X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=2beb3d95dfa5d58b14bbbdf62c299c413bf68b24;hb=237972562c84b83dbd287071cdd839d97aaf7d4b;hp=aa494f531e7217fe9f4304273bb3f07187e9fa58;hpb=713db61b4724485414159cfc145f9ffa4a24bb6d;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index aa494f5..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
@@ -29,7 +29,6 @@ import java.io.File;
 import jalview.io.*;
 import java.util.*;
 
-
 public class SequenceFetcher
     extends JPanel implements Runnable
 {
@@ -45,6 +44,7 @@ public class SequenceFetcher
     database.addItem("EMBL");
     database.addItem("EMBLCDS");
     database.addItem("PDB");
+    database.addItem("PFAM");
 
     try
     {
@@ -57,12 +57,15 @@ public class SequenceFetcher
 
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    if(System.getProperty("os.name").startsWith("Mac"))
-      Desktop.addInternalFrame(frame, ((af==null) ?
-                                       "New " : "Additional ")+"Sequence Fetcher (WSDBfetch@EBI)", 400, 140);
+    if (System.getProperty("os.name").startsWith("Mac"))
+      Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);
     else
-      Desktop.addInternalFrame(frame, ((af==null) ?
-                                       "New " : "Additional ")+"Sequence Fetcher (WSDBfetch@EBI)", 400, 125);
+      Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);
+  }
+
+  private String getFrameTitle()
+  {
+    return ( (alignFrame == null) ? "New " : "Additional ") + "Sequence Fetcher";
   }
 
   private void jbInit()
@@ -84,12 +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));
@@ -101,7 +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,
@@ -116,18 +119,18 @@ 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();
   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
     {
@@ -139,22 +142,21 @@ 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();
   }
 
-  private void resetDialog() {
+  private void resetDialog()
+  {
     database.setEnabled(true);
     textfield.setEnabled(true);
     ok.setEnabled(true);
-    cancel.setEnabled(true);
-    frame.setTitle("Sequence Fetcher (WSDBfetch@EBI)");
+    close.setEnabled(true);
   }
 
   public void run()
@@ -162,89 +164,130 @@ 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+","");
+    com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");
     textfield.setText(empty.replaceAll(textfield.getText()));
-    if (textfield.getText().length()==0)
-      error+="Please enter a (semi-colon separated list of) database id(s)";
-    if (error.length()>0) {
+    if (textfield.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();
+    result = new StringBuffer();
     if (database.getSelectedItem().equals("Uniprot"))
     {
       getUniprotFile(textfield.getText());
     }
     else if (database.getSelectedItem().equals("EMBL")
-        || database.getSelectedItem().equals("EMBLCDS"))
+             || 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");
+        }
+      }
 
-      for (int i = 0; i < reply.length; i++)
-        result.append(reply[i] + "\n");
+      if(result!=null)
+      {
+        System.out.println(result.toString());
 
-      parseResult(result.toString());
+        parseResult(result.toString(), null);
+      }
     }
     else if (database.getSelectedItem().equals("PDB"))
     {
-      result = getPDBFile(textfield.getText().toUpperCase());
-      if (result!=null)
-        parseResult(result.toString());
+      StringTokenizer qset = new StringTokenizer(textfield.getText(), ";");
+      String query;
+      while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))
+      {
+        StringBuffer respart = getPDBFile(query.toUpperCase());
+        if(respart!=null)
+          result.append(respart);
+      }
+
+
+      if (result.length()>0)
+        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);
+    File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
 
-    if(entries!=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" );
+
+        StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");
         Enumeration en2 = entry.getAccession().elements();
-        while(en2.hasMoreElements())
+        while (en2.hasMoreElements())
         {
           name.append("|");
           name.append(en2.nextElement());
         }
         en2 = entry.getName().elements();
-        while(en2.hasMoreElements())
+        while (en2.hasMoreElements())
         {
           name.append("|");
           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());
+        result.append(name + "\n" + entry.getUniprotSequence().getContent() +
+                      "\n");
 
       }
 
       //Then read in the features and apply them to the dataset
-      SequenceI [] sequence = parseResult(result.toString());
-      for(int i=0; i<entries.size(); i++)
+      SequenceI[] sequence = parseResult(result.toString(), null);
+      for (int i = 0; i < entries.size(); i++)
       {
         UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
         Enumeration e = entry.getDbReference().elements();
@@ -258,131 +301,203 @@ 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 );
+          }
+        }
       }
     }
   }
 
-    StringBuffer getPDBFile(String id)
+  StringBuffer getPDBFile(String id)
+  {
+    StringBuffer result = new StringBuffer();
+    String chain = null;
+    if (id.indexOf(":") > -1)
     {
-      StringBuffer result = new StringBuffer();
-      String chain = null;
-      if (id.indexOf(":") > -1)
-      {
-        chain = id.substring(id.indexOf(":") + 1);
-        id = id.substring(0, id.indexOf(":"));
-      }
+      chain = id.substring(id.indexOf(":") + 1);
+      id = id.substring(0, id.indexOf(":"));
+    }
 
