X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=10e1b5999f10614cc1cba4374768b2ff6eb1b1c0;hb=40ecea964afaaf404465d75873ec915b901117a3;hp=989227bbca69577a400bb543d699baaf86929e89;hpb=12ce4678159da9497740a02b4790d962c7625cbd;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 989227b..10e1b59 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,581 +1,604 @@
-/*
- * 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)
-      {
-        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
+ * 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 jalview.ws.DBRefFetcher;
+import jalview.ws.EBIFetchClient;
+
+import java.awt.Rectangle;
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+
+public class SequenceFetcher
+extends JPanel implements Runnable
+{
+  jalview.ws.SequenceFetcher sfetch; 
+  JInternalFrame frame;
+  AlignFrame alignFrame;
+  StringBuffer result;
+  final String noDbSelected = "-- Select Database --";
+  public SequenceFetcher(AlignFrame af)
+  {
+    alignFrame = af;
+    sfetch = new jalview.ws.SequenceFetcher();
+    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");
+
+    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)
+      {
+        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);
+      }
+    });
+  }
+}
+