/* 
 *
 * created: 2006
 *
 * This file is part of Artemis
 *
 * Copyright (C) 2006  Genome Research Limited
 *
 * 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., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */

package uk.ac.sanger.artemis.components.genebuilder;

import java.awt.Cursor;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.IOException;

import java.sql.SQLException;
import java.util.List;
import java.util.Vector;


import javax.swing.JButton;
import javax.swing.JOptionPane;

import javax.swing.JPasswordField;
import javax.swing.JTextField;

import javax.swing.JComboBox;
import javax.swing.JPanel;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
import javax.swing.UIManager;

import org.gmod.schema.organism.Organism;

import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.Feature;
import uk.ac.sanger.artemis.Options;
import uk.ac.sanger.artemis.Selection;
import uk.ac.sanger.artemis.SimpleEntryGroup;
import uk.ac.sanger.artemis.chado.*;
import uk.ac.sanger.artemis.io.FeatureVector;
import uk.ac.sanger.artemis.io.DatabaseDocumentEntry;
import uk.ac.sanger.artemis.io.EntryInformationException;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
import uk.ac.sanger.artemis.io.PartialSequence;
import uk.ac.sanger.artemis.sequence.NoSequenceException;
import uk.ac.sanger.artemis.util.DatabaseDocument;
import uk.ac.sanger.artemis.util.InputStreamProgressListener;
import uk.ac.sanger.artemis.util.OutOfRangeException;
import uk.ac.sanger.artemis.components.Splash;
import uk.ac.sanger.artemis.components.SwingWorker;
import uk.ac.sanger.artemis.components.database.DatabaseEntrySource;


/**
 * Chado data access example code. This searches for features by their
 * uniquename and returns their properties and attributes.
 */
public class GeneEdit
{
  /** JDBC DAO */
  private JdbcDAO jdbcDAO = null;

  /** iBatis DAO */
  private IBatisDAO connIB = null;

  /** password fields */
  private JPasswordField pfield;
  
  private String geneName;

  /**
   * Standalone gene editing (i.e. outside of Artemis)
   */
  public GeneEdit()
  {
    try
    {
      DatabaseEntrySource entry_source = new DatabaseEntrySource();
      entry_source.setLocation(true);
      final String location = entry_source.getLocation();
      pfield = entry_source.getPfield();
      
      final GmodDAO dao = getDAO(location);
      showFeatureSearchPanel(dao, location);
    }
    catch(java.net.ConnectException ce)
    {
      ce.printStackTrace();
    }
    catch(SQLException sqlExp)
    {
      JOptionPane.showMessageDialog(null, "SQL Problems...\n"
          + sqlExp.getMessage(), "SQL Error", JOptionPane.ERROR_MESSAGE);
      sqlExp.printStackTrace();
    }
  }
  
  public GeneEdit(final String geneName)
  {
    DatabaseEntrySource entry_source = new DatabaseEntrySource();
    this.geneName = geneName;
    
    boolean promptUser = true;
    if(System.getProperty("read_only") != null)
      promptUser = false;
    entry_source.setLocation(promptUser);
    final String location = entry_source.getLocation();
    pfield = entry_source.getPfield();

    if(System.getProperty("show_log") != null)
      GeneSplash.showLog();
    openGeneBuilder(null, location, null);
  }

  /**
   * Display a window for searching for features.
   * 
   * @throws java.net.ConnectException
   * @throws SQLException
   */
  private void showFeatureSearchPanel(final GmodDAO dao,
                                      final String location)
      throws java.net.ConnectException, SQLException
  {
    int index = location.indexOf('=') + 1;
    String schema = location.substring(index);

    final List<Organism> schemas = dao.getOrganisms(); //dao.getSchema();