-      EBIFetchClient ebi = new EBIFetchClient();
-      String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");
-      if (reply==null)
-        return null;
-      try
-      {
-        PDBfile pdbfile = new PDBfile(reply);
-        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() +
-                          "\n"
-                          +
-                          ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
-                          getSequence());
-        }
-      }
-      catch (Exception ex) // Problem parsing PDB file
+    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++)
       {
-        jalview.bin.Cache.log.warn("Exception when retrieving " + textfield.getText() + " from " +
-            database.getSelectedItem(), ex);
-        return null;
+        if (chain == null ||
+            ( (PDBChain) pdbfile.chains.elementAt(i)).id.
+            toUpperCase().equals(chain))
+
+          result.append("\n>PDB|" + id + "|" +
+                        ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
+                        getName() +
+                        "\n"
+                        +
+                        ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
+                        getSequence());
       }
-
-      return result;
+    }
+    catch (Exception ex) // Problem parsing PDB file
+    {
+      jalview.bin.Cache.log.warn("Exception when retrieving " +
+                                 textfield.getText() + " from " +
+                                 database.getSelectedItem(), ex);
+      return null;
     }
 
-    SequenceI[] parseResult(String result)
+    return result;
+  }
+
+  SequenceI[] parseResult(String result, String title)
+  {
+    String format = new IdentifyFile().Identify(result, "Paste");
+    SequenceI[] sequences = null;
+
+    if (FormatAdapter.isValidFormat(format))
     {
-      String format = IdentifyFile.Identify(result, "Paste");
-      SequenceI[] sequences = null;
+      sequences = null;
+      try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",
+                                               format);}
+      catch(Exception ex){}
 
-      if (FormatAdapter.formats.contains(format))
+      if (sequences != null && sequences.length > 0)
       {
-        sequences = new FormatAdapter().readFile(result.toString(), "Paste", format);
-        if (sequences != null && sequences.length>0)
+        if (alignFrame == null)
         {
-          if(alignFrame==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
           {
-            AlignFrame af = new AlignFrame(new Alignment(sequences));
-            af.currentFileFormat = format;
-            Desktop.addInternalFrame(af, "Retrieved from "+database.getSelectedItem(),
-                                     AlignFrame.NEW_WINDOW_WIDTH,
-                                     AlignFrame.NEW_WINDOW_HEIGHT);
-            af.statusBar.setText("Successfully pasted alignment file");
-            try
-            {
-              af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
-            }
-            catch (Exception ex)
-            {}
+            af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
           }
-          else
+          catch (Exception ex)
+          {}
+        }
+        else
+        {
+          for (int i = 0; i < sequences.length; i++)
           {
-            for (int i = 0; i < sequences.length; i++)
-            {
-              alignFrame.viewport.alignment.addSequence(sequences[i]);
-
-              ////////////////////////////
-              //Datset needs extension;
-              /////////////////////////////
-              Sequence ds = new Sequence(sequences[i].getName(),
-                                         AlignSeq.extractGaps("-. ",
-                  sequences[i].getSequence()),
-                                         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());
-
+            alignFrame.viewport.alignment.addSequence(sequences[i]);
+
+            ////////////////////////////
+            //Dataset needs extension;
+            /////////////////////////////
+            Sequence ds = new Sequence(sequences[i].getName(),
+                                       AlignSeq.extractGaps("-. ",
+                sequences[i].getSequence()),
+                                       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 (database.getSelectedItem().equals("PDB"))
+        }
+
+        if (database.getSelectedItem().equals("PDB"))
+        {
+          // Parse out the ids from the structured names
+          boolean errors = false;
+          for (int i = 0; i < sequences.length; i++)
           {
-            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()))
             {
-              PDBEntry entry = new PDBEntry();
-              entry.setId(textfield.getText());
+              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());
         }
-        else
-          showErrorMessage( "Error retrieving "+textfield.getText()
-                            +" from "+database.getSelectedItem());
+
       }
+      else
+        showErrorMessage("Error retrieving " + textfield.getText()
+                         + " from " + database.getSelectedItem());
+    }
 
-      return sequences;
+    return sequences;
 
   }
 
-  void showErrorMessage(String error)
+  void showErrorMessage(final String error)
   {
-    JOptionPane.showInternalMessageDialog(Desktop.desktop,
-         error, "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
+    resetDialog();
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                              error, "Error Retrieving Data",
+                                          JOptionPane.WARNING_MESSAGE);
+      }
+    });
   }
 }
 
-
-
-