X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=1b1e76577485cab08941e9f966afa91616b4ae02;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=4d21506d49b0ca2d488e3ac4ab644b9412b084bc;hpb=9749ae4861ba174e80afe4de8bd2dd039e5334ba;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 4d21506..1b1e765 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,582 +1,915 @@
-/*
- * 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
- */
-package jalview.gui;
-
-import java.io.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import MCview.*;
-import jalview.datamodel.*;
-import jalview.datamodel.xdb.embl.*;
-import java.io.File;
-import jalview.io.*;
-import java.awt.Rectangle;
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-
-public class SequenceFetcher
-extends JPanel implements Runnable
-{
-  JInternalFrame frame;
-  AlignFrame alignFrame;
-  StringBuffer result;
-  final String noDbSelected = "-- Select Database --";
-  public SequenceFetcher(AlignFrame af)
-  {
-    alignFrame = af;
-    database.addItem(noDbSelected);
-    database.addItem("Uniprot");
-    database.addItem("EMBL");
-    database.addItem("EMBLCDS");
-    database.addItem("PDB");
-    database.addItem("PFAM");
-
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-
-    frame = new JInternalFrame();
-    frame.setContentPane(this);
-    if (System.getProperty("os.name").startsWith("Mac"))
-    {
-      Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);
-    }
-    else
-    {
-      Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);
-    }
-  }
-
-  private String getFrameTitle()
-  {
-    return ( (alignFrame == null) ? "New " : "Additional ") +
-    "Sequence Fetcher";
-  }
-
-  private void jbInit()
-  throws Exception
-  {
-    this.setLayout(borderLayout2);
-
-    database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
-    jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
-    jLabel1.setText(
-    "Separate multiple accession ids with semi colon \";\"");
-    ok.setText("OK");
-    ok.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        ok_actionPerformed();
-      }
-    });
-    close.setText("Close");
-    close.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        close_actionPerformed(e);
-      }
-    });
-    textArea.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    textArea.setLineWrap(true);
-    textArea.addKeyListener(new KeyAdapter()
-    {
-      public void keyPressed(KeyEvent e)
-      {
-        System.out.println(e.getKeyCode()+" "+KeyEvent.VK_ENTER);
-        if(e.getKeyCode()==KeyEvent.VK_ENTER)
-          ok_actionPerformed();
-      }
-    });
-    jPanel3.setLayout(borderLayout1);
-    borderLayout1.setVgap(5);
-    jPanel1.add(ok);
-    jPanel1.add(close);
-    jPanel3.add(jPanel2, java.awt.BorderLayout.WEST);
-    jPanel2.add(database);
-    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);
-    jScrollPane1.getViewport().add(textArea);
-
-  }
-
-  JComboBox database = new JComboBox();
-  JLabel jLabel1 = new JLabel();
-  JButton ok = 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();
-  BorderLayout borderLayout1 = new BorderLayout();
-  BorderLayout borderLayout2 = new BorderLayout();
-  public void close_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      frame.setClosed(true);
-    }
-    catch (Exception ex)
-    {}
-  }
-
-  public void ok_actionPerformed()
-  {
-    database.setEnabled(false);
-    textArea.setEnabled(false);
-    ok.setEnabled(false);
-    close.setEnabled(false);
-
-    Thread worker = new Thread(this);
-    worker.start();
-  }
-
-  private void resetDialog()
-  {
-    database.setEnabled(true);
-    textArea.setEnabled(true);
-    ok.setEnabled(true);
-    close.setEnabled(true);
-  }
-
-  public void run()
-  {
-    String error = "";
-    if (database.getSelectedItem().equals(noDbSelected))
-    {
-      error += "Please select the source database\n";
-    }
-    com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");
-    textArea.setText(empty.replaceAll(textArea.getText()));
-    if (textArea.getText().length() == 0)
-    {
-      error += "Please enter a (semi-colon separated list of) database id(s)";
-    }
-    if (error.length() > 0)
-    {
-      showErrorMessage(error);
-      resetDialog();
-      return;
-    }
-
-    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();
-
-        File reply = dbFetch.fetchDataAsFile(
-            database.getSelectedItem().toString().toLowerCase(
-            ) + ":" + st.nextToken(),
-            "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=null;
-        }
-      }
-      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;
-  }
-  Alignment parseResult(String result, String title)
-  {
-    String format = new IdentifyFile().Identify(result, "Paste");
-    Alignment sequences = null;
-    if (FormatAdapter.isValidFormat(format))
-    {
-      sequences = null;
-      try
-      {
-        sequences = new FormatAdapter().readFile(result.toString(), "Paste",
-            format);
-      }
-      catch (Exception ex)
-      {}
-
-      if (sequences!=null)
-      {
-        return parseResult(sequences, title, format);
-      }
-    }
-    else
-    {
-      showErrorMessage("Error retrieving " + textArea.getText()
-          + " from " + database.getSelectedItem());
-    }
-
-    return null;
-  }
-
-  Alignment parseResult(Alignment 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)
-        {
-          af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT FORMAT FOR NON-FormatAdapter Sourced Alignments?
