From: jprocter <Jim Procter>
Date: Tue, 5 Aug 2008 14:51:23 +0000 (+0000)
Subject: ensure das sequence sources are refreshed when das registry is changed
X-Git-Tag: Release_2_4~63
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3b24654f2ada868e8a3771427cc9b180f78f2020;p=jalview.git

ensure das sequence sources are refreshed when das registry is changed
---

diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
index e695d3d..807aa4b 100755
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -46,8 +46,7 @@ public class DasSourceBrowser
    * true if thread is running and we are talking to DAS registry service
    */
   public boolean loadingDasSources = false;
-
-  public DasSourceBrowser()
+  protected static String getDasRegistryURL()
   {
     String registry = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
         DEFAULT_REGISTRY);
@@ -57,7 +56,12 @@ public class DasSourceBrowser
       jalview.bin.Cache.setProperty("DAS_REGISTRY_URL", DEFAULT_REGISTRY);
       registry = DEFAULT_REGISTRY;
     }
-
+    return registry;
+  }
+  public DasSourceBrowser()
+  {
+    String registry = getDasRegistryURL();
+    
     registryURL.setText(registry);
 
     setSelectedFromProperties();
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index a66ec2f..c82f383 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -40,73 +40,90 @@ 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 --";
+
   Hashtable sources = new Hashtable();
-  private static jalview.ws.SequenceFetcher sfetch=null;
+
+  private static jalview.ws.SequenceFetcher sfetch = null;
+
+  private static String dasRegistry = null;
+
   public SequenceFetcher(IProgressIndicator guiIndic)
   {
-      final IProgressIndicator guiWindow = guiIndic;
-      final SequenceFetcher us = this;
-      // launch initialiser thread
-      Thread sf = new Thread(new Runnable() {
+    final IProgressIndicator guiWindow = guiIndic;
+    final SequenceFetcher us = this;
+    // launch initialiser thread
+    Thread sf = new Thread(new Runnable()
+    {
 
-        public void run()
+      public void run()
+      {
+        if (sfetch == null
+                || dasRegistry != DasSourceBrowser.getDasRegistryURL())
         {
-          if (sfetch==null)
-          {
-            /**
-           * give a visual indication that sequence fetcher construction is occuring
+          /**
+           * give a visual indication that sequence fetcher construction is
+           * occuring
            */
-          if ( guiWindow!=null )
-            {
-              guiWindow.setProgressBar("Initialising Sequence Database Fetchers", this.hashCode());
-            }
-            jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
-            if ( guiWindow!=null )
-            {
-              guiWindow.setProgressBar("Initialising Sequence Database Fetchers", this.hashCode());
-            }
-            sfetch = sf;
-            
+          if (guiWindow != null)
+          {
+            guiWindow.setProgressBar(
+                    "Initialising Sequence Database Fetchers", this
+                            .hashCode());
           }
-          us.initGui(guiWindow);
+          dasRegistry = DasSourceBrowser.getDasRegistryURL();
+          jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
+          if (guiWindow != null)
+          {
+            guiWindow.setProgressBar(
+                    "Initialising Sequence Database Fetchers", this
+                            .hashCode());
+          }
+          sfetch = sf;
+
         }
-      });
-      sf.start();
+        us.initGui(guiWindow);
+      }
+    });
+    sf.start();
   }
+
   /**
    * called by thread spawned by constructor
+   * 
    * @param guiWindow
    */
-  private void initGui(IProgressIndicator 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. 
+     * 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++)
+    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))
@@ -114,14 +131,13 @@ extends JPanel implements Runnable
           database.addItem(name);
         }
         // overwrite with latest version of the retriever for this source
-        sources.put(name, dbs[i]);        
+        sources.put(name, dbs[i]);
       }
     }
     try
     {
       jbInit();
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
     }
@@ -140,12 +156,11 @@ extends JPanel implements Runnable
 
   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);
 
