X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=2f92333a679a3e4a76ecd58f1d510b5fa153e303;hb=ea7870f9bf9ae81876afbe3fdd4d9bd9022b4014;hp=f4e289b05f4070d7406cca38c72157bc6a547ee1;hpb=451619e33c0a90c8130c7d79ffa38161af1c6e0f;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index f4e289b..2f92333 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -18,20 +18,29 @@
  */
 package jalview.gui;
 
-import javax.swing.*;
+import java.io.*;
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import jalview.io.EBIFetchClient;
+import javax.swing.*;
+
 import MCview.*;
 import jalview.datamodel.*;
-import jalview.analysis.AlignSeq;
+import jalview.datamodel.xdb.embl.*;
 import java.io.File;
 import jalview.io.*;
-import java.util.*;
+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
+extends JPanel implements Runnable
 {
+  jalview.ws.SequenceFetcher sfetch; 
   JInternalFrame frame;
   AlignFrame alignFrame;
   StringBuffer result;
@@ -39,7 +48,26 @@ public class SequenceFetcher
   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");
@@ -58,33 +86,37 @@ public class SequenceFetcher
     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";
+    return ( (alignFrame == null) ? "New " : "Additional ") +
+    "Sequence Fetcher";
   }
 
   private void jbInit()
-      throws Exception
+  throws Exception
   {
-    this.setLayout(gridBagLayout1);
+    this.setLayout(borderLayout2);
 
     database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    database.setMinimumSize(new Dimension(160, 21));
-    database.setPreferredSize(new Dimension(160, 21));
     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
+    jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
     jLabel1.setText(
-        "Separate multiple accession ids with semi colon \";\"");
+    "Separate multiple accession ids with semi colon \";\"");
     ok.setText("OK");
     ok.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        ok_actionPerformed(e);
+        ok_actionPerformed();
       }
     });
     close.setText("Close");
@@ -95,32 +127,28 @@ public class SequenceFetcher
         close_actionPerformed(e);
       }
     });
-    textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    textfield.addActionListener(new ActionListener()
+    textArea.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    textArea.setLineWrap(true);
+    textArea.addKeyListener(new KeyAdapter()
     {
-      public void actionPerformed(ActionEvent e)
+      public void keyPressed(KeyEvent e)
       {
-        ok_actionPerformed(e);
+        if(e.getKeyCode()==KeyEvent.VK_ENTER)
+          ok_actionPerformed();
       }
     });
+    jPanel3.setLayout(borderLayout1);
+    borderLayout1.setVgap(5);
     jPanel1.add(ok);
     jPanel1.add(close);
-    this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0
-                                             , GridBagConstraints.WEST,
-                                             GridBagConstraints.NONE,
-                                             new Insets(7, 4, 0, 6), 77, 6));
-    this.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0
-                                             , GridBagConstraints.WEST,
-                                             GridBagConstraints.BOTH,
-                                             new Insets(7, -2, 7, 12), 241, -2));
-    this.add(database, new GridBagConstraints(0, 1, 1, 1, 1.0, 0.0
-                                              , GridBagConstraints.WEST,
-                                              GridBagConstraints.NONE,
-                                              new Insets(0, 4, 0, 0), 1, 0));
-    this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
-                                               , GridBagConstraints.CENTER,
-                                               GridBagConstraints.NONE,
-                                               new Insets(0, 0, 0, 6), 211, 1));
+    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();
@@ -128,8 +156,12 @@ public class SequenceFetcher
   JButton ok = new JButton();
   JButton close = new JButton();
   JPanel jPanel1 = new JPanel();
-  JTextField textfield = new JTextField();
-  GridBagLayout gridBagLayout1 = new GridBagLayout();
+  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
@@ -140,10 +172,10 @@ public class SequenceFetcher
     {}
   }
 
-  public void ok_actionPerformed(ActionEvent e)
+  public void ok_actionPerformed()
   {
     database.setEnabled(false);
-    textfield.setEnabled(false);
+    textArea.setEnabled(false);
     ok.setEnabled(false);
     close.setEnabled(false);
 
