X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=fc8f042fcdce14a099f219c02b3101b12d5f107a;hb=e651bfd6da43bae19e157d6fdf1efbb484acda76;hp=65145cc79898274c8380f59876852e24490d868d;hpb=7854b5718c659c3768b738f0211bf27e604cf3ff;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 65145cc..fc8f042 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -44,6 +44,7 @@ public class SequenceFetcher
     database.addItem("EMBL");
     database.addItem("EMBLCDS");
     database.addItem("PDB");
+    database.addItem("PFAM");
 
     try
     {
@@ -64,8 +65,7 @@ public class SequenceFetcher
 
   private String getFrameTitle()
   {
-    return ( (alignFrame == null) ? "New " : "Additional ") +
-        "Sequence Fetcher (WSDBfetch@EBI)";
+    return ( (alignFrame == null) ? "New " : "Additional ") + "Sequence Fetcher";
   }
 
   private void jbInit()
@@ -87,12 +87,12 @@ public class SequenceFetcher
         ok_actionPerformed(e);
       }
     });
-    cancel.setText("Cancel");
-    cancel.addActionListener(new ActionListener()
+    close.setText("Close");
+    close.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        cancel_actionPerformed(e);
+        close_actionPerformed(e);
       }
     });
     textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
@@ -104,7 +104,7 @@ public class SequenceFetcher
       }
     });
     jPanel1.add(ok);
-    jPanel1.add(cancel);
+    jPanel1.add(close);
     this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0
                                              , GridBagConstraints.WEST,
                                              GridBagConstraints.NONE,
@@ -126,11 +126,11 @@ public class SequenceFetcher
   JComboBox database = new JComboBox();
   JLabel jLabel1 = new JLabel();
   JButton ok = new JButton();
-  JButton cancel = new JButton();
+  JButton close = new JButton();
   JPanel jPanel1 = new JPanel();
   JTextField textfield = new JTextField();
   GridBagLayout gridBagLayout1 = new GridBagLayout();
-  public void cancel_actionPerformed(ActionEvent e)
+  public void close_actionPerformed(ActionEvent e)
   {
     try
     {
@@ -142,11 +142,10 @@ public class SequenceFetcher
 
   public void ok_actionPerformed(ActionEvent e)
   {
-    frame.setTitle("Sequence Fetcher (WSDBfetch@EBI) - Fetching Sequence...");
     database.setEnabled(false);
     textfield.setEnabled(false);
     ok.setEnabled(false);
-    cancel.setEnabled(false);
+    close.setEnabled(false);
 
     Thread worker = new Thread(this);
     worker.start();
@@ -157,8 +156,7 @@ public class SequenceFetcher
     database.setEnabled(true);
     textfield.setEnabled(true);
     ok.setEnabled(true);
-    cancel.setEnabled(true);
-    frame.setTitle(getFrameTitle());
+    close.setEnabled(true);
   }
 
   public void run()
@@ -191,10 +189,13 @@ public class SequenceFetcher
           ) + ":" + textfield.getText(),
           "fasta", "raw");
 
-      for (int i = 0; i < reply.length; i++)
-        result.append(reply[i] + "\n");
+      if(reply!=null)
+      {
+        for (int i = 0; i < reply.length; i++)
+          result.append(reply[i] + "\n");
 
-      parseResult(result.toString());
+        parseResult(result.toString(), null);
+      }
     }
     else if (database.getSelectedItem().equals("PDB"))
     {
@@ -209,21 +210,36 @@ public class SequenceFetcher
 
 
       if (result.length()>0)
-        parseResult(result.toString());
+        parseResult(result.toString(), null);
+    }
+    else if( database.getSelectedItem().equals("PFAM"))
+    {
+      try{
+        result.append(new FastaFile(
+           "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="
+           +  textfield.getText().toUpperCase(), "URL").print()
+           );
+
+         if(result.length()>0)
+           parseResult( result.toString(), textfield.getText().toUpperCase() );
+
+      }catch(java.io.IOException ex)
+      {   result = null;    }
     }
 
     if (result == null || result.length() == 0)
       showErrorMessage("Error retrieving " + textfield.getText()
                        + " from " + database.getSelectedItem());
-    else
-      textfield.setText("");
+
     resetDialog();
+    return;
   }
 
   void getUniprotFile(String id)
   {
     EBIFetchClient ebi = new EBIFetchClient();
     File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
+   // File file = new File("H:/jalview/classes/fer1.xml");
     SequenceFeatureFetcher sff = new SequenceFeatureFetcher();
     Vector entries = sff.getUniprotEntries(file);
 
