DatabaseDocument.java

/* DatabaseDocument.java
 *
 * created: 2005
 *
 * This file is part of Artemis
 * 
 * Copyright (C) 2005  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.util;

import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
import uk.ac.sanger.artemis.io.ReadFormatException;

import uk.ac.sanger.artemis.chado.ArtemisUtils;
import uk.ac.sanger.artemis.chado.IBatisDAO;
import uk.ac.sanger.artemis.chado.JdbcDAO;
import uk.ac.sanger.artemis.chado.GmodDAO;
import uk.ac.sanger.artemis.chado.ChadoTransaction;
import uk.ac.sanger.artemis.components.database.DatabaseEntrySource;
import uk.ac.sanger.artemis.components.Splash;

import org.gmod.schema.sequence.Feature;
import org.gmod.schema.sequence.FeatureProp;
import org.gmod.schema.sequence.FeatureLoc;
import org.gmod.schema.sequence.FeaturePub;
import org.gmod.schema.sequence.FeatureRelationship;
import org.gmod.schema.sequence.FeatureSynonym;
import org.gmod.schema.sequence.FeatureCvTerm;
import org.gmod.schema.sequence.FeatureCvTermProp;
import org.gmod.schema.sequence.FeatureCvTermDbXRef;
import org.gmod.schema.sequence.FeatureCvTermPub;
import org.gmod.schema.cv.CvTerm;
import org.gmod.schema.general.Db;
import org.gmod.schema.general.DbXRef;
import org.gmod.schema.pub.PubDbXRef;
import org.gmod.schema.pub.Pub;

import java.sql.*;
import java.text.SimpleDateFormat;
import java.io.*;
import java.net.ConnectException;
import java.util.Hashtable;
import java.util.HashMap;
import java.util.Vector;
import java.util.Enumeration;
import java.util.List;
import java.util.Iterator;
import java.util.Collection;

import javax.swing.JOptionPane;
import javax.swing.JPasswordField;

/**
 * Objects of this class are Documents created from a relational database.
 * 
 */

public class DatabaseDocument extends Document
{
  private String name = null;

  /** source feature_id */
  private String srcFeatureId = "1";

  /** database schema */
  private String schema = "public";

  private static Hashtable cvterms;
  
  private InputStreamProgressListener progress_listener;

  /** JDBC DAO */
  private JdbcDAO jdbcDAO = null;

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

  private ByteBuffer[] gff_buffer;

  private ByteBuffer gff_buff;

  /** entries to split into */
  private String[] types = { "exon", "gene", "CDS", "transcript" };

  /** true if splitting the GFF into entries */
  private boolean splitGFFEntry;

  private boolean iBatis = false;

  private JPasswordField pfield;

  private List schema_list;
  
  private boolean gene_builder;
  
  // controlled vocabulary
  /** controlled_curation controlled vocabulary */
  public static String CONTROLLED_CURATION_TAG_CVNAME = 
                                 "CC_";
  /** product controlled vocabulary */
  public static String PRODUCTS_TAG_CVNAME = "genedb_products";
  public static String RILEY_TAG_CVNAME = "RILEY";
  
  private static org.apache.log4j.Logger logger4j = 
    org.apache.log4j.Logger.getLogger(DatabaseDocument.class);
  
  /**
   * 
   * Create a new Document from a database.
   * 
   * @param location
   *          This should be a URL string giving:
   *          jdbc:postgresql://host:port/datbase_name?user=username
   * 
   */
  public DatabaseDocument(String location, JPasswordField pfield)
  {
    super(location);
    this.pfield = pfield;

    if(location.indexOf('=') > -1)
      this.schema = location.substring( location.indexOf('=')+ 1);
    
    if(System.getProperty("ibatis") != null)
    {
      iBatis = true;
      System.setProperty("chado", location);
    }
  }