@@ -153,8 +168,8 @@ extends JPanel implements Runnable
     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 \";\"");
     ok.setText("OK");
     ok.addActionListener(new ActionListener()
     {
@@ -194,7 +209,7 @@ extends JPanel implements Runnable
     {
       public void keyPressed(KeyEvent e)
       {
-        if(e.getKeyCode()==KeyEvent.VK_ENTER)
+        if (e.getKeyCode() == KeyEvent.VK_ENTER)
           ok_actionPerformed();
       }
     });
@@ -206,15 +221,18 @@ extends JPanel implements Runnable
     jPanel1.add(close);
     jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
     jPanel2.setLayout(borderLayout3);
-    
-    database.addActionListener(new ActionListener() {
+
+    database.addActionListener(new ActionListener()
+    {
 
       public void actionPerformed(ActionEvent e)
       {
-        DbSourceProxy db=null;
-        try {
-          db = sfetch.getSourceProxy((String)sources.get(database.getSelectedItem()));
-          dbeg.setText("Example query: "+db.getTestQuery());
+        DbSourceProxy db = null;
+        try
+        {
+          db = sfetch.getSourceProxy((String) sources.get(database
+                  .getSelectedItem()));
+          dbeg.setText("Example query: " + db.getTestQuery());
         } catch (Exception ex)
         {
           dbeg.setText("");
@@ -230,16 +248,18 @@ extends JPanel implements Runnable
     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);
+    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()));
+    DbSourceProxy db = null;
+    try
+    {
+      db = sfetch.getSourceProxy((String) sources.get(database
+              .getSelectedItem()));
       textArea.setText(db.getTestQuery());
     } catch (Exception ex)
     {
@@ -252,31 +272,47 @@ extends JPanel implements Runnable
     textArea.setText("");
     jPanel3.repaint();
   }
+
   JLabel dbeg = new JLabel();
+
   JComboBox database = new JComboBox();
+
   JLabel jLabel1 = new JLabel();
+
   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()
@@ -317,339 +353,189 @@ extends JPanel implements Runnable
       resetDialog();
       return;
     }
-    AlignmentI aresult=null;
-    try {
-      guiWindow.setProgressBar("Fetching Sequences from "+database.getSelectedItem(), Thread.currentThread().hashCode());
-      aresult = sfetch.getSourceProxy((String)sources.get(database.getSelectedItem()))
-      .getSequenceRecords(textArea.getText());
-      
-    }
-    catch (Exception e)
+    AlignmentI aresult = null;
+    try
     {
-      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");
+      guiWindow.setProgressBar("Fetching Sequences from "
+              + database.getSelectedItem(), Thread.currentThread()
+              .hashCode());
+      aresult = sfetch.getSourceProxy(
+              (String) sources.get(database.getSelectedItem()))
+              .getSequenceRecords(textArea.getText());
+
+    } 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)
+    } catch (OutOfMemoryError e)
     {
-      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");
+      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)
+    } catch (Error e)
     {
       showErrorMessage("Serious Error retrieving " + textArea.getText()
               + " from " + database.getSelectedItem());
       e.printStackTrace();
     }
     guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
-    if (aresult!=null)
+    if (aresult != null)
     {
       parseResult(aresult, null, null);
     }
     resetDialog();
   }
-    /*
-    result = new StringBuffer();
-    if (database.getSelectedItem().equals("Uniprot"))
-    {
-      getUniprotFile(textArea.getText());
-    }
-    else if (database.getSelectedItem().equals("EMBL")
-        || database.getSelectedItem().equals("EMBLCDS"))
-    {
-      String DBRefSource = database.getSelectedItem().equals("EMBLCDS")
-      ? jalview.datamodel.DBRefSource.EMBLCDS
-          : jalview.datamodel.DBRefSource.EMBL;
 
