X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=3fa00f5d491c1a6583f1b56db8bde4cbfe0b5035;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=70dff688f25c5a18b03887d8cc2b3fac4baa00f0;hpb=0eda2ac2f334f55f6e5f137789453a9f4dfe4d73;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 70dff68..3fa00f5 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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 
+ * 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/>.
  */
 package jalview.gui;
 
@@ -23,6 +22,7 @@ import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
+
 import javax.swing.*;
 
 import MCview.*;
@@ -33,53 +33,176 @@ import jalview.io.*;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.ebi.EBIFetchClient;
 import jalview.ws.seqfetcher.ASequenceFetcher;
+import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.awt.Rectangle;
 import java.awt.BorderLayout;
 import java.awt.Dimension;
 
-public class SequenceFetcher
-extends JPanel implements Runnable
+public class SequenceFetcher extends JPanel implements Runnable
 {
-  ASequenceFetcher sfetch; 
+  // ASequenceFetcher sfetch;
   JInternalFrame frame;
+
+  IProgressIndicator guiWindow;
+
   AlignFrame alignFrame;
+
   StringBuffer result;
+
   final String noDbSelected = "-- Select Database --";
-  public SequenceFetcher(AlignFrame af)
+
+  Hashtable sources = new Hashtable();
+
+  private static jalview.ws.SequenceFetcher sfetch = null;
+
+  private static String dasRegistry = null;
+
+  private static boolean _initingFetcher = false;
+
+  private static Thread initingThread = null;
+
+  /**
+   * 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
+   */
+  public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
+          final IProgressIndicator guiWindow)
   {
-    alignFrame = af;
-    sfetch = new jalview.ws.SequenceFetcher();
+    if (_initingFetcher && initingThread != null && initingThread.isAlive())
+    {
+      if (guiWindow != null)
+      {
+        guiWindow.setProgressBar(
+                "Waiting for Sequence Database Fetchers to initialise",
+                Thread.currentThread().hashCode());
+      }
+      // initting happening on another thread - so wait around to see if it
+      // finishes.
+      while (_initingFetcher && initingThread != null
+              && initingThread.isAlive())
+      {
+        try
+        {
+          Thread.sleep(10);
+        } catch (Exception e)
+        {
+        }
+        ;
+      }
+      if (guiWindow != null)
+      {
+        guiWindow.setProgressBar(
+                "Waiting for Sequence Database Fetchers to initialise",
+                Thread.currentThread().hashCode());
+      }
+    }
+    if (sfetch == null
+            || dasRegistry != DasSourceBrowser.getDasRegistryURL())
+    {
+      _initingFetcher = true;
+      initingThread = Thread.currentThread();
+      /**
+       * give a visual indication that sequence fetcher construction is occuring
+       */
+      if (guiWindow != null)
+      {
+        guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
+                Thread.currentThread().hashCode());
+      }
+      dasRegistry = DasSourceBrowser.getDasRegistryURL();
+      jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
+      if (guiWindow != null)
+      {
+        guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
+                Thread.currentThread().hashCode());
+      }
+      sfetch = sf;
+      _initingFetcher = false;
+      initingThread = null;
+    }
+    return sfetch;
+  }
+
+  public SequenceFetcher(IProgressIndicator guiIndic)
+  {
+    final IProgressIndicator guiWindow = guiIndic;
+    final SequenceFetcher us = this;
+    // launch initialiser thread
+    Thread sf = new Thread(new Runnable()
+    {
+
+      public void run()
+      {
+        if (getSequenceFetcherSingleton(guiWindow) != null)
+        {
+          us.initGui(guiWindow);
+        }
+        else
+        {
+          javax.swing.SwingUtilities.invokeLater(new Runnable()
+          {
+            public void run()
+            {
+              JOptionPane
+                      .showInternalMessageDialog(
+                              Desktop.desktop,
+                              "Could not create the sequence fetcher client. Check error logs for details.",
+                              "Couldn't create SequenceFetcher",
+                              JOptionPane.ERROR_MESSAGE);
+            }
+          });
+
+          // raise warning dialog
+        }
+      }
+    });
+    sf.start();
+  }
+
+  /**
+   * called by thread spawned by constructor
+   * 
+   * @param guiWindow
+   */
+  private void initGui(IProgressIndicator guiWindow)
+  {
+    this.guiWindow = guiWindow;
+    if (guiWindow instanceof AlignFrame)
+    {
+      alignFrame = (AlignFrame) guiWindow;
+    }
+
     database.addItem(noDbSelected);
     /*
-     * Dynamically generated database list
-     * will need a translation function from
-     * internal source to externally distinct names.
-     * UNIPROT and UP_NAME are identical DB sources,
-     * and should be collapsed. 
-     *
-     
-     String dbs[] = sfetch.getSupportedDb();
-    for (int i=0; i<dbs.length;i++)
-    {
-      if (DBRefSource.isPrimaryDb(dbs[i]))
-      {  
-        database.addItem(dbs[i]);
-        // should have some kind of human readable description of each database displayed when
-         * that combo is selected.
-      }
-    }*/
-    database.addItem("Uniprot");
-    database.addItem("EMBL");
-    database.addItem("EMBLCDS");
-    database.addItem("PDB");
-    database.addItem("PFAM");
+     * Dynamically generated database list will need a translation function from
+     * internal source to externally distinct names. UNIPROT and UP_NAME are
+     * identical DB sources, and should be collapsed.
+     */
 