@@ -154,7 +186,7 @@ public class SequenceFetcher
   private void resetDialog()
   {
     database.setEnabled(true);
-    textfield.setEnabled(true);
+    textArea.setEnabled(true);
     ok.setEnabled(true);
     close.setEnabled(true);
   }
@@ -163,11 +195,15 @@ public class SequenceFetcher
   {
     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+", "");
-    textfield.setText(empty.replaceAll(textfield.getText()));
-    if (textfield.getText().length() == 0)
+    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);
@@ -178,68 +214,133 @@ public class SequenceFetcher
     result = new StringBuffer();
     if (database.getSelectedItem().equals("Uniprot"))
     {
-      getUniprotFile(textfield.getText());
+      getUniprotFile(textArea.getText());
     }
     else if (database.getSelectedItem().equals("EMBL")
-             || database.getSelectedItem().equals("EMBLCDS"))
+        || database.getSelectedItem().equals("EMBLCDS"))
     {
-      StringTokenizer st = new StringTokenizer(textfield.getText(), ";");
+      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[] reply = dbFetch.fetchData(
-            database.getSelectedItem().toString().toLowerCase(
-            ) + ":" + st.nextToken(),
-            "fasta", "raw");
-//
-        if (reply != null)
+        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())
         {
-          for (int i = 0; i < reply.length; i++)
-            result.append(reply[i] + "\n");
+          efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
         }
-      }
-
-      if(result!=null && result.length()>1) // arbitrary minimum length for a seuqence file
-      {
-        System.out.println(result.toString());
+        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;
 
-        parseResult(result.toString(), null);
+            }
+          }
+        } 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(textfield.getText(), ";");
+      StringTokenizer qset = new StringTokenizer(textArea.getText(), ";");
       String query;
+      SequenceI[] seqs = null;
       while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))
       {
-        StringBuffer respart = getPDBFile(query.toUpperCase());
-        if(respart!=null)
-          result.append(respart);
+        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");
+        }
       }
-
-
-      if (result.length()>0)
-        parseResult(result.toString(), null);
     }
     else if( database.getSelectedItem().equals("PFAM"))
     {
-      try{
+      try
+      {
         result.append(new FastaFile(
-           "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="
-           +  textfield.getText().toUpperCase(), "URL").print()
-           );
+            "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(), textfield.getText().toUpperCase() );
+        if(result.length()>0)
+        {
+          parseResult( result.toString(), textArea.getText().toUpperCase() );
+        }
 
-      }catch(java.io.IOException ex)
-      {   result = null;    }
+      }
+      catch (java.io.IOException ex)
+      {
+        result = null;
+      }
     }
 
     if (result == null || result.length() == 0)
-      showErrorMessage("Error retrieving " + textfield.getText()
-                       + " from " + database.getSelectedItem());
+    {
+      showErrorMessage("Error retrieving " + textArea.getText()
+          + " from " + database.getSelectedItem());
+    }
 
     resetDialog();
     return;
@@ -277,16 +378,16 @@ public class SequenceFetcher
 
         if (entry.getProtein() != null)
         {
-           name.append(" " + entry.getProtein().getName().elementAt(0));
+          name.append(" " + entry.getProtein().getName().elementAt(0));
         }
 
         result.append(name + "\n" + entry.getUniprotSequence().getContent() +
-                      "\n");
+        "\n");
 
       }
 
       //Then read in the features and apply them to the dataset
-      SequenceI[] sequence = parseResult(result.toString(), null);
+      Alignment al = parseResult(result.toString(), null);
       for (int i = 0; i < entries.size(); i++)
       {
         UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
@@ -296,7 +397,9 @@ public class SequenceFetcher
         {
           PDBEntry pdb = (PDBEntry) e.nextElement();
           if (!pdb.getType().equals("PDB"))
+          {
             continue;
+          }
 
           onlyPdbEntries.addElement(pdb);
         }
@@ -304,15 +407,16 @@ public class SequenceFetcher
         Enumeration en2 = entry.getAccession().elements();
         while (en2.hasMoreElements())
         {
-          sequence[i].getDatasetSequence().addDBRef(new DBRefEntry(DBRefSource.UNIPROT,
-                    "0",
-                    en2.nextElement().toString()));
+          al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(
+              DBRefSource.UNIPROT,
+              "0",
+              en2.nextElement().toString()));
         }
 
 
 
 
-        sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
+        al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries);
         if (entry.getFeature() != null)
         {
           e = entry.getFeature().elements();
@@ -320,16 +424,16 @@ public class SequenceFetcher
           {
             SequenceFeature sf = (SequenceFeature) e.nextElement();
             sf.setFeatureGroup("Uniprot");
-            sequence[i].getDatasetSequence().addSequenceFeature( sf );
+            al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf );
           }
         }
       }
     }
   }
 
-  StringBuffer getPDBFile(String id)
+  SequenceI[] getPDBFile(String id)
   {
-    StringBuffer result = new StringBuffer();
+    Vector result = new Vector();
     String chain = null;
     if (id.indexOf(":") > -1)
     {
@@ -338,9 +442,12 @@ public class SequenceFetcher
     }
 
     EBIFetchClient ebi = new EBIFetchClient();
-    String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
+    String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").
+    getAbsolutePath();
     if (file == null)
+    {
       return null;
+    }
     try
     {
       PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);
@@ -349,141 +456,137 @@ public class SequenceFetcher
         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());
+        }
+      }
 