    Vector<String> v_schemas = new Vector<String>(schemas.size());
    for(int i=0; i<schemas.size(); i++)
      v_schemas.add( schemas.get(i).getCommonName() );
    
    v_schemas.add(0, "All");

    final JPanel panel = new JPanel(new GridBagLayout());
    GridBagConstraints c = new GridBagConstraints();
    
    final JComboBox schema_list = new JComboBox(v_schemas);
    schema_list.setSelectedItem(schema);

    final JTextField gene_text = new JTextField(20);
    gene_text.setText("Smp_000130"); //"SPAC212.04c");
    
    c.gridx = 0;
    c.gridy = 0;
    panel.add(gene_text,c);
    c.gridx = 1;
    panel.add(schema_list,c);
    gene_text.selectAll();
    
    final GeneSplash frame = new GeneSplash();
    final JButton findButt = new JButton("OPEN GENE BUILDER");
    findButt.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent event)
      {
        GeneEdit.this.geneName = gene_text.getText().trim();
        final String schema = (String)schema_list.getSelectedItem();
        List schema_search;
        if(schema.equalsIgnoreCase("All"))
          schema_search = schemas;
        else
        {
          schema_search = new Vector();
          schema_search.add(schema);
        }

        openGeneBuilder(schema, location, frame);
      }
    });

    c.gridx = 1;
    c.gridy = 1;
    panel.add(findButt, c);
    
    frame.getContentPane().add(panel);
    frame.setJMenuBar(getJMenuBar(dao));
    frame.pack();
    frame.setVisible(true);
  }

  private void openGeneBuilder(final String organism,
                               final String location,
                               final GeneSplash frame)
  {
    SwingWorker entryWorker = new SwingWorker()
    {
      public Object construct()
      {
        if(frame != null)
          frame.setCursor(new Cursor(Cursor.WAIT_CURSOR));
        DatabaseDocumentEntry entry = makeEntry(organism, 
                                                location, pfield);
        
        if(System.getProperty("read_only") != null)
          entry.setReadOnly(true);
        showGeneEditor(organism, geneName, entry);
        
        if(frame != null)
          frame.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
        return null;
      }
    };
    entryWorker.start();  
  }
  
  private DatabaseDocumentEntry makeEntry(final String schema, 
                                          final String location,
                                          final JPasswordField pfield)
  {
    DatabaseDocumentEntry db_entry = null;
    DatabaseDocument doc = new DatabaseDocument(location, pfield, 
                                                 geneName,
                                                schema, true);
    doc.setLazyFeatureLoad(false);

    try
    {
      db_entry = new DatabaseDocumentEntry(doc, null);
    }
    catch(Exception e)
    {
      org.gmod.schema.sequence.Feature chadoFeature = 
        doc.getChadoGeneByAnyCurrentName(geneName);
      if(chadoFeature != null)
      {
        JOptionPane.showMessageDialog(null, 
            geneName+" appears to be a synonym for "+chadoFeature.getUniqueName()+
            "\nNow opening "+chadoFeature.getUniqueName(), 
            geneName, JOptionPane.INFORMATION_MESSAGE);
        geneName = chadoFeature.getUniqueName();
        db_entry = makeEntry(schema, location, pfield);
      }
    }

    return db_entry;  
  }
  
  /**
   * Build a <code>JMenuBar</code>.
   * 
   * @return a <code>JMenuBar</code>
   */
  public JMenuBar getJMenuBar(final GmodDAO dao)
  {
    JMenuBar mbar = new JMenuBar();
    JMenu file = new JMenu("File");
    mbar.add(file);

    JMenuItem showLog = new JMenuItem("Show Log Window");
    showLog.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent event)
      {
        GeneSplash.showLog();
      }
    });
    file.add(showLog);
    
    JMenuItem exit = new JMenuItem("Exit");
    exit.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent event)
      {
        System.exit(0);
      }
    });
    file.add(exit);

    return mbar;
  }

  /**
   * Make an entry for a single gene.
   * @param organism
   * @param uniquename
   * @param doc
   * @param stream_progress_listener
   * @return
   */
  public static DatabaseDocumentEntry makeGeneEntry(final String organism, 
                                      final String uniquename,
                                      final DatabaseDocument doc,
                                      final InputStreamProgressListener stream_progress_listener)
  {
    DatabaseDocumentEntry db_entry = null;
    DatabaseDocument newdoc = new DatabaseDocument(doc, 
            uniquename, organism, true, stream_progress_listener);
    newdoc.setLazyFeatureLoad(false);
    
