }
         }
diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 2ede9ed..c23f03c 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -60,7 +60,7 @@ public class SeqsetUtils
       }
     }
     sqinfo.put("SeqFeatures", sfeat);
-    sqinfo.put("PdbId", (seq.getPDBId() != null) ? seq.getPDBId()
+    sqinfo.put("PdbId", (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
             : new Vector<PDBEntry>());
     sqinfo.put("datasetSequence",
             (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index f16da84..0dd73ea 100644
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -896,9 +896,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   void addPDB()
   {
-    if (seq.getPDBId() != null)
+    if (seq.getAllPDBEntries() != null)
     {
-      PDBEntry entry = seq.getPDBId().firstElement();
+      PDBEntry entry = seq.getAllPDBEntries().firstElement();
 
       if (ap.av.applet.jmolAvailable)
       {
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 0225dc7..688ea53 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -3950,7 +3950,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     boolean needtoadd = false;
     if (toaddpdb != null)
     {
-      Vector pdbe = toaddpdb.getPDBId();
+      Vector pdbe = toaddpdb.getAllPDBEntries();
       PDBEntry pdbentry = null;
       if (pdbe != null && pdbe.size() > 0)
       {
diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index c1035bd..929a871 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -139,7 +139,7 @@ public class ExtJmol extends JalviewJmolBinding
     SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
     for (int s = 0; s < sq.length; s++)
     {
-      Vector<PDBEntry> pdbids = sq[s].getPDBId();
+      Vector<PDBEntry> pdbids = sq[s].getAllPDBEntries();
       if (pdbids != null)
       {
         for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index db792e2..d0cef5d 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -167,4 +167,8 @@ public class PDBEntry
     this.chainCode = chainCode;
   }
 
+  public String toString()
+  {
+    return id;
+  }
 }
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 916d785..19ad30f 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -260,9 +260,9 @@ public class Sequence extends ASequence implements SequenceI
         }
       }
     }
-    if (seq.getPDBId() != null)
+    if (seq.getAllPDBEntries() != null)
     {
-      Vector ids = seq.getPDBId();
+      Vector ids = seq.getAllPDBEntries();
       Enumeration e = ids.elements();
       while (e.hasMoreElements())
       {
@@ -410,7 +410,7 @@ public class Sequence extends ASequence implements SequenceI
    * @return DOCUMENT ME!
    */
   @Override
-  public Vector<PDBEntry> getPDBId()
+  public Vector<PDBEntry> getAllPDBEntries()
   {
     return pdbIds;
   }
@@ -1057,7 +1057,7 @@ public class Sequence extends ASequence implements SequenceI
       // move database references onto dataset sequence
       datasetSequence.setDBRef(getDBRef());
       setDBRef(null);
-      datasetSequence.setPDBId(getPDBId());
+      datasetSequence.setPDBId(getAllPDBEntries());
       setPDBId(null);
       datasetSequence.updatePDBIds();
       if (annotation != null)
@@ -1221,9 +1221,9 @@ public class Sequence extends ASequence implements SequenceI
     }
 
     // transfer PDB entries
-    if (entry.getPDBId() != null)
+    if (entry.getAllPDBEntries() != null)
     {
-      Enumeration e = entry.getPDBId().elements();
+      Enumeration e = entry.getAllPDBEntries().elements();
       while (e.hasMoreElements())
       {
         PDBEntry pdb = (PDBEntry) e.nextElement();
@@ -1307,4 +1307,23 @@ public class Sequence extends ASequence implements SequenceI
     return getDisplayId(false);
   }
 
+  @Override
+  public PDBEntry getPDBEntry(String pdbIdStr)
+  {
+    if (getDatasetSequence() == null
+            || getDatasetSequence().getAllPDBEntries() == null)
+    {
+      return null;
+    }
+    List<PDBEntry> entries = getDatasetSequence().getAllPDBEntries();
+    for (PDBEntry entry : entries)
+    {
+      if (entry.getId().equalsIgnoreCase(pdbIdStr))
+      {
+        return entry;
+      }
+    }
+    return null;
+  }
+
 }
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index f69c8b6..2ff619b 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -274,7 +274,7 @@ public interface SequenceI extends ASequenceI
    * 
    * @return DOCUMENT ME!
    */
-  public Vector<PDBEntry> getPDBId();
+  public Vector<PDBEntry> getAllPDBEntries();
 