-          result.append("\n>PDB|" + id + "|" +
-                        ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
-                        getName() +
-                        "\n"
-                        +
-                        ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
-                        getSequenceAsString());
+      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 " +
-                                 textfield.getText() + " from " +
-                                 database.getSelectedItem(), ex);
+          textArea.getText() + " from " +
+          database.getSelectedItem(), ex);
       return null;
     }
 
-    return result;
-  }
 
-  SequenceI[] parseResult(String result, String title)
+    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");
-    SequenceI[] sequences = null;
-
+    Alignment sequences = null;
     if (FormatAdapter.isValidFormat(format))
     {
       sequences = null;
-      try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",
-                                               format);}
-      catch(Exception ex){}
+      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 (sequences != null && sequences.length > 0)
+    if (al != null && al.getHeight() > 0)
+    {
+      if (alignFrame == null)
       {
-        if (alignFrame == null)
+        AlignFrame af = new AlignFrame(al,
+            AlignFrame.DEFAULT_WIDTH,
+            AlignFrame.DEFAULT_HEIGHT);
+        if (currentFileFormat!=null)
         {
-          AlignFrame af = new AlignFrame(new Alignment(sequences),
-                                           AlignFrame.DEFAULT_WIDTH,
-                                           AlignFrame.DEFAULT_HEIGHT
-);
-          af.currentFileFormat = format;
-          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)
-          {}
+          af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT FORMAT FOR NON-FormatAdapter Sourced Alignments?
         }
-        else
-        {
-          for (int i = 0; i < sequences.length; i++)
-          {
-            alignFrame.viewport.alignment.addSequence(sequences[i]);
-
-            ////////////////////////////
-            //Dataset needs extension;
-            /////////////////////////////
-            Sequence ds = new Sequence(sequences[i].getName(),
-                                       AlignSeq.extractGaps("-. ",
-                sequences[i].getSequenceAsString()),
-                                       sequences[i].getStart(),
-                                       sequences[i].getEnd());
-            sequences[i].setDatasetSequence(ds);
-            alignFrame.viewport.alignment.getDataset().addSequence(ds);
-          }
-          alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.
-                                        getHeight());
-          alignFrame.viewport.alignment.getWidth();
-          alignFrame.viewport.firePropertyChange("alignment", null,
-                                                 alignFrame.viewport.
-                                                 getAlignment().getSequences());
 
+        if(title==null)
+        {
+          title = "Retrieved from " + database.getSelectedItem();
         }
 
-        if (database.getSelectedItem().equals("PDB"))
+        Desktop.addInternalFrame(af,
+            title,
+            AlignFrame.DEFAULT_WIDTH,
+            AlignFrame.DEFAULT_HEIGHT);
+
+        af.statusBar.setText("Successfully pasted alignment file");
+
+        try
         {
-          // Parse out the ids from the structured names
-          boolean errors = false;
-          for (int i = 0; i < sequences.length; i++)
-          {
-            PDBEntry entry = new PDBEntry();
-            com.stevesoft.pat.Regex idbits = new com.stevesoft.pat.Regex(
-                "PDB\\|([0-9A-z]{4})\\|(.)");
-            if (idbits.search(sequences[i].getName()))
-            {
-              String pdbid = idbits.substring(1);
-              String pdbccode = idbits.substring(2);
-              // Construct the PDBEntry
-              entry.setId(pdbid);
-              if (entry.getProperty() == null)
-                entry.setProperty(new Hashtable());
-              entry.getProperty().put("chains",
-                                      pdbccode
-                                      + "=" + sequences[i].getStart()
-                                      + "-" + sequences[i].getEnd());
-              sequences[i].getDatasetSequence().addPDBId(entry);
-
-              // 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",pdbid);
-              sequences[i].getDatasetSequence().addDBRef(dbentry);
-            }
-            else
-            {
-              // don't add an entry for this chain, but this is probably a bug
-              // that the user should know about.
-              jalview.bin.Cache.log.warn(
-                  "No PDBEntry constructed for sequence " + i + " : " +
-                  sequences[i].getName());
-              errors = true;
-            }
-          }
-          if (errors)
-            jalview.bin.Cache.log.warn(
-                "Query string that resulted in PDBEntry construction failure was :\n" +
-                textfield.getText());
+          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
         }
-
+        catch (Exception ex)
+        {}
       }
       else
-        showErrorMessage("Error retrieving " + textfield.getText()
-                         + " from " + database.getSelectedItem());
+      {
+        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 sequences;
-
+    return al;
   }
 
   void showErrorMessage(final String error)
@@ -494,8 +597,8 @@ public class SequenceFetcher
       public void run()
       {
         JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                              error, "Error Retrieving Data",
-                                          JOptionPane.WARNING_MESSAGE);
+            error, "Error Retrieving Data",
+            JOptionPane.WARNING_MESSAGE);
       }
     });
   }