+    String dbs[] = sfetch.getOrderedSupportedSources();
+    for (int i = 0; i < dbs.length; i++)
+    {
+      if (!sources.containsValue(dbs[i]))
+      {
+        String name = sfetch.getSourceProxy(dbs[i]).getDbName();
+        // duplicate source names are thrown away, here.
+        if (!sources.containsKey(name))
+        {
+          database.addItem(name);
+        }
+        // overwrite with latest version of the retriever for this source
+        sources.put(name, dbs[i]);
+      }
+    }
     try
     {
       jbInit();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -88,30 +211,34 @@ extends JPanel implements Runnable
     frame.setContentPane(this);
     if (new jalview.util.Platform().isAMac())
     {
-      Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);
+      Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
     }
     else
     {
-      Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);
+      Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
     }
   }
 
   private String getFrameTitle()
   {
-    return ( (alignFrame == null) ? "New " : "Additional ") +
-    "Sequence Fetcher";
+    return ((alignFrame == null) ? "New " : "Additional ")
+            + "Sequence Fetcher";
   }
 
-  private void jbInit()
-  throws Exception
+  private void jbInit() throws Exception
   {
     this.setLayout(borderLayout2);
 
-    database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    database.setFont(JvSwingUtils.getLabelFont());
+    dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
-    jLabel1.setText(
-    "Separate multiple accession ids with semi colon \";\"");
+    jLabel1.setText("Separate multiple accession ids with semi colon \";\"");
+
+    replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
+    replacePunctuation
+            .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
+    replacePunctuation.setText("Replace commas with semi-colons");
     ok.setText("OK");
     ok.addActionListener(new ActionListener()
     {
@@ -120,6 +247,23 @@ extends JPanel implements Runnable
         ok_actionPerformed();
       }
     });
+    clear.setText("Clear");
+    clear.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        clear_actionPerformed();
+      }
+    });
+
+    example.setText("Example");
+    example.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        example_actionPerformed();
+      }
+    });
     close.setText("Close");
     close.addActionListener(new ActionListener()
     {
@@ -128,49 +272,124 @@ extends JPanel implements Runnable
         close_actionPerformed(e);
       }
     });
-    textArea.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    textArea.setFont(JvSwingUtils.getLabelFont());
     textArea.setLineWrap(true);
     textArea.addKeyListener(new KeyAdapter()
     {
       public void keyPressed(KeyEvent e)
       {
-        if(e.getKeyCode()==KeyEvent.VK_ENTER)
+        if (e.getKeyCode() == KeyEvent.VK_ENTER)
           ok_actionPerformed();
       }
     });
     jPanel3.setLayout(borderLayout1);
     borderLayout1.setVgap(5);
     jPanel1.add(ok);
+    jPanel1.add(example);
+    jPanel1.add(clear);
     jPanel1.add(close);
-    jPanel3.add(jPanel2, java.awt.BorderLayout.WEST);
-    jPanel2.add(database);
+    jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
+    jPanel2.setLayout(borderLayout3);
+
+    database.addActionListener(new ActionListener()
+    {
+
+      public void actionPerformed(ActionEvent e)
+      {
+        DbSourceProxy db = null;
+        try
+        {
+          db = sfetch.getSourceProxy((String) sources.get(database
+                  .getSelectedItem()));
+          String eq = db.getTestQuery();
+          dbeg.setText("Example query: " + eq);
+          replacePunctuation.setEnabled(!(eq != null && eq.indexOf(",") > -1));
+        } catch (Exception ex)
+        {
+          dbeg.setText("");
+          replacePunctuation.setEnabled(true);
+        }
+        jPanel2.repaint();
+      }
+    });
+    dbeg.setText("");
+    jPanel2.add(database, java.awt.BorderLayout.NORTH);
+    jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
+    JPanel jPanel2a = new JPanel(new BorderLayout());
+    jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
+    jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
+    jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
+    // jPanel2.setPreferredSize(new Dimension())
     jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
-    jPanel3.add(jLabel1, java.awt.BorderLayout.NORTH);
     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
     this.add(jPanel3, java.awt.BorderLayout.CENTER);
+    this.add(jPanel2, java.awt.BorderLayout.NORTH);
     jScrollPane1.getViewport().add(textArea);
 
