/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 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
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
package jalview.gui;

import javax.swing.*;
import java.awt.*;
import java.awt.event.*;
import jalview.io.EBIFetchClient;
import MCview.*;
import jalview.datamodel.*;
import jalview.analysis.AlignSeq;
import java.io.File;
import jalview.io.*;
import java.util.*;

public class SequenceFetcher
    extends JPanel implements Runnable
{
  JInternalFrame frame;
  AlignFrame alignFrame;
  StringBuffer result;
  final String noDbSelected = "-- Select Database --";
  public SequenceFetcher(AlignFrame af)
  {
    alignFrame = af;
    database.addItem(noDbSelected);
    database.addItem("Uniprot");
    database.addItem("EMBL");
    database.addItem("EMBLCDS");
    database.addItem("PDB");
    database.addItem("PFAM");

    try
    {
      jbInit();
    }
    catch (Exception ex)
    {
      ex.printStackTrace();
    }

    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";
  }

  private void jbInit()
      throws Exception
  {
    this.setLayout(gridBagLayout1);

    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.setText(
        "Separate multiple accession ids with semi colon \";\"");
    ok.setText("OK");
    ok.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        ok_actionPerformed(e);
      }
    });
    close.setText("Close");
    close.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        close_actionPerformed(e);
      }
    });
    textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
    textfield.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        ok_actionPerformed(e);
      }
    });
    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.HORIZONTAL,
                                               new Insets(0, 0, 0, 6), 200, 1));
  }

  JComboBox database = new JComboBox();
  JLabel jLabel1 = new JLabel();
  JButton ok = new JButton();
  JButton close = new JButton();
  JPanel jPanel1 = new JPanel();
  JTextField textfield = new JTextField();
  GridBagLayout gridBagLayout1 = new GridBagLayout();
  public void close_actionPerformed(ActionEvent e)
  {
    try
    {
      frame.setClosed(true);
    }
    catch (Exception ex)
    {}
  }

  public void ok_actionPerformed(ActionEvent e)
  {
    database.setEnabled(false);
    textfield.setEnabled(false);
    ok.setEnabled(false);
    close.setEnabled(false);

    Thread worker = new Thread(this);
    worker.start();
  }

  private void resetDialog()
  {
    database.setEnabled(true);
    textfield.setEnabled(true);
    ok.setEnabled(true);
    close.setEnabled(true);
  }

  public void run()
  {
    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)
      error += "Please enter a (semi-colon separated list of) database id(s)";
    if (error.length() > 0)
    {
      showErrorMessage(error);
      resetDialog();
      return;
    }

    result = new StringBuffer();
    if (database.getSelectedItem().equals("Uniprot"))
    {
      getUniprotFile(textfield.getText());
    }
    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");

      if(reply!=null)
      {
        for (int i = 0; i < reply.length; i++)
          result.append(reply[i] + "\n");

        parseResult(result.toString(), null);
      }
    }
    else if (database.getSelectedItem().equals("PDB"))
    {
      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());

    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);

    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.getProteinName() != null)
          name.append(" " + entry.getProteinName().elementAt(0));

        result.append(name + "\n" + entry.getUniprotSequence().getContent() +
                      "\n");

      }

      //Then read in the features and apply them to the dataset
      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();
        Vector onlyPdbEntries = new Vector();
        while (e.hasMoreElements())
        {
          PDBEntry pdb = (PDBEntry) e.nextElement();
          if (!pdb.getType().equals("PDB"))
            continue;

          onlyPdbEntries.addElement(pdb);
        }

        sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
        e = entry.getFeature().elements();
        while(e.hasMoreElements())
        {
          sequence[i].getDatasetSequence().addSequenceFeature((SequenceFeature)e.nextElement());
        }
      }
    }
  }

  StringBuffer getPDBFile(String id)
  {
    StringBuffer result = new StringBuffer();
    String chain = null;
    if (id.indexOf(":") > -1)
    {
      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
    {
      jalview.bin.Cache.log.warn("Exception when retrieving " +
                                 textfield.getText() + " from " +
                                 database.getSelectedItem(), ex);
      return null;
    }

    return result;
  }

  SequenceI[] parseResult(String result, String title)
  {
    String format = new IdentifyFile().Identify(result, "Paste");
    SequenceI[] sequences = null;

    if (FormatAdapter.formats.contains(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,
                                   title,
                                   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)
          {}
        }
        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].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"))
        {
          // 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("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());
    }

    return sequences;

  }

  void showErrorMessage(String error)
  {
    resetDialog();
    JOptionPane.showInternalMessageDialog(Desktop.desktop,
                                          error, "Error Retrieving Data",
                                          JOptionPane.WARNING_MESSAGE);
    return;
  }
}