X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=9c51409ae83802cf809f05913ec995ebb727e9b8;hb=5646f33d5e9dcbf30339abb53f2fca40d0f768b3;hp=5ea5768a3c2848892afdd1941b08923e7c15a8a3;hpb=d31b471f53501f7c9344efcf15c2aec1ac1d8ec2;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 5ea5768..9c51409 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,37 +1,35 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- * 
+ *
  * 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 
+ * 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 
+ *
+ * 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/>.
  */
 package jalview.gui;
 
 import java.util.*;
+import java.util.List;
 
 import java.awt.*;
 import java.awt.event.*;
 
 import javax.swing.*;
 import javax.swing.tree.DefaultMutableTreeNode;
-import javax.swing.tree.MutableTreeNode;
-import javax.swing.tree.TreeModel;
-
 import jalview.datamodel.*;
 import jalview.io.*;
+import jalview.util.DBRefUtils;
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
 import jalview.ws.seqfetcher.DbSourceProxy;
-
 import java.awt.BorderLayout;
 
 public class SequenceFetcher extends JPanel implements Runnable
@@ -60,7 +58,7 @@ public class SequenceFetcher extends JPanel implements Runnable
   /**
    * Blocking method that initialises and returns the shared instance of the
    * SequenceFetcher client
-   * 
+   *
    * @param guiWindow
    *          - where the initialisation delay message should be shown
    * @return the singleton instance of the sequence fetcher client
@@ -139,6 +137,7 @@ public class SequenceFetcher extends JPanel implements Runnable
     Thread sf = new Thread(new Runnable()
     {
 
+      @Override
       public void run()
       {
         if (getSequenceFetcherSingleton(guiWindow) != null)
@@ -149,6 +148,7 @@ public class SequenceFetcher extends JPanel implements Runnable
         {
           javax.swing.SwingUtilities.invokeLater(new Runnable()
           {
+            @Override
             public void run()
             {
               JOptionPane
@@ -179,7 +179,7 @@ public class SequenceFetcher extends JPanel implements Runnable
 
   /**
    * called by thread spawned by constructor
-   * 
+   *
    * @param guiWindow
    */
   private void initGui(IProgressIndicator guiWindow)
@@ -233,6 +233,7 @@ public class SequenceFetcher extends JPanel implements Runnable
     ok.setText("OK");
     ok.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         ok_actionPerformed();
@@ -241,6 +242,7 @@ public class SequenceFetcher extends JPanel implements Runnable
     clear.setText("Clear");
     clear.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         clear_actionPerformed();
@@ -250,6 +252,7 @@ public class SequenceFetcher extends JPanel implements Runnable
     example.setText("Example");
     example.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         example_actionPerformed();
@@ -258,6 +261,7 @@ public class SequenceFetcher extends JPanel implements Runnable
     close.setText("Close");
     close.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         close_actionPerformed(e);
@@ -267,6 +271,7 @@ public class SequenceFetcher extends JPanel implements Runnable
     textArea.setLineWrap(true);
     textArea.addKeyListener(new KeyAdapter()
     {
+      @Override
       public void keyPressed(KeyEvent e)
       {
         if (e.getKeyCode() == KeyEvent.VK_ENTER)
@@ -286,9 +291,9 @@ public class SequenceFetcher extends JPanel implements Runnable
     database.addActionListener(new ActionListener()
     {
 
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        DbSourceProxy db = null;
         try
         {
           databaseButt.setText(database.getSelectedItem()
@@ -297,7 +302,16 @@ public class SequenceFetcher extends JPanel implements Runnable
                           + " others)" : ""));
           String eq = database.getExampleQueries();
           dbeg.setText("Example query: " + eq);
-          replacePunctuation.setEnabled(!(eq != null && eq.indexOf(",") > -1));
+          boolean enablePunct=!(eq != null && eq.indexOf(",") > -1);
+          for (DbSourceProxy dbs:database.getSelectedSources()) {
+            if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
+            {
+              enablePunct = false;
+              break;
+            }
+          }
+          replacePunctuation.setEnabled(enablePunct);
+
         } catch (Exception ex)
         {
           dbeg.setText("");
@@ -405,6 +419,7 @@ public class SequenceFetcher extends JPanel implements Runnable
     close.setEnabled(true);
   }
 