-        }
-
-        if(title==null)
-        {
-          title = "Retrieved from " + database.getSelectedItem();
-        }
-
-        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));
-        }
-        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.setEndSeq(alignFrame.viewport.alignment.
-            getHeight());
-        alignFrame.viewport.alignment.getWidth();
-        alignFrame.viewport.firePropertyChange("alignment", null,
-            alignFrame.viewport.
-            getAlignment().getSequences());
-      }
-    }
-    return al;
-  }
-
-  void showErrorMessage(final String error)
-  {
-    resetDialog();
-    javax.swing.SwingUtilities.invokeLater(new Runnable()
-    {
-      public void run()
-      {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
-            error, "Error Retrieving Data",
-            JOptionPane.WARNING_MESSAGE);
-      }
-    });
-  }
-}
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.SwingConstants;
+import javax.swing.tree.DefaultMutableTreeNode;
+
+import com.stevesoft.pat.Regex;
+
+public class SequenceFetcher extends JPanel implements Runnable
+{
+  JLabel dbeg = new JLabel();
+
+  JDatabaseTree database;
+
+  JButton databaseButt;
+
+  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();
+
+  JInternalFrame frame;
+
+  IProgressIndicator guiWindow;
+
+  AlignFrame alignFrame;
+
+  StringBuffer result;
+
+  final String noDbSelected = "-- Select Database --";
+
+  private static jalview.ws.SequenceFetcher sfetch = null;
+
+  private static long lastDasSourceRegistry = -3;
+
+  private static DasSourceRegistryI dasRegistry = null;
+
+  private static boolean _initingFetcher = false;
+
+  private static Thread initingThread = null;
+
+  int debounceTrap = 0;
+
+  /**
+   * 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)
+  {
+    if (_initingFetcher && initingThread != null && initingThread.isAlive())
+    {
+      if (guiWindow != null)
+      {
+        guiWindow
+                .setProgressBar(
+                        MessageManager
+                                .getString("status.waiting_sequence_database_fetchers_init"),
+                        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(
+                        MessageManager
+                                .getString("status.waiting_sequence_database_fetchers_init"),
+                        Thread.currentThread().hashCode());
+      }
+    }
+    if (sfetch == null
+            || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
+            || lastDasSourceRegistry != (jalview.bin.Cache
+                    .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
+                    .getDasSourceRegistry().getLocalSourceString())
+                    .hashCode())
+    {
+      _initingFetcher = true;
+      initingThread = Thread.currentThread();
+      /**
+       * give a visual indication that sequence fetcher construction is occuring
+       */
+      if (guiWindow != null)
+      {
+        guiWindow.setProgressBar(MessageManager
+                .getString("status.init_sequence_database_fetchers"),
+                Thread.currentThread().hashCode());
+      }
+      dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
+      dasRegistry.refreshSources();
+
+      jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
+      if (guiWindow != null)
+      {
+        guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
+      }
+      lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
+              .getLocalSourceString()).hashCode();
+      sfetch = sf;
+      _initingFetcher = false;
+      initingThread = null;
+    }
+    return sfetch;
+  }
+
+  private IProgressIndicator progressIndicator;
+
+  public SequenceFetcher(IProgressIndicator guiIndic)
+  {
+    this.progressIndicator = guiIndic;
+    final SequenceFetcher us = this;
+    // launch initialiser thread
+    Thread sf = new Thread(new Runnable()
+    {
+
+      @Override
+      public void run()
+      {
+        if (getSequenceFetcherSingleton(progressIndicator) != null)
+        {
+          us.initGui(progressIndicator);
+        }
+        else
+        {
+          javax.swing.SwingUtilities.invokeLater(new Runnable()
+          {
+            @Override
+            public void run()
+            {
+              JOptionPane
+                      .showInternalMessageDialog(
+                              Desktop.desktop,
+                              MessageManager
+                                      .getString("warn.couldnt_create_sequence_fetcher_client"),
+                              MessageManager
+                                      .getString("label.couldnt_create_sequence_fetcher"),
+                              JOptionPane.ERROR_MESSAGE);
+            }
+          });
+
+          // raise warning dialog
+        }
+      }
+    });
+    sf.start();
+  }
+
+  private class DatabaseAuthority extends DefaultMutableTreeNode
+  {
+
+  };
+
+  private class DatabaseSource extends DefaultMutableTreeNode
+  {
+
+  };
+
+  /**
+   * called by thread spawned by constructor
+   * 
+   * @param guiWindow
+   */
+  private void initGui(IProgressIndicator guiWindow)
+  {
+    this.guiWindow = guiWindow;
+    if (guiWindow instanceof AlignFrame)
+    {
+      alignFrame = (AlignFrame) guiWindow;
+    }
+    database = new JDatabaseTree(sfetch);
+    try
+    {