    try
    {
      db_entry = new DatabaseDocumentEntry(newdoc, null);
    }
    catch(EntryInformationException e)
    {
      e.printStackTrace();
    }
    catch(IOException e)
    {
      e.printStackTrace();
    }
    catch(NullPointerException npe)
    {
      JOptionPane.showMessageDialog(null, organism+":"+uniquename+
          " not found!", "Warning", JOptionPane.WARNING_MESSAGE);
    }
    return db_entry;
  }
  
  
  
  /**
   * 
   * @param organism
   * @param uniqueName
   * @param dbentry
   */
  public static void showGeneEditor(final String organism,
                                    final String uniqueName,
                                    final DatabaseDocumentEntry dbentry)
  {
    DatabaseDocument doc = (DatabaseDocument)dbentry.getDocument();
    PartialSequence sequence = doc.getChadoSequence(uniqueName);
    dbentry.setPartialSequence(sequence);
    
    FeatureVector features = dbentry.getAllFeatures();
    Feature gff_gene_feature = null;

    SimpleEntryGroup entry_group = new SimpleEntryGroup();
    try
    {
      // create Entry
      new Entry(dbentry);
    }
    catch(OutOfRangeException e)
    {
      e.printStackTrace();
    }
    catch(NoSequenceException e)
    {
      e.printStackTrace();
    }
    
    for(int i = 0; i < features.size(); i++)
    {
      GFFStreamFeature this_embl_feature = (GFFStreamFeature) features.get(i);
      String this_uniquename = (String) this_embl_feature.getQualifierByName("ID")
          .getValues().get(0);

      Feature this_feature;
      
      if(this_embl_feature.getUserData() == null)
        this_feature = new Feature(this_embl_feature);
      else
        this_feature = (Feature)this_embl_feature.getUserData();
      
      if(uniqueName.equals(this_uniquename))
        gff_gene_feature = this_feature;
    }

    Selection selection = new Selection(null);
    selection.add(gff_gene_feature);
    
    entry_group.addElement(gff_gene_feature.getEntry());
    
    ChadoTransactionManager ctm = new ChadoTransactionManager();
    entry_group.addFeatureChangeListener(ctm);
    entry_group.addEntryChangeListener(ctm);
    ctm.setEntryGroup(entry_group);
    
    if(System.getProperty("basic") == null)
      new GeneBuilderFrame(gff_gene_feature, entry_group, selection, null, ctm); 
    else
      new BasicGeneBuilderFrame(gff_gene_feature, entry_group, selection, ctm); 
  }
  
  /**
   * Get the data access object (DAO).
   * 
   * @return data access object
   */
  private GmodDAO getDAO(final String location) 
          throws java.net.ConnectException, SQLException
  {
    if(System.getProperty("ibatis") == null)
    {
      if(jdbcDAO == null)
        jdbcDAO = new JdbcDAO(location, pfield);
      return jdbcDAO;
    }
    else
    {
      if(connIB == null)
      {
        System.setProperty("chado", location);
        connIB = new IBatisDAO(pfield);
      }

      return connIB;
    }
  }

  class GeneSplash extends Splash
  {
    /** */
    private static final long serialVersionUID = 1L;

    public GeneSplash()
    {
      super("Gene Search", "Gene Builder");  
    }
    
    protected void exit()
    {   
    }
    
  }
  

  
  public static void main(String args[])
  {
    final javax.swing.plaf.FontUIResource font_ui_resource =
      Options.getOptions().getFontUIResource();

    java.util.Enumeration<Object> keys = UIManager.getDefaults().keys();
    while(keys.hasMoreElements()) 
    {
      Object key = keys.nextElement();
      Object value = UIManager.get(key);
      if(value instanceof javax.swing.plaf.FontUIResource) 
        UIManager.put(key, font_ui_resource);
    }
    if(args.length == 1)
      new GeneEdit(args[0]);
    else
      new GeneEdit();
    
  }
}