+  @Override
   public void run()
   {
     String error = "";
@@ -438,283 +453,248 @@ public class SequenceFetcher extends JPanel implements Runnable
       resetDialog();
       return;
     }
-    ArrayList<String> aresultq = new ArrayList<String>();
-    ArrayList<AlignmentI> aresult = new ArrayList<AlignmentI>();
-    DbSourceProxy proxy = database.getSelectedSources().get(0);
-    Enumeration en = new StringTokenizer(textArea.getText(), ";");
-    boolean isAliSource = false;
-    try
-    {
-      guiWindow.setProgressBar(
-              "Fetching Sequences from " + proxy.getDbName(), Thread
-                      .currentThread().hashCode());
-      isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
-      if (proxy.getAccessionSeparator() == null)
+    // indicate if successive sources should be merged into one alignment.
+    boolean addToLast=false;
+    ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
+    ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
+    Iterator<DbSourceProxy> proxies = database.getSelectedSources()
+            .iterator();
+    String[] qries;
+    List<String> nextfetch = Arrays.asList(qries = textArea.getText()
+            .split(";"));
+    Iterator<String> en = Arrays.asList(new String[0]).iterator();
+    int nqueries = qries.length;
+    while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
+    {
+      if (!en.hasNext() && nextfetch.size() > 0)
+      {
+        en = nextfetch.iterator();
+        nqueries = nextfetch.size();
+        // save the remaining queries in the original array
+        qries = nextfetch.toArray(new String[nqueries]);
+        nextfetch = new ArrayList<String>();
+      }
+
+      DbSourceProxy proxy = proxies.next();
+      boolean isAliSource = false;
+      try
       {
-        while (en.hasMoreElements())
+        // update status
+        guiWindow.setProgressBar("Fetching " + nqueries
+                + " sequence queries from " + proxy.getDbName(), Thread
+                .currentThread().hashCode());
+        isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
+        if (proxy.getAccessionSeparator() == null)
         {
-          String item = (String) en.nextElement();
-          try
+          while (en.hasNext())
           {
-            if (aresult != null)
+            String item = en.next();
+            try
             {
+              if (aresult != null)
+              {
+                try
+                {
+                  // give the server a chance to breathe
+                  Thread.sleep(5);
+                } catch (Exception e)
+                {
+                  //
+                }
+
+              }
+
+              AlignmentI indres = null;
               try
               {
-                // give the server a chance to breathe
-                Thread.sleep(5);
-              } catch (Exception e)
+                indres = proxy.getSequenceRecords(item);
+              } catch (OutOfMemoryError oome)
               {
-                //
+                new OOMWarning("fetching " + item + " from "
+                        + proxy.getDbName(), oome, this);
               }
-
+              if (indres != null)
+              {
+                aresultq.add(item);
+                aresult.add(indres);
+              }
+              else
+              {
+                nextfetch.add(item);
+              }
+            } catch (Exception e)
+            {
+              jalview.bin.Cache.log.info("Error retrieving " + item
+                      + " from " + proxy.getDbName(), e);
+              nextfetch.add(item);
             }
-
-            AlignmentI indres = null;
-            try
+          }
+        }
+        else
+        {
+          StringBuffer multiacc = new StringBuffer();
+          ArrayList<String> tosend = new ArrayList<String>();
+          while (en.hasNext())
+          {
+            String nel = en.next();
+            tosend.add(nel);
+            multiacc.append(nel);
+            if (en.hasNext())
             {
-              indres = proxy.getSequenceRecords(item);
-            } catch (OutOfMemoryError oome)
+              multiacc.append(proxy.getAccessionSeparator());
+            }
+          }
+          try
+          {
+            AlignmentI rslt;
+            SequenceI[] rs;
+            List<String> nores = new ArrayList<String>();
+            rslt = proxy.getSequenceRecords(multiacc.toString());
+            if (rslt == null || rslt.getHeight() == 0)
             {
-              new OOMWarning("fetching " + item + " from "
-                      + proxy.getDbName(), oome, this);
+              // no results - pass on all queries to next source
+              nextfetch.addAll(tosend);
             }
-            if (indres != null)
+            else
             {
-              aresultq.add(item);
-              aresult.add(indres);
+              aresultq.add(multiacc.toString());
+              aresult.add(rslt);
+
+              rs = rslt.getSequencesArray();
+              // search for each query in the dbrefs associated with each
+              // sequence
+              // returned.
+              // ones we do not find will be used to query next source (if any)
+              for (String q : tosend)
+              {
+                DBRefEntry dbr = new DBRefEntry(), found[] = null;
+                dbr.setSource(proxy.getDbSource());
+                boolean rfound = false;
+                for (int r = 0; r < rs.length; r++)
+                {
+                  if (rs[r] != null
+                          && (found = DBRefUtils.searchRefs(
+                                  rs[r].getDBRef(), dbr)) != null
+                          && found.length > 0)
+                  {
+                    rfound = true;
+                    rs[r] = null;
+                    continue;
+                  }
+                }
+                if (!rfound)
+                {
+                  nextfetch.add(q);