   /**
    * add entry to the vector of PDBIds, if it isn't in the list already
@@ -420,4 +420,12 @@ public interface SequenceI extends ASequenceI
    */
   public List<int[]> getInsertions();
 
+  /**
+   * Given a pdbId String, return the equivalent PDBEntry if available in the
+   * given sequence
+   * 
+   * @param pdbId
+   * @return
+   */
+  public PDBEntry getPDBEntry(String pdbId);
 }
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 29c4fde..9ed953f 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -669,7 +669,7 @@ public class AlignViewport extends AlignmentViewport implements
       for (SequenceI sq : alignment.getSequences())
       {
         Vector<PDBEntry> pdbs = sq
-                .getDatasetSequence().getPDBId();
+                .getDatasetSequence().getAllPDBEntries();
         if (pdbs == null)
         {
           continue;
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 7876346..bd1cc88 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -628,7 +628,7 @@ public class AppJmol extends StructureViewerBase
           {
             // just transfer the file name from the first sequence's first
             // PDBEntry
-            file = new File(pdbseq.getSequenceAt(0).getPDBId()
+            file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
                     .elementAt(0).getFile()).getAbsolutePath();
             jmb.getPdbEntry(pi).setFile(file);
 
diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index f644e95..1d60d6c 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -434,7 +434,7 @@ public class ChimeraViewFrame extends StructureViewerBase
         String chain = null;
         if (seq.getDatasetSequence() != null)
         {
-          Vector<PDBEntry> pdbrefs = seq.getDatasetSequence().getPDBId();
+          Vector<PDBEntry> pdbrefs = seq.getDatasetSequence().getAllPDBEntries();
           if (pdbrefs != null && pdbrefs.size() > 0)
           {
             chain = pdbrefs.get(0).getChainCode();
@@ -950,7 +950,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     if (pdbseq != null && pdbseq.getHeight() > 0)
     {
       // just use the file name from the first sequence's first PDBEntry
-      filePath = new File(pdbseq.getSequenceAt(0).getPDBId()
+      filePath = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
               .elementAt(0).getFile()).getAbsolutePath();
       processingEntry.setFile(filePath);
     }
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 3b90bf6..23b09de 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -776,9 +776,9 @@ public class Jalview2XML
         }
       }
 
-      if (jdatasq.getPDBId() != null)
+      if (jdatasq.getAllPDBEntries() != null)
       {
-        Enumeration en = jdatasq.getPDBId().elements();
+        Enumeration en = jdatasq.getAllPDBEntries().elements();
         while (en.hasMoreElements())
         {
           Pdbids pdb = new Pdbids();
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 5699d9e..45b5394 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -561,7 +561,7 @@ public class PopupMenu extends JPopupMenu
       SequenceI sqass = null;
       for (SequenceI sq : ap.av.getSequenceSelection())
       {
-        Vector<PDBEntry> pes = sq.getDatasetSequence().getPDBId();
+        Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
         if (pes != null && pes.size() > 0)
         {
           reppdb.put(pes.get(0).getId(), pes.get(0));
diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 765c214..266690e 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -39,7 +39,6 @@ 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;
 
@@ -47,7 +46,7 @@ import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JLabel;
 import javax.swing.JOptionPane;
-import javax.swing.table.DefaultTableModel;
+import javax.swing.table.AbstractTableModel;
 
 /**
  * Provides the behaviors for the Structure chooser Panel
@@ -76,7 +75,6 @@ public class StructureChooser extends GStructureChooser
 
   private boolean isValidPBDEntry;
 
-  private static Hashtable<String, PDBEntry> cachedEntryMap;
 