  
  /**
   * 
   * Create a new Document from a database.
   * 
   * @param location
   *          This should be a URL string giving:
   *          jdbc:postgresql://host:port/database_name?user=username
   * @param feature_id
   *          ID of a feature to be extracted.
   * 
   */
  public DatabaseDocument(String location, JPasswordField pfield,
                          String srcFeatureId, String schema)
  {
    super(location);
    this.pfield = pfield;

    this.srcFeatureId = srcFeatureId;
    this.schema = schema;

    if(System.getProperty("ibatis") != null)
    {
      iBatis = true;
      System.setProperty("chado", location);
    }
  }

  /**
   * 
   * Create a new Document from a database.
   * 
   * @param location
   *          This should be a URL string giving:
   *          jdbc:postgresql://host:port/datbase_name?user=username
   * @param srcFeatureId
   *          ID of a feature to be extracted.
   * @param splitGFFEntry
   *          split into separate entries based on feature types.
   * @param progress_listener
   *          input stream progress listener
   * 
   */
  public DatabaseDocument(String location, JPasswordField pfield,
                          String srcFeatureId, String schema, boolean splitGFFEntry,
                          InputStreamProgressListener progress_listener)
  {
    super(location);
    this.pfield = pfield;
    this.srcFeatureId = srcFeatureId;
    this.schema = schema;
    this.splitGFFEntry = splitGFFEntry;
    this.progress_listener = progress_listener;
    if(System.getProperty("ibatis") != null)
    {
      iBatis = true;
      System.setProperty("chado", location);
    }
    
    reset(location, schema);
  }

  /**
   * Used by the gene builder to read a database entry
   * for a single gene.
   * @param location
   * @param pfield
   * @param srcFeatureId
   * @param schema
   * @param gene_builder
   */
  public DatabaseDocument(String location, JPasswordField pfield,
          String srcFeatureId, String schema, boolean gene_builder)
  {
    super(location);
    this.pfield = pfield;
    this.srcFeatureId = srcFeatureId;
    this.schema = schema;
    this.gene_builder = gene_builder;

    if(System.getProperty("ibatis") != null)
    {
      iBatis = true;
      System.setProperty("chado", location);
    }
  }
  
  public DatabaseDocument(String location, JPasswordField pfield,
                          String srcFeatureId, String schema,
                          ByteBuffer gff_buff, String name)
  {
    super(location);
    this.pfield = pfield;
    this.srcFeatureId = srcFeatureId;
    this.schema = schema;
    this.gff_buff = gff_buff;
    this.name = name;
    if(System.getProperty("ibatis") != null)
    {
      iBatis = true;
      System.setProperty("chado", location);
    }
  }
  
  /**
   * Reset the schema.
   * @param location
   * @param schema
   */
  private void reset(String location, String schema)
  {
    this.schema = schema;

    if(!location.endsWith("="+schema))
    {
      int index = location.lastIndexOf('=');
      setLocation(location.substring(0,index+1) + schema);
      if(iBatis && connIB != null)
      {
        try
        {
          connIB.close();
        }
        catch(SQLException e)
        {
          logger4j.warn(e.getMessage());
        }
        connIB  = null;
      }
      
      jdbcDAO = null;
      System.setProperty("chado", (String)getLocation());
      logger4j.debug((String)getLocation());
    }
  }

  /**
   * Append a String to the Document location.
   * @param name  the name to append.
   */
  public Document append(String name) throws IOException
  {
    return new DatabaseDocument( ((String)getLocation()) + name, pfield);
  }

  /**
   * Return the name of this Document (the last element of the Document
   * location).
   */
  public String getName()
  {
    if(name == null)
    {
      int ind     = ((String) getLocation()).indexOf("?");
      String name = ((String) getLocation()).substring(0, ind);
      ind = name.lastIndexOf("/");
      return name.substring(ind + 1);
    }
    return name;
  }


  /**
  *  Set the name of this document.
  */
  public void setName(String name)
  {
    this.name = name;
  }


  public DatabaseDocument createDatabaseDocument()
  {
    return new DatabaseDocument( (String)getLocation(), pfield,
                                  srcFeatureId, schema );
  }
  