+                }
+              }
             }
-          } catch (Exception e)
+          } catch (OutOfMemoryError oome)
           {
-            jalview.bin.Cache.log.info("Error retrieving " + item
-                    + " from " + proxy.getDbName(), e);
+            new OOMWarning("fetching " + multiacc + " from "
+                    + database.getSelectedItem(), oome, this);
           }
         }
+
+      } catch (Exception e)
+      {
+        showErrorMessage("Error retrieving " + textArea.getText()
+                + " from " + database.getSelectedItem());
+        // error
+        // +="Couldn't retrieve sequences from "+database.getSelectedItem();
+        System.err.println("Retrieval failed for source ='"
+                + database.getSelectedItem() + "' and query\n'"
+                + textArea.getText() + "'\n");
+        e.printStackTrace();
+      } catch (OutOfMemoryError e)
+      {
+        // resets dialog box - so we don't use OOMwarning here.
+        showErrorMessage("Out of Memory when retrieving "
+                + textArea.getText()
+                + " from "
+                + database.getSelectedItem()
+                + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
+        e.printStackTrace();
+      } catch (Error e)
+      {
+        showErrorMessage("Serious Error retrieving " + textArea.getText()
+                + " from " + database.getSelectedItem());
+        e.printStackTrace();
       }
-      else
+      // Stack results ready for opening in alignment windows
+      if (aresult != null && aresult.size() > 0)
       {
-        StringBuffer multiacc = new StringBuffer();
-        while (en.hasMoreElements())
+        AlignmentI ar = null;
+        if (isAliSource)
         {
-          multiacc.append(en.nextElement());
-          if (en.hasMoreElements())
+          addToLast=false;
+          // new window for each result
+          while (aresult.size() > 0)
           {
-            multiacc.append(proxy.getAccessionSeparator());
+            presult.add(aresult.remove(0));
+            presultTitle.add(aresultq.remove(0) + " "
+                    + getDefaultRetrievalTitle());
           }
         }
-        try
-        {
-          aresultq.add(multiacc.toString());
-          aresult.add(proxy.getSequenceRecords(multiacc.toString()));
-        } catch (OutOfMemoryError oome)
+        else
         {
-          new OOMWarning("fetching " + multiacc + " from "
-                  + database.getSelectedItem(), oome, this);
+          String titl=null;
+          if (addToLast && presult.size()>0)
+          {
+            ar=presult.remove(presult.size()-1);
+            titl=presultTitle.remove(presultTitle.size()-1);
+          }
+          // concatenate all results in one window
+          while (aresult.size() > 0)
+          {
+            if (ar == null)
+            {
+              ar = aresult.remove(0);
+            }
+            else
+            {
+              ar.append(aresult.remove(0));
+            }
+            ;
+          }
+          addToLast=true;
+          presult.add(ar);
+          presultTitle.add(titl);
         }
-
       }
-
-    } catch (Exception e)
-    {
-      showErrorMessage("Error retrieving " + textArea.getText() + " from "
-              + database.getSelectedItem());
-      // error +="Couldn't retrieve sequences from "+database.getSelectedItem();
-      System.err.println("Retrieval failed for source ='"
-              + database.getSelectedItem() + "' and query\n'"
-              + textArea.getText() + "'\n");
-      e.printStackTrace();
-    } catch (OutOfMemoryError e)
-    {
-      // resets dialog box - so we don't use OOMwarning here.
-      showErrorMessage("Out of Memory when retrieving "
-              + textArea.getText()
-              + " from "
-              + database.getSelectedItem()
-              + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
-      e.printStackTrace();
-    } catch (Error e)
-    {
-      showErrorMessage("Serious Error retrieving " + textArea.getText()
-              + " from " + database.getSelectedItem());
-      e.printStackTrace();
+      guiWindow.setProgressBar("Finished querying", Thread.currentThread().hashCode());
     }
-    if (aresult != null && aresult.size() > 0)
+    guiWindow.setProgressBar((presult.size()>0) ? "Parsing results.":"Processing ..", Thread.currentThread().hashCode());
+    // process results
+    while (presult.size() > 0)
     {
-      AlignmentI ar = null;
-      if (isAliSource)
+      parseResult(presult.remove(0), presultTitle.remove(0), null);
+    }
+    // only remove visual delay after we finished parsing.
+    guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
+    if (nextfetch.size() > 0)
+    {
+      StringBuffer sb = new StringBuffer();
+      sb.append("Didn't retrieve the following "
+              + (nextfetch.size() == 1 ? "query" : nextfetch.size()
+                      + " queries") + ": \n");
+      int l = sb.length(),lr=0;
+      for (String s : nextfetch)
       {
-        // new window for each result
-        while (aresult.size() > 0)
+        if (l != sb.length())
         {
-          parseResult(aresult.remove(0), aresultq.remove(0) + " "
-                  + getDefaultRetrievalTitle(), null);
+          sb.append("; ");
         }
-      }
-      else
-      {
-        // concatenate all results in one window
-        while (aresult.size() > 0)
+        if (lr-sb.length()>40)
         {
-          if (ar == null)
-          {
-            ar = aresult.remove(0);
-          }
-          else
-          {
-            ar.append(aresult.remove(0));
-          }
-          ;
+          sb.append("\n");
         }
-        parseResult(ar, null, null);
+        sb.append(s);
       }
+      showErrorMessage(sb.toString());
     }
-    // only remove visual delay after we finished parsing.
-    guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
     resetDialog();
   }
 