   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
           AlignmentPanel ap)
@@ -169,7 +167,6 @@ public class StructureChooser extends GStructureChooser
               && !resultList.getSearchSummary().isEmpty())
       {
         discoveredStructuresSet.addAll(resultList.getSearchSummary());
-        updateSequencePDBEntries(seq, resultList.getSearchSummary());
       }
     }
 
@@ -192,7 +189,6 @@ public class StructureChooser extends GStructureChooser
       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");
@@ -205,70 +201,27 @@ public class StructureChooser extends GStructureChooser
 
   public void loadLocalCachedPDBEntries()
   {
-    DefaultTableModel tableModel = new DefaultTableModel()
-    {
-      @Override
-      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>();
+    ArrayList<CachedPDB> entries = new ArrayList<CachedPDB>();
     for (SequenceI seq : selectedSequences)
     {
       if (seq.getDatasetSequence() != null
-              && seq.getDatasetSequence().getPDBId() != null)
+              && seq.getDatasetSequence().getAllPDBEntries() != null)
       {
-        for (PDBEntry pdbEntry : seq.getDatasetSequence().getPDBId())
+        for (PDBEntry pdbEntry : seq.getDatasetSequence().getAllPDBEntries())
         {
-
-          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);
+            entries.add(new CachedPDB(seq, pdbEntry));
           }
-          cachedEntryMap.put(pdbEntry.getId().toLowerCase(), pdbEntry);
         }
       }
     }
-    tbl_local_pdb.setModel(tableModel);
-  }
 
-  /**
-   * 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);
-    }
+    PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
+    tbl_local_pdb.setModel(tableModelx);
   }
 
+
   /**
    * Builds a query string for a given sequences using its DBRef entries
    * 
@@ -292,9 +245,9 @@ public class StructureChooser extends GStructureChooser
       }
     }
 
-    if (seq.getPDBId() != null)
+    if (seq.getAllPDBEntries() != null)
     {
-      for (PDBEntry entry : seq.getPDBId())
+      for (PDBEntry entry : seq.getAllPDBEntries())
       {
         if (isValidSeqName(entry.getId()))
         {
@@ -685,19 +638,20 @@ public class StructureChooser extends GStructureChooser
       PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
       int count = 0;
       ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
-      for (int summaryRow : selectedRows)
+      for (int row : selectedRows)
       {
-        String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdColIndex)
+        String pdbIdStr = tbl_summary.getValueAt(row, pdbIdColIndex)
                 .toString();
-        SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(
-                summaryRow, refSeqColIndex);
+        SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row,
+                refSeqColIndex);
         selectedSeqsToView.add(selectedSeq);
-        PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
+        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;
       }
@@ -718,13 +672,12 @@ public class StructureChooser extends GStructureChooser
       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);
+        PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
+                pdbIdColIndex);
+        pdbEntriesToView[count++] = pdbEntry;
         SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row,
                 refSeqColIndex);
         selectedSeqsToView.add(selectedSeq);
-
       }
       SequenceI[] selectedSeqs = selectedSeqsToView
               .toArray(new SequenceI[selectedSeqsToView.size()]);
@@ -741,15 +694,15 @@ public class StructureChooser extends GStructureChooser
       }
 
       String pdbIdStr = txt_search.getText();
-      PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
+      PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
       if (pdbEntry == null)
       {
         pdbEntry = new PDBEntry();
-        pdbEntry.setId(txt_search.getText());
+        pdbEntry.setId(pdbIdStr);
         pdbEntry.setType(PDBEntry.Type.PDB);
+        selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
       }
 
-      selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
       PDBEntry[] pdbEntriesToView = new PDBEntry[]
       { pdbEntry };
       launchStructureViewer(ap.getStructureSelectionManager(),
@@ -796,9 +749,6 @@ public class StructureChooser extends GStructureChooser
           }
           SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
           sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
-          // sViewer.viewStructures(pdbEntriesToView,
-          // alignPanel.av.collateForPDB(pdbEntriesToView),
-          // alignPanel);
         }
         else
         {
@@ -818,7 +768,6 @@ public class StructureChooser extends GStructureChooser
     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)
     {
@@ -909,4 +858,103 @@ public class StructureChooser extends GStructureChooser
     }
   }
 