  /**
   * Return true if and only if the Document refered to by this object exists
   * and is readable. Always returns true.
   */
  public boolean readable()
  {
    return true;
  }

  /**
   * Return true if and only if the Document refered to by this object exists
   * and can be written to. Always returns false.
   */
  public boolean writable()
  {
    return true;
  }

  /**
   * Create a new InputStream object from this Document. The contents of the
   * Document can be read from the InputStream.
   * 
   * @exception IOException
   *              Thrown if the Document can't be read from (for example if it
   *              doesn't exist).
   */
  public InputStream getInputStream() throws IOException
  {
    ByteArrayInputStream instream;

    if(gff_buff != null)
    {
      instream = new ByteArrayInputStream(gff_buff.getBytes());
      return instream;
    }

    try
    {
      GmodDAO dao = getDAO();

      // if creating a gene builder
      if(gene_builder)
      {
        List schemaList = new Vector();
        schemaList.add(schema);
          
        ByteBuffer bb = getGeneFeature(srcFeatureId,
                                       schemaList, dao);          
        return new ByteArrayInputStream(bb.getBytes());
      }

      ByteBuffer entry = new ByteBuffer();
      try
      {
        if(dao instanceof IBatisDAO)
          ((IBatisDAO) dao).startTransaction();

        gff_buffer = getGff(dao);
        
        if(splitGFFEntry)
        {
          if(gff_buffer[0].size() > 0)
            entry.append(gff_buffer[0]);

          getChadoSequence(dao, entry);
        }
        else
        {
          for(int i = 0; i < gff_buffer.length; i++)
          {
            if(gff_buffer[i].size() > 0)
              entry.append(gff_buffer[i]);
          }

          getChadoSequence(dao, entry);
        }

        if(dao instanceof IBatisDAO)
          ((IBatisDAO) dao).commitTransaction();
      }
      finally
      {
        if(dao instanceof IBatisDAO)
          ((IBatisDAO) dao).endTransaction();
      }

      instream = new ByteArrayInputStream(entry.getBytes());
      return instream;
    }
    catch(RuntimeException re)
    {
      JOptionPane.showMessageDialog(null, "Problems Reading...\n" +
          re.getMessage(),
          "Problems Reading From the Database ",
          JOptionPane.ERROR_MESSAGE);
      
      re.printStackTrace();
    }
    catch(java.sql.SQLException sqlExp)
    {
      JOptionPane.showMessageDialog(null, "Problems Reading...\n" +
          sqlExp.getMessage(),
          "Problems Reading From the Database ",
          JOptionPane.ERROR_MESSAGE);
      
      sqlExp.printStackTrace();
    }

    return null;
  }

  /**
   * 
   * Called (by DatabaseEntrySource) to retrieve all the documents for each
   * entry created.
   * 
   */
  public DatabaseDocument[] getGffDocuments(String location, String id,
                                            String schema)
  {
    int nentries = 0;
    for(int i = 1; i < gff_buffer.length; i++)
    {
      if(gff_buffer[i].size() > 0)
        nentries++;
    }

    DatabaseDocument[] new_docs = new DatabaseDocument[nentries];
    nentries = 0;
    for(int i = 1; i < gff_buffer.length; i++)
    {
      if(gff_buffer[i].size() == 0)
        continue;

      String name;
      if(i >= types.length)
        name = "other";
      else
        name = types[i];

      new_docs[nentries] = new DatabaseDocument(location, pfield, id, schema,
                                                gff_buffer[i], name);
      nentries++;
    }

    return new_docs;
  }

  /**
   * Create an array of GFF lines.
   * @param dao                 the data access object 
   * @param parentFeatureID     the parent identifier for the features to 
   *                            extract
   * @return   the <code>ByteBuffer</code> array of GFF lines
   */
  private ByteBuffer[] getGff(final GmodDAO dao)
  {
    final int srcfeature_id = Integer.parseInt(srcFeatureId);
    