-  /*
-   * result = new StringBuffer(); if
-   * (database.getSelectedItem().equals("Uniprot")) {
-   * getUniprotFile(textArea.getText()); } else if
-   * (database.getSelectedItem().equals("EMBL") ||
-   * database.getSelectedItem().equals("EMBLCDS")) { String DBRefSource =
-   * database.getSelectedItem().equals("EMBLCDS") ?
-   * jalview.datamodel.DBRefSource.EMBLCDS : jalview.datamodel.DBRefSource.EMBL;
-   * 
-   * StringTokenizer st = new StringTokenizer(textArea.getText(), ";");
-   * SequenceI[] seqs = null; while(st.hasMoreTokens()) { EBIFetchClient dbFetch
-   * = new EBIFetchClient(); String qry =
-   * database.getSelectedItem().toString().toLowerCase( ) + ":" +
-   * st.nextToken(); File reply = dbFetch.fetchDataAsFile( qry, "emblxml",null);
-   * 
-   * jalview.datamodel.xdb.embl.EmblFile efile=null; if (reply != null &&
-   * reply.exists()) { efile =
-   * jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply); } if (efile!=null)
-   * { for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) { EmblEntry
-   * entry = (EmblEntry) i.next(); SequenceI[] seqparts =
-   * entry.getSequences(false,true, DBRefSource); if (seqparts!=null) {
-   * SequenceI[] newseqs = null; int si=0; if (seqs==null) { newseqs = new
-   * SequenceI[seqparts.length]; } else { newseqs = new
-   * SequenceI[seqs.length+seqparts.length];
-   * 
-   * for (;si<seqs.length; si++) { newseqs[si] = seqs[si]; seqs[si] = null; } }
-   * for (int j=0;j<seqparts.length; si++, j++) { newseqs[si] =
-   * seqparts[j].deriveSequence(); // place DBReferences on dataset and refer }
-   * seqs=newseqs; } } } else { result.append("# no response for "+qry); } } if
-   * (seqs!=null && seqs.length>0) { if (parseResult(new Alignment(seqs), null,
-   * null)!=null) { result.append("# Successfully parsed the
-   * "+database.getSelectedItem()+" Queries into an Alignment"); } } } else if
-   * (database.getSelectedItem().equals("PDB")) { StringTokenizer qset = new
-   * StringTokenizer(textArea.getText(), ";"); String query; SequenceI[] seqs =
-   * null; while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null)) {
-   * SequenceI[] seqparts = getPDBFile(query.toUpperCase()); if (seqparts !=
-   * null) { if (seqs == null) { seqs = seqparts; } else { SequenceI[] newseqs =
-   * new SequenceI[seqs.length+seqparts.length]; int i=0; for (; i <
-   * seqs.length; i++) { newseqs[i] = seqs[i]; seqs[i] = null; } for (int
-   * j=0;j<seqparts.length; i++, j++) { newseqs[i] = seqparts[j]; }
-   * seqs=newseqs; } result.append("# Success for "+query.toUpperCase()+"\n"); }
-   * } if (seqs != null && seqs.length > 0) { if (parseResult(new
-   * Alignment(seqs), null, null)!=null) { result.append( "# Successfully parsed
-   * the PDB File Queries into an
-   * Alignment"); } } } else if( database.getSelectedItem().equals("PFAM")) {
-   * try { result.append(new FastaFile(
-   * "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc=" +
-   * textArea.getText().toUpperCase(), "URL").print() );
-   * 
-   * if(result.length()>0) { parseResult( result.toString(),
-   * textArea.getText().toUpperCase() ); } } catch (java.io.IOException ex) {
-   * result = null; } }
-   * 
-   * if (result == null || result.length() == 0) { showErrorMessage("Error
-   * retrieving " + textArea.getText() + " from " + database.getSelectedItem());
-   * }
-   * 
-   * resetDialog(); return; }
-   * 
-   * void getUniprotFile(String id) { EBIFetchClient ebi = new EBIFetchClient();
-   * File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
-   * 
-   * DBRefFetcher dbref = new DBRefFetcher(); Vector entries =
-   * dbref.getUniprotEntries(file);
-   * 
-   * if (entries != null) { //First, make the new sequences Enumeration en =
-   * entries.elements(); while (en.hasMoreElements()) { UniprotEntry entry =
-   * (UniprotEntry) en.nextElement();
-   * 
-   * StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot"); Enumeration
-   * en2 = entry.getAccession().elements(); while (en2.hasMoreElements()) {
-   * name.append("|"); name.append(en2.nextElement()); } en2 =