@@ -234,7 +250,8 @@ public class SequenceFetcher
       while (en.hasMoreElements())
       {
         UniprotEntry entry = (UniprotEntry) en.nextElement();
-        StringBuffer name = new StringBuffer(">Uniprot/Swiss-Prot");
+
+        StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");
         Enumeration en2 = entry.getAccession().elements();
         while (en2.hasMoreElements())
         {
@@ -248,8 +265,10 @@ public class SequenceFetcher
           name.append(en2.nextElement());
         }
 
-        if (entry.getProteinName() != null)
-          name.append(" " + entry.getProteinName().elementAt(0));
+        if (entry.getProtein() != null)
+        {
+           name.append(" " + entry.getProtein().getName().elementAt(0));
+        }
 
         result.append(name + "\n" + entry.getUniprotSequence().getContent() +
                       "\n");
@@ -257,7 +276,7 @@ public class SequenceFetcher
       }
 
       //Then read in the features and apply them to the dataset
-      SequenceI[] sequence = parseResult(result.toString());
+      SequenceI[] sequence = parseResult(result.toString(), null);
       for (int i = 0; i < entries.size(); i++)
       {
         UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
@@ -273,8 +292,16 @@ public class SequenceFetcher
         }
 
         sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
-        sequence[i].getDatasetSequence().setSequenceFeatures(entry.getFeature());
-
+        if (entry.getFeature() != null)
+        {
+          e = entry.getFeature().elements();
+          while (e.hasMoreElements())
+          {
+            SequenceFeature sf = (SequenceFeature) e.nextElement();
+            sf.setFeatureGroup("Uniprot");
+            sequence[i].getDatasetSequence().addSequenceFeature( sf );
+          }
+        }
       }
     }
   }
@@ -321,23 +348,28 @@ public class SequenceFetcher
     return result;
   }
 
-  SequenceI[] parseResult(String result)
+  SequenceI[] parseResult(String result, String title)
   {
-    String format = IdentifyFile.Identify(result, "Paste");
+    String format = new IdentifyFile().Identify(result, "Paste");
     SequenceI[] sequences = null;
 
     if (FormatAdapter.formats.contains(format))
     {
-      sequences = new FormatAdapter().readFile(result.toString(), "Paste",
-                                               format);
+      sequences = null;
+      try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",
+                                               format);}
+      catch(Exception ex){}
+
       if (sequences != null && sequences.length > 0)
       {
         if (alignFrame == null)
         {
           AlignFrame af = new AlignFrame(new Alignment(sequences));
           af.currentFileFormat = format;
+          if(title==null)
+            title = "Retrieved from " + database.getSelectedItem();
           Desktop.addInternalFrame(af,
-                                   "Retrieved from " + database.getSelectedItem(),
+                                   title,
                                    AlignFrame.NEW_WINDOW_WIDTH,
                                    AlignFrame.NEW_WINDOW_HEIGHT);
           af.statusBar.setText("Successfully pasted alignment file");
@@ -355,7 +387,7 @@ public class SequenceFetcher
             alignFrame.viewport.alignment.addSequence(sequences[i]);
 
             ////////////////////////////
-            //Datset needs extension;
+            //Dataset needs extension;
             /////////////////////////////
             Sequence ds = new Sequence(sequences[i].getName(),
                                        AlignSeq.extractGaps("-. ",
@@ -396,6 +428,11 @@ public class SequenceFetcher
                                       + "=" + 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("PDB","0",pdbid);
+              sequences[i].getDatasetSequence().addDBRef(dbentry);
             }
             else
             {
@@ -425,9 +462,11 @@ public class SequenceFetcher
 
   void showErrorMessage(String error)
   {
+    resetDialog();
     JOptionPane.showInternalMessageDialog(Desktop.desktop,
                                           error, "Error Retrieving Data",
                                           JOptionPane.WARNING_MESSAGE);
+    return;
   }
 }