    Splash.logger4j.debug("Build GFF");
    
    // build srcfeature object
    FeatureLoc featureloc = new FeatureLoc();
    Feature srcFeature = new Feature();
    srcFeature.setFeatureId(srcfeature_id);
    featureloc.setFeatureBySrcFeatureId(srcFeature);
    
    //featureloc.setSrcfeature_id(srcfeature_id);
    Feature parent = new Feature();
    parent.setFeatureLoc(featureloc);
    
    List featList = dao.getFeaturesByLocatedOnFeature(parent);

    ByteBuffer[] buffers = new ByteBuffer[types.length + 1];
    for(int i = 0; i < buffers.length; i++)
      buffers[i] = new ByteBuffer();

    final Feature parentFeature = dao.getFeatureById(srcfeature_id);
    
    ByteBuffer this_buff;

    int feature_size = featList.size();
    Hashtable id_store = new Hashtable(feature_size);

    // build feature name store
    for(int i = 0; i < feature_size; i++)
    {
      Feature feat = (Feature)featList.get(i);
      String name       = feat.getUniqueName();
      String featureId = Integer.toString(feat.getFeatureId());

      id_store.put(featureId, name);
    }
    
    // get all dbrefs & synonyms
    Hashtable dbxrefs = IBatisDAO.mergeDbXRef(
                 dao.getFeatureDbXRefsByFeatureUniquename(null));
    Hashtable synonym = getAllFeatureSynonyms(dao, null);

    Hashtable featureCvTerms = getFeatureCvTermsByFeature(dao, null);
    Hashtable featureCvTermDbXRefs = getFeatureCvTermDbXRef(dao, null);
    Hashtable featureCvTermPubs = getFeatureCvTermPub(dao, null);
    
    Hashtable featurePubs = getFeaturePubsBySrcFeatureId(dao,srcfeature_id);
    
    List pubDbXRefs= dao.getPubDbXRef();

    // create gff byte stream
    for(int i = 0; i < feature_size; i++)
    { 
      // select buffer based on feature type
      Feature feat = (Feature)featList.get(i);
      int type_id = feat.getCvTerm().getCvTermId();
      String typeName = getCvtermName(type_id, dao);
      this_buff = buffers[types.length];
      for(int j = 0; j < types.length; j++)
      {
        if(types[j].equals(typeName))
          this_buff = buffers[j];
      }
      
      
      chadoToGFF(feat, parentFeature.getUniqueName(),
                 dbxrefs, synonym, featureCvTerms,
                 pubDbXRefs, featureCvTermDbXRefs, featureCvTermPubs,
                 featurePubs,
                 id_store, dao, 
                 feat.getFeatureLoc(), this_buff);
       
      if( i%10 == 0 || i == feature_size-1)
        progress_listener.progressMade("Read from database: " + 
                                       feat.getUniqueName());
    }

    return buffers;
  }

  /**
   * Get a <code>Hashtable</code> of feature_id keys and their corresponding 
   * feature_synonym
   * 
   */
  private Hashtable getAllFeatureSynonyms(final GmodDAO dao, 
          final String uniquename) 
  {
    List list = dao.getFeatureSynonymsByFeatureUniquename(uniquename);  
    
    Hashtable synonym = new Hashtable();
    Integer featureId;
    List value;
    FeatureSynonym alias;
    
    for(int i=0; i<list.size(); i++)
    {
      alias = (FeatureSynonym)list.get(i);
      featureId = new Integer(alias.getFeature().getFeatureId());
      if(synonym.containsKey(featureId))
        value = (Vector)synonym.get(featureId);
      else
        value = new Vector();
      
      value.add(alias);
      synonym.put(featureId, value);
    }
    
    return synonym;
  }
  
  /**
   * Get FeaturePub's (i.e. /literature qualifiers).
   * @param dao
   * @param srcfeature_id
   * @return
   */
  private Hashtable getFeaturePubsBySrcFeatureId(final GmodDAO dao,
                                                 final int srcfeature_id)
  {
    List list = dao.getFeaturePubsBySrcFeatureId(srcfeature_id);
    