-      StringTokenizer st = new StringTokenizer(textArea.getText(), ";");
-      SequenceI[] seqs = null;
-      while(st.hasMoreTokens())
-      {
-        EBIFetchClient dbFetch = new EBIFetchClient();
-        String qry = database.getSelectedItem().toString().toLowerCase(
-        ) + ":" + st.nextToken();
-        File reply = dbFetch.fetchDataAsFile(
-            qry,
-            "emblxml",null);
-
-        jalview.datamodel.xdb.embl.EmblFile efile=null;
-        if (reply != null && reply.exists())
-        {
-          efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
-        }
-        if (efile!=null) {
-          for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) {
-            EmblEntry entry = (EmblEntry) i.next();
-            SequenceI[] seqparts = entry.getSequences(false,true, DBRefSource);
-            if (seqparts!=null) {
-              SequenceI[] newseqs = null;
-              int si=0;
-              if (seqs==null) {
-                newseqs = new SequenceI[seqparts.length];
-              } else {
-                newseqs  = new SequenceI[seqs.length+seqparts.length];
-
-                for (;si<seqs.length; si++) {
-                  newseqs[si] = seqs[si];
-                  seqs[si] = null;
-                }
-              }
-              for (int j=0;j<seqparts.length; si++, j++) {
-                newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on dataset and refer
-              }
-              seqs=newseqs;
-
-            }
-          }
-        } else {
-          result.append("# no response for "+qry);
-        }
-      }
-      if (seqs!=null && seqs.length>0) {
-        if (parseResult(new Alignment(seqs), null, null)!=null)
-        {
-            result.append("# Successfully parsed the "+database.getSelectedItem()+" Queries into an Alignment");
-        }
-      }
-    }
-    else if (database.getSelectedItem().equals("PDB"))
-    {
-      StringTokenizer qset = new StringTokenizer(textArea.getText(), ";");
-      String query;
-      SequenceI[] seqs = null;
-      while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))
-      {
-        SequenceI[] seqparts = getPDBFile(query.toUpperCase());
-        if (seqparts != null)
-        {
-          if (seqs == null)
-          {
-            seqs = seqparts;
-          }
-          else
-          {
-            SequenceI[] newseqs = new SequenceI[seqs.length+seqparts.length];
-            int i=0;
-            for (; i < seqs.length; i++)
-            {
-              newseqs[i] = seqs[i];
-              seqs[i] = null;
-            }
-            for (int j=0;j<seqparts.length; i++, j++)
-            {
-              newseqs[i] = seqparts[j];
-            }
-            seqs=newseqs;
-          }
-          result.append("# Success for "+query.toUpperCase()+"\n");
-        }
-      }
-      if (seqs != null && seqs.length > 0)
-      {
-        if (parseResult(new Alignment(seqs), null, null)!=null)
-        {
-          result.append(
-          "# Successfully parsed the PDB File Queries into an Alignment");
-        }
-      }
-    }
-    else if( database.getSelectedItem().equals("PFAM"))
-    {
-      try
-      {
-        result.append(new FastaFile(
-            "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="
-            +  textArea.getText().toUpperCase(), "URL").print()
-        );
-
-        if(result.length()>0)
-        {
-          parseResult( result.toString(), textArea.getText().toUpperCase() );
-        }
-
-      }
-      catch (java.io.IOException ex)
-      {
-        result = null;
-      }
-    }
-
-    if (result == null || result.length() == 0)
-    {
-      showErrorMessage("Error retrieving " + textArea.getText()
-          + " from " + database.getSelectedItem());
-    }
-
-    resetDialog();
-    return;
-  }
-
-  void getUniprotFile(String id)
-  {
-    EBIFetchClient ebi = new EBIFetchClient();
-    File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
-
-    DBRefFetcher dbref = new DBRefFetcher();
-    Vector entries = dbref.getUniprotEntries(file);
-
-    if (entries != null)
-    {
-      //First, make the new sequences
-      Enumeration en = entries.elements();
-      while (en.hasMoreElements())
-      {
-        UniprotEntry entry = (UniprotEntry) en.nextElement();
-
-        StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");
-        Enumeration en2 = entry.getAccession().elements();
-        while (en2.hasMoreElements())
-        {
-          name.append("|");
-          name.append(en2.nextElement());
-        }
-        en2 = entry.getName().elements();
-        while (en2.hasMoreElements())
-        {
-          name.append("|");
-          name.append(en2.nextElement());
-        }
-
-        if (entry.getProtein() != null)