-   * entry.getName().elements(); while (en2.hasMoreElements()) {
-   * name.append("|"); name.append(en2.nextElement()); }
-   * 
-   * if (entry.getProtein() != null) { name.append(" " +
-   * entry.getProtein().getName().elementAt(0)); }
-   * 
-   * result.append(name + "\n" + entry.getUniprotSequence().getContent() +
-   * "\n"); }
-   * 
-   * //Then read in the features and apply them to the dataset Alignment al =
-   * parseResult(result.toString(), null); for (int i = 0; i < entries.size();
-   * i++) { UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
-   * Enumeration e = entry.getDbReference().elements(); Vector onlyPdbEntries =
-   * new Vector(); while (e.hasMoreElements()) { PDBEntry pdb = (PDBEntry)
-   * e.nextElement(); if (!pdb.getType().equals("PDB")) { continue; }
-   * 
-   * onlyPdbEntries.addElement(pdb); }
-   * 
-   * Enumeration en2 = entry.getAccession().elements(); while
-   * (en2.hasMoreElements()) {
-   * al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(
-   * DBRefSource.UNIPROT, "0", en2.nextElement().toString())); }
-   * 
-   * 
-   * 
-   * 
-   * al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries); if
-   * (entry.getFeature() != null) { e = entry.getFeature().elements(); while
-   * (e.hasMoreElements()) { SequenceFeature sf = (SequenceFeature)
-   * e.nextElement(); sf.setFeatureGroup("Uniprot");
-   * al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf ); } } } }
-   * }
-   * 
-   * SequenceI[] getPDBFile(String id) { Vector result = new Vector(); String
-   * chain = null; if (id.indexOf(":") > -1) { chain =
-   * id.substring(id.indexOf(":") + 1); id = id.substring(0, id.indexOf(":")); }
-   * 
-   * EBIFetchClient ebi = new EBIFetchClient(); String file =
-   * ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw"). getAbsolutePath(); if (file
-   * == null) { return null; } try { PDBfile pdbfile = new PDBfile(file,
-   * jalview.io.AppletFormatAdapter.FILE); for (int i = 0; i <
-   * pdbfile.chains.size(); i++) { if (chain == null || ( (PDBChain)
-   * pdbfile.chains.elementAt(i)).id. toUpperCase().equals(chain)) { PDBChain
-   * pdbchain = (PDBChain) pdbfile.chains.elementAt(i); // Get the Chain's
-   * Sequence - who's dataset includes any special features added from the PDB
-   * file SequenceI sq = pdbchain.sequence; // Specially formatted name for the
-   * PDB chain sequences retrieved from the PDB
-   * sq.setName("PDB|"+id+"|"+sq.getName()); // Might need to add more metadata
-   * to the PDBEntry object // like below /* PDBEntry entry = new PDBEntry(); //
-   * Construct the PDBEntry entry.setId(id); if (entry.getProperty() == null)
-   * entry.setProperty(new Hashtable()); entry.getProperty().put("chains",
-   * pdbchain.id + "=" + sq.getStart() + "-" + sq.getEnd());
-   * sq.getDatasetSequence().addPDBId(entry); // Add PDB DB Refs // We make a
-   * DBRefEtntry because we have obtained the PDB file from a verifiable source
-   * // JBPNote - PDB DBRefEntry should also carry the chain and mapping
-   * information DBRefEntry dbentry = new
-   * DBRefEntry(jalview.datamodel.DBRefSource.PDB, "0", id + pdbchain.id);
-   * sq.addDBRef(dbentry); // and add seuqence to the retrieved set
-   * result.addElement(sq.deriveSequence()); } }
-   * 
-   * if (result.size() < 1) { throw new Exception("WsDBFetch for PDB id resulted
-   * in zero result size"); } } catch (Exception ex) // Problem parsing PDB file
-   * { jalview.bin.Cache.log.warn("Exception when retrieving " +
-   * textArea.getText() + " from " + database.getSelectedItem(), ex); return
-   * null; }
-   * 
-   * 
-   * SequenceI[] results = new SequenceI[result.size()]; for (int i = 0, j =
-   * result.size(); i < j; i++) { results[i] = (SequenceI) result.elementAt(i);
-   * result.setElementAt(null,i); } return results; }
-   */
   AlignmentI parseResult(String result, String title)
   {
     String format = new IdentifyFile().Identify(result, "Paste");
@@ -745,7 +725,7 @@ public class SequenceFetcher extends JPanel implements Runnable
   }
 