+      jbInit();
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    if (new jalview.util.Platform().isAMac())
+    {
+      Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
+    }
+    else
+    {
+      Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
+    }
+  }
+
+  private String getFrameTitle()
+  {
+    return ((alignFrame == null) ? MessageManager
+            .getString("label.new_sequence_fetcher") : MessageManager
+            .getString("label.additional_sequence_fetcher"));
+  }
+
+  private void jbInit() throws Exception
+  {
+    this.setLayout(borderLayout2);
+
+    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(MessageManager
+            .getString("label.separate_multiple_accession_ids"));
+
+    replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
+    replacePunctuation
+            .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
+    replacePunctuation.setText(MessageManager
+            .getString("label.replace_commas_semicolons"));
+    ok.setText(MessageManager.getString("action.ok"));
+    ok.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        ok_actionPerformed();
+      }
+    });
+    clear.setText(MessageManager.getString("action.clear"));
+    clear.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        clear_actionPerformed();
+      }
+    });
+
+    example.setText(MessageManager.getString("label.example"));
+    example.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        example_actionPerformed();
+      }
+    });
+    close.setText(MessageManager.getString("action.close"));
+    close.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        close_actionPerformed(e);
+      }
+    });
+    textArea.setFont(JvSwingUtils.getLabelFont());
+    textArea.setLineWrap(true);
+    textArea.addKeyListener(new KeyAdapter()
+    {
+      @Override
+      public void keyPressed(KeyEvent e)
+      {
+        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.CENTER);
+    jPanel2.setLayout(borderLayout3);
+    databaseButt = database.getDatabaseSelectorButton();
+    databaseButt.setFont(JvSwingUtils.getLabelFont());
+    database.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        debounceTrap++;
+        String currentSelection = database.getSelectedItem();
+        if (!currentSelection.equalsIgnoreCase("pdb"))
+        {
+          otherSourceAction();
+        }
+        if (currentSelection.equalsIgnoreCase("pdb")
+                && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
+        {
+          pdbSourceAction();
+        }
+        database.action = -1;
+      }
+    });
+
+    dbeg.setText("");
+    jPanel2.add(databaseButt, 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);
+    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);
+
+  }
+
+  private void pdbSourceAction()
+  {
+    databaseButt.setText(database.getSelectedItem());
+    new PDBSearchPanel(this);
+    frame.dispose();
+  }
+
+  private void otherSourceAction()
+  {
+    try
+    {
+      databaseButt.setText(database.getSelectedItem()
+              + (database.getSelectedSources().size() > 1 ? " (and "
+                      + database.getSelectedSources().size() + " others)"
+                      : ""));
+      String eq = database.getExampleQueries();
+      dbeg.setText(MessageManager.formatMessage(
+              "label.example_query_param", new String[] { eq }));
+      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("");
+      replacePunctuation.setEnabled(true);
+    }
+    jPanel2.repaint();
+  }
+
+  protected void example_actionPerformed()
+  {
+    DbSourceProxy db = null;
+    try
+    {
+      textArea.setText(database.getExampleQueries());
+    } catch (Exception ex)
+    {
+    }
+    jPanel3.repaint();
+  }
+
+  protected void clear_actionPerformed()
+  {
+    textArea.setText("");
+    jPanel3.repaint();
+  }
+
+  public void close_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      frame.setClosed(true);
+    } catch (Exception ex)
+    {
+    }
+  }
+
+  public void ok_actionPerformed()
+  {
+    databaseButt.setEnabled(false);
+    example.setEnabled(false);
+    textArea.setEnabled(false);
+    ok.setEnabled(false);
+    close.setEnabled(false);
+
+    Thread worker = new Thread(this);
+    worker.start();
+  }
+
+  private void resetDialog()
+  {
+    databaseButt.setEnabled(true);
+    example.setEnabled(true);
+    textArea.setEnabled(true);
+    ok.setEnabled(true);
+    close.setEnabled(true);
+  }
+
+  @Override
+  public void run()
+  {
+    String error = "";
+    if (!database.hasSelection())
+    {
+      error += "Please select the source database\n";
+    }
+    // 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()));
+    // 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)";
+    }
+    if (error.length() > 0)
+    {
+      showErrorMessage(error);
+      resetDialog();
+      return;
+    }
+    // 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
+      {
+        // update status
+        guiWindow
+                .setProgressBar(MessageManager.formatMessage(
+                        "status.fetching_sequence_queries_from",
+                        new String[] {
+                            Integer.valueOf(nqueries).toString(),
+                            proxy.getDbName() }), Thread.currentThread()
+                        .hashCode());