   }
 
+  protected void example_actionPerformed()
+  {
+    DbSourceProxy db = null;
+    try
+    {
+      db = sfetch.getSourceProxy((String) sources.get(database
+              .getSelectedItem()));
+      textArea.setText(db.getTestQuery());
+    } catch (Exception ex)
+    {
+    }
+    jPanel3.repaint();
+  }
+
+  protected void clear_actionPerformed()
+  {
+    textArea.setText("");
+    jPanel3.repaint();
+  }
+
+  JLabel dbeg = new JLabel();
+
   JComboBox database = new JComboBox();
+
   JLabel jLabel1 = new JLabel();
+
+  JCheckBox replacePunctuation = new JCheckBox();
+
   JButton ok = new JButton();
+
+  JButton clear = new JButton();
+
+  JButton example = new JButton();
+
   JButton close = new JButton();
+
   JPanel jPanel1 = new JPanel();
+
   JTextArea textArea = new JTextArea();
+
   JScrollPane jScrollPane1 = new JScrollPane();
+
   JPanel jPanel2 = new JPanel();
+
   JPanel jPanel3 = new JPanel();
+
+  JPanel jPanel4 = new JPanel();
+
   BorderLayout borderLayout1 = new BorderLayout();
+
   BorderLayout borderLayout2 = new BorderLayout();
+
+  BorderLayout borderLayout3 = new BorderLayout();
+
   public void close_actionPerformed(ActionEvent e)
   {
     try
     {
       frame.setClosed(true);
+    } catch (Exception ex)
+    {
     }
-    catch (Exception ex)
-    {}
   }
 