   /**
-   * 
+   *
    * @return a standard title for any results retrieved using the currently
    *         selected source and settings
    */
@@ -777,19 +757,21 @@ public class SequenceFetcher extends JPanel implements Runnable
           title = getDefaultRetrievalTitle();
         }
         SequenceFeature[] sfs = null;
-        for (Enumeration sq = al.getSequences().elements(); sq
-                .hasMoreElements();)
+        List<SequenceI> alsqs;
+        synchronized (alsqs = al.getSequences())
         {
-          if ((sfs = ((SequenceI) sq.nextElement()).getDatasetSequence()
-                  .getSequenceFeatures()) != null)
+          for (SequenceI sq : alsqs)
           {
-            if (sfs.length > 0)
+            if ((sfs = (sq).getDatasetSequence().getSequenceFeatures()) != null)
             {
-              af.setShowSeqFeatures(true);
-              break;
+              if (sfs.length > 0)
+              {
+                af.setShowSeqFeatures(true);
+                break;
+              }
             }
-          }
 
+          }
         }
         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
@@ -831,6 +813,7 @@ public class SequenceFetcher extends JPanel implements Runnable
     resetDialog();
     javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
+      @Override
       public void run()
       {
         JOptionPane.showInternalMessageDialog(Desktop.desktop, error,