-        {
-          name.append(" " + entry.getProtein().getName().elementAt(0));
-        }
-
-        result.append(name + "\n" + entry.getUniprotSequence().getContent() +
-        "\n");
-
-      }
-
-      //Then read in the features and apply them to the dataset
-      Alignment al = parseResult(result.toString(), null);
-      for (int i = 0; i < entries.size(); i++)
-      {
-        UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
-        Enumeration e = entry.getDbReference().elements();
-        Vector onlyPdbEntries = new Vector();
-        while (e.hasMoreElements())
-        {
-          PDBEntry pdb = (PDBEntry) e.nextElement();
-          if (!pdb.getType().equals("PDB"))
-          {
-            continue;
-          }
-
-          onlyPdbEntries.addElement(pdb);
-        }
-
-        Enumeration en2 = entry.getAccession().elements();
-        while (en2.hasMoreElements())
-        {
-          al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(
-              DBRefSource.UNIPROT,
-              "0",
-              en2.nextElement().toString()));
-        }
-
-
-
-
-        al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries);
-        if (entry.getFeature() != null)
-        {
-          e = entry.getFeature().elements();
-          while (e.hasMoreElements())
-          {
-            SequenceFeature sf = (SequenceFeature) e.nextElement();
-            sf.setFeatureGroup("Uniprot");
-            al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf );
-          }
-        }
-      }
-    }
-  }
-
-  SequenceI[] getPDBFile(String id)
-  {
-    Vector result = new Vector();
-    String chain = null;
-    if (id.indexOf(":") > -1)
-    {
-      chain = id.substring(id.indexOf(":") + 1);
-      id = id.substring(0, id.indexOf(":"));
-    }
-
-    EBIFetchClient ebi = new EBIFetchClient();
-    String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").
-    getAbsolutePath();
-    if (file == null)
-    {
-      return null;
-    }
-    try
-    {
-      PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);
-      for (int i = 0; i < pdbfile.chains.size(); i++)
-      {
-        if (chain == null ||
-            ( (PDBChain) pdbfile.chains.elementAt(i)).id.
-            toUpperCase().equals(chain))
-        {
-          PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);
-          // Get the Chain's Sequence - who's dataset includes any special features added from the PDB file
-          SequenceI sq = pdbchain.sequence;
-          // Specially formatted name for the PDB chain sequences retrieved from the PDB
-          sq.setName("PDB|"+id+"|"+sq.getName());
-          // Might need to add more metadata to the PDBEntry object
-          // like below
-          /*
-           * PDBEntry entry = new PDBEntry();
-            // Construct the PDBEntry
-            entry.setId(id);
-            if (entry.getProperty() == null)
-                entry.setProperty(new Hashtable());
-            entry.getProperty().put("chains",
-                        pdbchain.id
-                        + "=" + sq.getStart()
-                        + "-" + sq.getEnd());
-            sq.getDatasetSequence().addPDBId(entry);
-           *
-          // Add PDB DB Refs
-          // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source
-          // JBPNote - PDB DBRefEntry should also carry the chain and mapping information
-          DBRefEntry dbentry = new DBRefEntry(jalview.datamodel.DBRefSource.PDB,
-              "0", id + pdbchain.id);
-          sq.addDBRef(dbentry);
-          // and add seuqence to the retrieved set
-          result.addElement(sq.deriveSequence());
-        }
-      }
-
-      if (result.size() < 1)
-      {
-        throw new Exception("WsDBFetch for PDB id resulted in zero result size");
-      }
-    }
-    catch (Exception ex) // Problem parsing PDB file
-    {
-      jalview.bin.Cache.log.warn("Exception when retrieving " +
-          textArea.getText() + " from " +
-          database.getSelectedItem(), ex);
-      return null;
-    }
-
-
-    SequenceI[] results = new SequenceI[result.size()];
-    for (int i = 0, j = result.size(); i < j; i++)
-    {
-      results[i] = (SequenceI) result.elementAt(i);
-      result.setElementAt(null,i);
-    }
-    return results; 
-  }*/
+  /*
+   * 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");
@@ -659,72 +545,78 @@ 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;
   }
 
-  AlignmentI parseResult(AlignmentI al, String title, String currentFileFormat)
+  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();
         }
 
-        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;
@@ -737,11 +629,9 @@ 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);
       }
     });
   }
 }
-