   public void ok_actionPerformed()
@@ -199,9 +418,23 @@ extends JPanel implements Runnable
     {
       error += "Please select the source database\n";
     }
-    com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");
+    // TODO: make this transformation more configurable
+    com.stevesoft.pat.Regex empty;
+    if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
+    {
+      empty = new com.stevesoft.pat.Regex(
+      // replace commas and spaces with a semicolon
+              "(\\s|[,; ])+", ";");
+    }
+    else
+    {
+      // just turn spaces and semicolons into single semicolons
+      empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
+    }
     textArea.setText(empty.replaceAll(textArea.getText()));
-    if (textArea.getText().length() == 0)
+    // see if there's anthing to search with
+    if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
+            .getText()))
     {
       error += "Please enter a (semi-colon separated list of) database id(s)";
     }
@@ -211,306 +444,275 @@ extends JPanel implements Runnable
       resetDialog();
       return;
     }
-
-    result = new StringBuffer();
-    if (database.getSelectedItem().equals("Uniprot"))
-    {
-      getUniprotFile(textArea.getText());
-    }
-    else if (database.getSelectedItem().equals("EMBL")
-        || database.getSelectedItem().equals("EMBLCDS"))
+    ArrayList<String> aresultq=new ArrayList<String>();
+    ArrayList<AlignmentI> aresult = new ArrayList<AlignmentI>();
+    Object source = database.getSelectedItem();
+    Enumeration en = new StringTokenizer(textArea.getText(), ";");
+    boolean isAliSource=false;
+    try
     {
-      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())
+      guiWindow.setProgressBar(
+              "Fetching Sequences from " + database.getSelectedItem(),
+              Thread.currentThread().hashCode());
+      DbSourceProxy proxy = sfetch.getSourceProxy((String) sources
+              .get(source));
+      isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
+      if (proxy.getAccessionSeparator() == null)
       {
-        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())
+        while (en.hasMoreElements())
         {
-          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
+          String item = (String) en.nextElement();
+          try
+          {
+            if (aresult != null)
+            {
+              try
+              {
+                // give the server a chance to breathe
+                Thread.sleep(5);
+              } catch (Exception e)
+              {
+                //
               }
-              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++)
+
+            AlignmentI indres = null;
+            try
+            {
+              indres = proxy.getSequenceRecords(item);
+            } catch (OutOfMemoryError oome)
             {
-              newseqs[i] = seqs[i];
-              seqs[i] = null;
+              new OOMWarning("fetching " + item + " from "
+                      + database.getSelectedItem(), oome, this);
             }
-            for (int j=0;j<seqparts.length; i++, j++)
+            if (indres != null)
             {
-              newseqs[i] = seqparts[j];
+              aresultq.add(item);
+              aresult.add(indres);
             }
-            seqs=newseqs;
+          } catch (Exception e)
+          {
+            jalview.bin.Cache.log.info("Error retrieving " + item
+                    + " from " + source, e);
           }
-          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++)
+      else
       {
-        UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
-        Enumeration e = entry.getDbReference().elements();
-        Vector onlyPdbEntries = new Vector();
-        while (e.hasMoreElements())
+        StringBuffer multiacc = new StringBuffer();
+        while (en.hasMoreElements())
         {
-          PDBEntry pdb = (PDBEntry) e.nextElement();
-          if (!pdb.getType().equals("PDB"))
+          multiacc.append(en.nextElement());
+          if (en.hasMoreElements())
           {
-            continue;
+            multiacc.append(proxy.getAccessionSeparator());
           }
-
-          onlyPdbEntries.addElement(pdb);
         }
-
-        Enumeration en2 = entry.getAccession().elements();
-        while (en2.hasMoreElements())
+        try
         {
-          al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(
-              DBRefSource.UNIPROT,
-              "0",
-              en2.nextElement().toString()));
-        }
-
-
-
-
-        al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries);
-        if (entry.getFeature() != null)
+          aresultq.add(multiacc.toString());
+          aresult.add(proxy.getSequenceRecords(multiacc.toString()));
+        } catch (OutOfMemoryError oome)
         {
-          e = entry.getFeature().elements();
-          while (e.hasMoreElements())
-          {
-            SequenceFeature sf = (SequenceFeature) e.nextElement();
-            sf.setFeatureGroup("Uniprot");
-            al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf );
-          }
+          new OOMWarning("fetching " + multiacc + " from "
+                  + database.getSelectedItem(), oome, this);
         }
+
       }
-    }
-  }
 