+  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;
+    }
+
+  }
 }
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 0705422..65f2a57 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -346,9 +346,9 @@ public class FileLoader implements Runnable
             {
               sq = sq.getDatasetSequence();
             }
-            if (sq.getPDBId() != null)
+            if (sq.getAllPDBEntries() != null)
             {
-              for (PDBEntry pdbe : sq.getPDBId())
+              for (PDBEntry pdbe : sq.getAllPDBEntries())
               {
                 // register PDB entries with desktop's structure selection
                 // manager
diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index c75a36f..836e211 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -140,7 +140,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
         {
           String chid = null;
           // Mapping map=null;
-          for (PDBEntry pid : pdbcs.getPDBId())
+          for (PDBEntry pid : pdbcs.getAllPDBEntries())
           {
             if (pid.getFile() == file)
             {
diff --git a/test/MCview/PDBfileTest.java b/test/MCview/PDBfileTest.java
index 1dfeba9..3e24f52 100644
--- a/test/MCview/PDBfileTest.java
+++ b/test/MCview/PDBfileTest.java
@@ -71,8 +71,8 @@ public class PDBfileTest
     assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
     assertEquals("3W5V|A", chainA.sequence.getName());
     assertNull(chainA.sequence.getAnnotation());
-    assertEquals(1, chainA.sequence.getPDBId().size());
-    PDBEntry pdb = chainA.sequence.getPDBId().get(0);
+    assertEquals(1, chainA.sequence.getAllPDBEntries().size());
+    PDBEntry pdb = chainA.sequence.getAllPDBEntries().get(0);
     assertEquals("A", pdb.getChainCode());
     assertEquals("PDB", pdb.getType());
     assertEquals("3W5V", pdb.getId());
@@ -107,8 +107,8 @@ public class PDBfileTest
     assertEquals("3W5V|B", seqs.get(1).getName());
     assertEquals("3W5V|C", seqs.get(2).getName());
     assertEquals("3W5V|D", seqs.get(3).getName());
-    assertEquals(1, seqs.get(0).getPDBId().size());
-    PDBEntry pdbe = seqs.get(0).getPDBId().get(0);
+    assertEquals(1, seqs.get(0).getAllPDBEntries().size());
+    PDBEntry pdbe = seqs.get(0).getAllPDBEntries().get(0);
     assertEquals("A", pdbe.getChainCode());
     assertEquals("3W5V", pdbe.getId());
     assertEquals(PDBEntry.Type.PDB.toString(), pdbe.getType());
diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
index 0c5d7fa..4bfabb3 100644
--- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
+++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
@@ -56,15 +56,15 @@ public class JalviewChimeraView
       {
         dsq = dsq.getDatasetSequence();
       }
-      if (dsq.getPDBId() != null && dsq.getPDBId().size() > 0)
+      if (dsq.getAllPDBEntries() != null && dsq.getAllPDBEntries().size() > 0)
       {
-        for (int q = 0; q < dsq.getPDBId().size(); q++)
+        for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
         {
           final StructureViewer structureViewer = new StructureViewer(af
                   .getViewport().getStructureSelectionManager());
           structureViewer.setViewerType(ViewerType.JMOL);
           JalviewStructureDisplayI jmolViewer = structureViewer
-                  .viewStructures(dsq.getPDBId().elementAt(q),
+                  .viewStructures(dsq.getAllPDBEntries().elementAt(q),
                           new SequenceI[]
                   { sq }, af.getCurrentView().getAlignPanel());
           /*
@@ -100,15 +100,15 @@ public class JalviewChimeraView
       {
         dsq = dsq.getDatasetSequence();
       }
-      if (dsq.getPDBId() != null && dsq.getPDBId().size() > 0)
+      if (dsq.getAllPDBEntries() != null && dsq.getAllPDBEntries().size() > 0)
       {
-        for (int q = 0; q < dsq.getPDBId().size(); q++)
+        for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
         {
           final StructureViewer structureViewer = new StructureViewer(af
                   .getViewport().getStructureSelectionManager());
           structureViewer.setViewerType(ViewerType.CHIMERA);
           JalviewStructureDisplayI chimeraViewer = structureViewer
-                  .viewStructures(dsq.getPDBId().elementAt(q),
+                  .viewStructures(dsq.getAllPDBEntries().elementAt(q),
                           new SequenceI[]
                           { sq }, af.getCurrentView().getAlignPanel());
           /*
diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index 31bfd9d..150ee59 100644
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -43,7 +43,7 @@ public class AnnotatedPDBFileInputTest
     AlignFrame af = loader.LoadFileWaitTillLoaded(pdbStr,
             FormatAdapter.FILE);
     al = af.getViewport().getAlignment();
-    pdbId = al.getSequenceAt(0).getDatasetSequence().getPDBId()
+    pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
             .get(0).getId();
   }
 