    Hashtable featurePubs = new Hashtable();
    Integer featureId;
    List value;
    FeaturePub featurePub;
    
    for(int i=0; i<list.size(); i++)
    {
      featurePub = (FeaturePub)list.get(i);
      featureId = new Integer(featurePub.getFeature().getFeatureId());
      if(featurePubs.containsKey(featureId))
        value = (Vector)featurePubs.get(featureId);
      else
        value = new Vector();
      
      value.add(featurePub);
      featurePubs.put(featureId, value);
    }
    
    return featurePubs;
  }
  
  /**
   * 
   * @param dao
   * @param chadoFeature null if we want them all
   * @return
   */
  private Hashtable getFeatureCvTermsByFeature(final GmodDAO dao, 
                                               final Feature chadoFeature)
  {
    List list = dao.getFeatureCvTermsByFeature(chadoFeature);
    
    Hashtable featureCvTerms = new Hashtable();
    Integer featureId;
    List value;
    FeatureCvTerm feature_cvterm;
    
    for(int i=0; i<list.size(); i++)
    {
      feature_cvterm = (FeatureCvTerm)list.get(i);
      featureId = new Integer(feature_cvterm.getFeature().getFeatureId());
      if(featureCvTerms.containsKey(featureId))
        value = (Vector)featureCvTerms.get(featureId);
      else
        value = new Vector();
      
      value.add(feature_cvterm);
      featureCvTerms.put(featureId, value);
    }
    
    return featureCvTerms;
  }
  
  /**
   * 
   * @param dao
   * @param chadoFeature null if we want all
   * @return
   */
  private Hashtable getFeatureCvTermDbXRef(final GmodDAO dao, final Feature chadoFeature)
  {
    List list = dao.getFeatureCvTermDbXRefByFeature(chadoFeature);
    if(list == null || list.size() == 0)
      return null;
    
    Integer featureCvTermDbXRefId;
    List value;
    
    Hashtable featureCvTermDbXRefs = new Hashtable(list.size());
    for(int i=0; i<list.size(); i++)
    {
      FeatureCvTermDbXRef featureCvTermDbXRef =
        (FeatureCvTermDbXRef)list.get(i);
      
      featureCvTermDbXRefId = new Integer(
          featureCvTermDbXRef.getFeatureCvTerm().getFeatureCvTermId());
      
      if(featureCvTermDbXRefs.containsKey(featureCvTermDbXRefId))
        value = (Vector)featureCvTermDbXRefs.get(featureCvTermDbXRefId);
      else
        value = new Vector();
      
      value.add(featureCvTermDbXRef);
      featureCvTermDbXRefs.put(featureCvTermDbXRefId, value);
    }
     
    return featureCvTermDbXRefs;
  }
  
  private Hashtable getFeatureCvTermPub(final GmodDAO dao,
                                        final Feature chadoFeature)
  {
    List list = dao.getFeatureCvTermPubByFeature(chadoFeature);
    if(list == null || list.size() == 0)
      return null;
    
    Integer featureCvTermId;
    List value;
    
    Hashtable featureCvTermPubs = new Hashtable(list.size());
    for(int i=0; i<list.size(); i++)
    {
      FeatureCvTermPub featureCvTermPub =
        (FeatureCvTermPub)list.get(i);
      
      featureCvTermId = new Integer(
          featureCvTermPub.getFeatureCvTerm().getFeatureCvTermId());
      
      if(featureCvTermPubs.containsKey(featureCvTermId))
        value = (Vector)featureCvTermPubs.get(featureCvTermId);
      else
        value = new Vector();
      
      value.add(featureCvTermPub);
      featureCvTermPubs.put(featureCvTermId, value);
    }
     