-  SequenceI[] getPDBFile(String id)
-  {
-    Vector result = new Vector();
-    String chain = null;
-    if (id.indexOf(":") > -1)
+    } catch (Exception e)
     {
-      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)
+      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)
     {
-      return null;
+      showErrorMessage("Serious Error retrieving " + textArea.getText()
+              + " from " + database.getSelectedItem());
+      e.printStackTrace();
     }
-    try
+    if (aresult != null && aresult.size()>0)
     {
-      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))
+      AlignmentI ar=null;
+      if (isAliSource) {
+        // new window for each result
+        while (aresult.size()>0)
         {
-          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());
+          parseResult(aresult.remove(0), aresultq.remove(0)+" "+getDefaultRetrievalTitle(), null);
         }
-      }
-
-      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);
+      } else {
+        // concatenate all results in one window
+        while (aresult.size()>0)
+        {
+          if (ar==null) { ar = aresult.remove(0);}
+          else { ar.append(aresult.remove(0)); };
+        }
+        parseResult(ar, null, null);
+      } 
     }
-    return results;
+    // only remove visual delay after we finished parsing.
+    guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
+    resetDialog();
   }
-  Alignment parseResult(String result, String title)
+
+  /*
+   * 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");
     Alignment sequences = null;
@@ -519,72 +721,99 @@ extends JPanel implements Runnable
       sequences = null;
       try
       {
-        sequences = new FormatAdapter().readFile(result.toString(), "Paste",
-            format);
+        sequences = new FormatAdapter().readFile(result.toString(),
+                "Paste", format);
+      } catch (Exception ex)
+      {
       }
-      catch (Exception ex)
-      {}
 
-      if (sequences!=null)
+      if (sequences != null)
       {
         return parseResult(sequences, title, format);
       }
     }
     else
     {
-      showErrorMessage("Error retrieving " + textArea.getText()
-          + " from " + database.getSelectedItem());
+      showErrorMessage("Error retrieving " + textArea.getText() + " from "
+              + database.getSelectedItem());
     }
 
     return null;
   }
 
-  Alignment parseResult(Alignment al, String title, String currentFileFormat)
+  /**
+   * 
+   * @return a standard title for any results retrieved using the currently selected source and settings
+   */
+  public String getDefaultRetrievalTitle() {
+    return "Retrieved from " + database.getSelectedItem();
+  }
+  AlignmentI parseResult(AlignmentI al, String title,
+          String currentFileFormat)
   {
 
     if (al != null && al.getHeight() > 0)
     {
       if (alignFrame == null)
       {
-        AlignFrame af = new AlignFrame(al,
-            AlignFrame.DEFAULT_WIDTH,
-            AlignFrame.DEFAULT_HEIGHT);
-        if (currentFileFormat!=null)
+        AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+                AlignFrame.DEFAULT_HEIGHT);
+        if (currentFileFormat != null)
         {
-          af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT FORMAT FOR NON-FormatAdapter Sourced Alignments?
+          af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
+          // FORMAT FOR
+          // NON-FormatAdapter Sourced
+          // Alignments?
         }
 
-        if(title==null)
+        if (title == null)
         {
-          title = "Retrieved from " + database.getSelectedItem();
+          title = getDefaultRetrievalTitle();
         }
+        SequenceFeature[] sfs = null;
+        for (Enumeration sq = al.getSequences().elements(); sq
+                .hasMoreElements();)
+        {
+          if ((sfs = ((SequenceI) sq.nextElement()).getDatasetSequence()
+                  .getSequenceFeatures()) != null)
+          {
+            if (sfs.length > 0)
+            {
+              af.setShowSeqFeatures(true);
+              break;
+            }
+          }
 
-        Desktop.addInternalFrame(af,
-            title,
-            AlignFrame.DEFAULT_WIDTH,
-            AlignFrame.DEFAULT_HEIGHT);
+        }
+        Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
+                AlignFrame.DEFAULT_HEIGHT);
 
         af.statusBar.setText("Successfully pasted alignment file");
 
         try
         {
-          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
+                  false));
+        } catch (Exception ex)
+        {
         }
-        catch (Exception ex)
-        {}
       }
       else
       {
         for (int i = 0; i < al.getHeight(); i++)
         {
-          alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this also creates dataset sequence entries
+          alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this
+          // also
+          // creates
+          // dataset
+          // sequence
+          // entries
         }
-        alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.
-            getHeight());
+        alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment
+                .getHeight());
         alignFrame.viewport.alignment.getWidth();
         alignFrame.viewport.firePropertyChange("alignment", null,
-            alignFrame.viewport.
-            getAlignment().getSequences());
+                alignFrame.viewport.getAlignment().getSequences());
       }
     }
     return al;
@@ -597,11 +826,9 @@ extends JPanel implements Runnable
     {
       public void run()
       {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
-            error, "Error Retrieving Data",
-            JOptionPane.WARNING_MESSAGE);
+        JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
+                "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
       }
     });
   }
 }
-