+        isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
+        if (proxy.getAccessionSeparator() == null)
+        {
+          while (en.hasNext())
+          {
+            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
+              {
+                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);
+            }
+          }
+        }
+        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())
+            {
+              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)
+            {
+              // no results - pass on all queries to next source
+              nextfetch.addAll(tosend);
+            }
+            else
+            {
+              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());
+                dbr.setVersion(null);
+                if (proxy.getAccessionValidator() != null)
+                {
+                  Regex vgr = proxy.getAccessionValidator();
+                  vgr.search(q);
+                  if (vgr.numSubs() > 0)
+                  {
+                    dbr.setAccessionId(vgr.stringMatched(1));
+                  }
+                  else
+                  {
+                    dbr.setAccessionId(vgr.stringMatched());
+                  }
+                }
+                else
+                {
+                  dbr.setAccessionId(q);
+                }
+                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 (OutOfMemoryError oome)
+          {
+            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();
+      }
+      // Stack results ready for opening in alignment windows
+      if (aresult != null && aresult.size() > 0)
+      {
+        AlignmentI ar = null;
+        if (isAliSource)
+        {
+          addToLast = false;
+          // new window for each result
+          while (aresult.size() > 0)
+          {
+            presult.add(aresult.remove(0));
+            presultTitle.add(aresultq.remove(0) + " "
+                    + getDefaultRetrievalTitle());
+          }
+        }
+        else
+        {
+          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);
+        }
+      }
+      guiWindow.setProgressBar(MessageManager
+              .getString("status.finshed_querying"), Thread.currentThread()
+              .hashCode());
+    }
+    guiWindow.setProgressBar(
+            (presult.size() > 0) ? MessageManager
+                    .getString("status.parsing_results") : MessageManager
+                    .getString("status.processing"), Thread.currentThread()
+                    .hashCode());
+    // process results
+    while (presult.size() > 0)
+    {
+      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)
+      {
+        if (l != sb.length())
+        {
+          sb.append("; ");
+        }
+        if (lr - sb.length() > 40)
+        {
+          sb.append("\n");
+        }
+        sb.append(s);
+      }
+      showErrorMessage(sb.toString());
+    }
+    resetDialog();
+  }
+
+  AlignmentI parseResult(String result, String title)
+  {
+    String format = new IdentifyFile().Identify(result, "Paste");
+    AlignmentI sequences = null;
+    if (FormatAdapter.isValidFormat(format))
+    {
+      sequences = null;
+      try
+      {
+        sequences = new FormatAdapter().readFile(result.toString(),
+                "Paste", format);
+      } catch (Exception ex)
+      {
+      }
+
+      if (sequences != null)
+      {
+        return parseResult(sequences, title, format);
+      }
+    }
+    else
+    {
+      showErrorMessage("Error retrieving " + textArea.getText() + " from "
+              + database.getSelectedItem());
+    }
+
+    return null;
+  }
+
+  /**
+   * 
+   * @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 (title == null)
+      {
+        title = getDefaultRetrievalTitle();
+      }
+      if (alignFrame == 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?
+        }
+
+        SequenceFeature[] sfs = null;
+        List<SequenceI> alsqs;
+        synchronized (alsqs = al.getSequences())
+        {
+          for (SequenceI sq : alsqs)
+          {
+            if ((sfs = sq.getSequenceFeatures()) != null)
+            {
+              if (sfs.length > 0)
+              {
+                af.setShowSeqFeatures(true);
+                break;
+              }
+            }
+
+          }
+        }
+        Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
+                AlignFrame.DEFAULT_HEIGHT);
+
+        af.statusBar.setText(MessageManager
+                .getString("label.successfully_pasted_alignment_file"));
+
+        try
+        {
+          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
+                  false));
+        } catch (Exception ex)
+        {
+        }
+      }
+      else
+      {
+        alignFrame.viewport.addAlignment(al, title);
+      }
+    }
+    return al;
+  }
+
+  void showErrorMessage(final String error)
+  {
+    resetDialog();
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
+                MessageManager.getString("label.error_retrieving_data"),
+                JOptionPane.WARNING_MESSAGE);
+      }
+    });
+  }
+
+  public IProgressIndicator getProgressIndicator()
+  {
+    return progressIndicator;
+  }
+
+  public void setProgressIndicator(IProgressIndicator progressIndicator)
+  {
+    this.progressIndicator = progressIndicator;
+  }
+}