X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=2beb3d95dfa5d58b14bbbdf62c299c413bf68b24;hb=237972562c84b83dbd287071cdd839d97aaf7d4b;hp=0884d44cc7cb7478ff870526901e10f1eb16d357;hpb=b7f7c7acc0afabdf3a6162c237094b860968219b;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 0884d44..2beb3d9 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) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 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
@@ -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()
@@ -119,8 +119,8 @@ public class SequenceFetcher
                                               new Insets(0, 4, 0, 0), 1, 0));
     this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
                                                , GridBagConstraints.CENTER,
-                                               GridBagConstraints.HORIZONTAL,
-                                               new Insets(0, 0, 0, 6), 200, 1));
+                                               GridBagConstraints.NONE,
+                                               new Insets(0, 0, 0, 6), 211, 1));
   }
 
   JComboBox database = new JComboBox();
@@ -142,7 +142,6 @@ 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);
@@ -158,7 +157,6 @@ public class SequenceFetcher
     textfield.setEnabled(true);
     ok.setEnabled(true);
     close.setEnabled(true);
-    frame.setTitle(getFrameTitle());
   }
 
   public void run()
@@ -185,18 +183,28 @@ public class SequenceFetcher
     else if (database.getSelectedItem().equals("EMBL")
              || database.getSelectedItem().equals("EMBLCDS"))
     {
-      EBIFetchClient dbFetch = new EBIFetchClient();
-      String[] reply = dbFetch.fetchData(
-          database.getSelectedItem().toString().toLowerCase(
-          ) + ":" + textfield.getText(),
-          "fasta", "raw");
+      StringTokenizer st = new StringTokenizer(textfield.getText(), ";");
+      while(st.hasMoreTokens())
+      {
+        EBIFetchClient dbFetch = new EBIFetchClient();
+
+        String[] reply = dbFetch.fetchData(
+            database.getSelectedItem().toString().toLowerCase(
+            ) + ":" + st.nextToken(),
+            "fasta", "raw");
+//
+        if (reply != null)
+        {
+          for (int i = 0; i < reply.length; i++)
+            result.append(reply[i] + "\n");
+        }
+      }
 
-      if(reply!=null)
+      if(result!=null)
       {
-        for (int i = 0; i < reply.length; i++)
-          result.append(reply[i] + "\n");
+        System.out.println(result.toString());
 
-        parseResult(result.toString());
+        parseResult(result.toString(), null);
       }
     }
     else if (database.getSelectedItem().equals("PDB"))
@@ -212,23 +220,38 @@ 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);
-    SequenceFeatureFetcher sff = new SequenceFeatureFetcher();
-    Vector entries = sff.getUniprotEntries(file);
+
+    DBRefFetcher dbref = new DBRefFetcher();
+    Vector entries = dbref.getUniprotEntries(file);
 
     if (entries != null)
     {
@@ -237,7 +260,8 @@ 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())
         {
@@ -251,8 +275,10 @@ 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");
@@ -260,7 +286,7 @@ 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);
@@ -275,9 +301,28 @@ public class SequenceFetcher
           onlyPdbEntries.addElement(pdb);
         }
 
-        sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
-        sequence[i].getDatasetSequence().setSequenceFeatures(entry.getFeature());
+        Enumeration en2 = entry.getAccession().elements();
+        while (en2.hasMoreElements())
+        {
+          sequence[i].getDatasetSequence().addDBRef(new DBRefEntry(DBRefSource.UNIPROT,
+                    "0",
+                    en2.nextElement().toString()));
+        }
+
+
 
+
+        sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
+        if (entry.getFeature() != null)
+        {
+          e = entry.getFeature().elements();
+          while (e.hasMoreElements())
+          {
+            SequenceFeature sf = (SequenceFeature) e.nextElement();
+            sf.setFeatureGroup("Uniprot");
+            sequence[i].getDatasetSequence().addSequenceFeature( sf );
+          }
+        }
       }
     }
   }
@@ -293,17 +338,18 @@ public class SequenceFetcher
     }
 
     EBIFetchClient ebi = new EBIFetchClient();
-    String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");
-    if (reply == null)
+    String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
+    if (file == null)
       return null;
     try
     {
-      PDBfile pdbfile = new PDBfile(reply);
+      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))
+
           result.append("\n>PDB|" + id + "|" +
                         ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
                         getName() +
@@ -324,26 +370,35 @@ 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))
+    if (FormatAdapter.isValidFormat(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));
+          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,
-                                   "Retrieved from " + database.getSelectedItem(),
-                                   AlignFrame.NEW_WINDOW_WIDTH,
-                                   AlignFrame.NEW_WINDOW_HEIGHT);
+                                   title,
+                                   AlignFrame.DEFAULT_WIDTH,
+                                   AlignFrame.DEFAULT_HEIGHT);
           af.statusBar.setText("Successfully pasted alignment file");
+
           try
           {
             af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
@@ -358,7 +413,7 @@ public class SequenceFetcher
             alignFrame.viewport.alignment.addSequence(sequences[i]);
 
             ////////////////////////////
-            //Datset needs extension;
+            //Dataset needs extension;
             /////////////////////////////
             Sequence ds = new Sequence(sequences[i].getName(),
                                        AlignSeq.extractGaps("-. ",
@@ -402,7 +457,7 @@ public class SequenceFetcher
 
               // 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);
+              DBRefEntry dbentry = new DBRefEntry(jalview.datamodel.DBRefSource.PDB,"0",pdbid);
               sequences[i].getDatasetSequence().addDBRef(dbentry);
             }
             else
@@ -431,11 +486,18 @@ public class SequenceFetcher
 
   }
 
-  void showErrorMessage(String error)
+  void showErrorMessage(final String error)
   {
-    JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                          error, "Error Retrieving Data",
+    resetDialog();
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                              error, "Error Retrieving Data",
                                           JOptionPane.WARNING_MESSAGE);
+      }
+    });
   }
 }