@@ -197,9 +197,9 @@ public class AnnotatedPDBFileInputTest
       {
         sq = sq.getDatasetSequence();
       }
-      assertNotNull(sq.getPDBId());
-      assertEquals("Expected only one PDB ID", sq.getPDBId().size(), 1);
-      for (PDBEntry pdbentry : sq.getPDBId())
+      assertNotNull(sq.getAllPDBEntries());
+      assertEquals("Expected only one PDB ID", sq.getAllPDBEntries().size(), 1);
+      for (PDBEntry pdbentry : sq.getAllPDBEntries())
       {
         System.err.println("PDB Entry " + pdbentry.getId() + " "
                 + pdbentry.getFile());
diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 2537002..7ef5cc6 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -58,9 +58,9 @@ public class StockholmFileTest
     int numpdb = 0;
     for (SequenceI sq : al.getSequences())
     {
-      if (sq.getPDBId() != null)
+      if (sq.getAllPDBEntries() != null)
       {
-        numpdb += sq.getPDBId().size();
+        numpdb += sq.getAllPDBEntries().size();
       }
     }
     assertTrue(
diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java
index b06132b..af5fd1e 100644
--- a/test/jalview/util/DBRefUtilsTest.java
+++ b/test/jalview/util/DBRefUtilsTest.java
@@ -129,7 +129,7 @@ public class DBRefUtilsTest
     assertEquals("EMBL", ref.getSource());
     assertEquals("1.2", ref.getVersion());
     assertEquals("a7890", ref.getAccessionId());
-    assertNull(seq.getPDBId());
+    assertNull(seq.getAllPDBEntries());
   }
 
   /**
@@ -148,8 +148,8 @@ public class DBRefUtilsTest
     assertEquals("1.2", ref.getVersion());
     // DBRef id is pdbId + chain code
     assertEquals("1WRIA", ref.getAccessionId());
-    assertEquals(1, seq.getPDBId().size());
-    PDBEntry pdbRef = seq.getPDBId().get(0);
+    assertEquals(1, seq.getAllPDBEntries().size());
+    PDBEntry pdbRef = seq.getAllPDBEntries().get(0);
     assertEquals("1WRI", pdbRef.getId());
     assertNull(pdbRef.getFile());
     assertEquals("A", pdbRef.getChainCode());
diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index 2963ef2..86439fc 100644
--- a/test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@ -61,7 +61,7 @@ public class PDBSequenceFetcherTest
     {
       assertTrue("No annotation transfered to sequence.",
               sq.getAnnotation().length > 0);
-      assertTrue("No PDBEntry on sequence.", sq.getPDBId().size() > 0);
+      assertTrue("No PDBEntry on sequence.", sq.getAllPDBEntries().size() > 0);
       assertTrue("No RNA annotation on sequence.", sq.getRNA() != null);
     }
   }