    return featureCvTermPubs;
  }
  
  /**
   * Use by the gene editor to retrieve the gene and related
   * features
   * @param search_gene     gene uniquename
   * @param schema_search   schema list to search
   * @param dao             data access method
   * @return  GFF byte buffer
   * @throws SQLException
   * @throws ReadFormatException
   * @throws ConnectException 
   */
  private ByteBuffer getGeneFeature(final String search_gene, 
                                    final List schema_search,
                                    GmodDAO dao) 
          throws SQLException, ReadFormatException, ConnectException
  {
    Hashtable id_store = new Hashtable();

    reset((String)getLocation(), (String)schema_search.get(0));
    dao = getDAO();
    Feature chadoFeature = 
      (Feature)(dao.getFeaturesByUniqueName(search_gene).get(0));
    
    ChadoCanonicalGene chado_gene = new ChadoCanonicalGene();
    id_store.put(Integer.toString(chadoFeature.getFeatureId()), 
                 chadoFeature.getUniqueName());

    List featurelocs = new Vector(chadoFeature.getFeatureLocsForFeatureId());
    FeatureLoc featureloc = (FeatureLoc) featurelocs.get(0);
    int src_id = featureloc.getSrcFeatureId();
    srcFeatureId = Integer.toString(src_id);

    Feature parent = new Feature();
    parent.setFeatureId(src_id);

    parent = dao.getFeatureById(src_id);
    
    chado_gene.setSeqlen(parent.getSeqLen());
    chado_gene.setSrcfeature_id(src_id);

    ByteBuffer buff = new ByteBuffer();
    
    buildGffLineFromId(dao, chadoFeature.getFeatureId(), 
        id_store, parent.getUniqueName(), src_id, buff, chadoFeature);
    

    // get children of gene
    List relations = new Vector(chadoFeature.getFeatureRelationshipsForObjectId());
    
    for(int i = 0; i < relations.size(); i++)
    {
      //Feature transcript = new Feature();
      
      int id = ((FeatureRelationship) relations.get(i)).getFeatureBySubjectId().getFeatureId();
      
      Feature transcript = buildGffLineFromId(dao, id, id_store, parent.getUniqueName(), 
                                              src_id, buff, null);

      // get children of transcript - exons and pp
      List transcipt_relations = new Vector(
          transcript.getFeatureRelationshipsForObjectId());

      for(int j = 0; j < transcipt_relations.size(); j++)
      {
        id = ((FeatureRelationship) transcipt_relations.get(j)).getFeatureBySubjectId().getFeatureId();

        buildGffLineFromId(dao, id, id_store, parent.getUniqueName(), 
                           src_id, buff, null);
      }
    }

    logger4j.debug( new String(buff.getBytes()) );
    return buff;
  }
  
  private Feature buildGffLineFromId(final GmodDAO dao, 
                                  final int featureId, 
                                  final Hashtable id_store,
                                  final String parentName,
                                  final int srcFeatureId,
                                  final ByteBuffer this_buff,
                                  Feature chadoFeature)
  {
    if(chadoFeature == null)
      chadoFeature = (Feature)dao.getFeatureById(featureId); 

    id_store.put(Integer.toString(chadoFeature.getFeatureId()), 
                 chadoFeature.getUniqueName());

    FeatureLoc loc = getFeatureLoc(new Vector(
        chadoFeature.getFeatureLocsForFeatureId()), srcFeatureId);
    Hashtable dbxrefs = IBatisDAO.mergeDbXRef(
        dao.getFeatureDbXRefsByFeatureUniquename(chadoFeature.getUniqueName()));
    Hashtable synonym = getAllFeatureSynonyms(dao, chadoFeature.getUniqueName());
    
    Hashtable featureCvTerms = getFeatureCvTermsByFeature(dao, chadoFeature);
    Hashtable featureCvTermDbXRefs = getFeatureCvTermDbXRef(dao, chadoFeature);
    Hashtable featureCvTermPubs = getFeatureCvTermPub(dao, chadoFeature);
    Hashtable featurePubs = getFeaturePubsBySrcFeatureId(dao,srcFeatureId);
    List pubDbXRefs= dao.getPubDbXRef();
    chadoToGFF(chadoFeature, parentName, dbxrefs, synonym, featureCvTerms,
        pubDbXRefs, featureCvTermDbXRefs, featureCvTermPubs, featurePubs, id_store, dao, loc, this_buff);  
    return chadoFeature;
  }
  
  /**
   * Convert the chado feature into a GFF line
   * @param feat           Chado feature
   * @param parentFeature  parent of this feature
   * @param dbxrefs        hashtable containing dbxrefs
   * @param synonym        hashtable containing synonynms
   * @param featureCvTerms
   * @param pubDbXRefs
   * @param featureCvTermDbXRefs
   * @param id_store       id store for looking up parent names
   * @param dao            chado data access
   * @param featureloc     feature location for this chado feature
   * @param this_buff      byte buffer of GFF line 
   */
  private static void chadoToGFF(final Feature feat,
                                 final String parentFeature,
                                 final Hashtable dbxrefs,
                                 final Hashtable synonym,
                                 final Hashtable featureCvTerms,
                                 final List pubDbXRefs,
                                 final Hashtable featureCvTermDbXRefs,
                                 final Hashtable featureCvTermPubs,
                                 final Hashtable featurePubs,
                                 final Hashtable id_store,
                                 final GmodDAO dao,
                                 final FeatureLoc featureloc,
                                 final ByteBuffer this_buff)
  {
    String gff_source = null;
    
    final int fmin          = featureloc.getFmin().intValue() + 1;
    final int fmax          = featureloc.getFmax().intValue();
    final int type_id       = feat.getCvTerm().getCvTermId();
    final Short strand      = featureloc.getStrand();
    final Integer phase     = featureloc.getPhase();
    final String name       = feat.getUniqueName();
    final String typeName   = getCvtermName(type_id, dao);
    final Integer featureId = new Integer(feat.getFeatureId());
    final String timelastmodified = Long.toString(feat.getTimeLastModified().getTime());

    String parent_id = null;
    String parent_relationship = null;
    int rank = -1;
/*    if(feat.getFeatureRelationship() != null)
    {
      FeatureRelationship feat_relationship = feat.getFeatureRelationship();
      parent_id = Integer.toString(feat_relationship.getFeatureByObjectId().getFeatureId());
      long parent_type_id = feat_relationship.getCvTerm().getCvTermId();
      
      parent_relationship = feat_relationship.getCvTerm().getName();
      
      rank= feat_relationship.getRank();
      if(parent_relationship == null)
        parent_relationship = getCvtermName(parent_type_id, dao);
    }
    else */
      
    if(feat.getFeatureRelationshipsForSubjectId() != null)
    {
      List relations = new Vector(feat.getFeatureRelationshipsForSubjectId());
      for(int i=0; i<relations.size(); i++)
      {
        FeatureRelationship feat_relationship = 
                            (FeatureRelationship)relations.get(i);
        parent_id = Integer.toString(feat_relationship.getFeatureByObjectId().getFeatureId());
        rank      = feat_relationship.getRank();
        
        if( feat_relationship.getCvTerm().getName() == null )
        {
          int parent_type_id = feat_relationship.getCvTerm().getCvTermId();
          parent_relationship = getCvtermName(parent_type_id, dao);
        }
        else
          parent_relationship = feat_relationship.getCvTerm().getName();
      }
    }
          
    if(parent_id != null && id_store != null &&  id_store.containsKey(parent_id))
      parent_id = (String)id_store.get(parent_id);
 
    // make gff format
    
    Vector dbxref = null;
    // append dbxrefs
    if(dbxrefs != null &&
       dbxrefs.containsKey(featureId))
    {
      dbxref = (Vector)dbxrefs.get(featureId);
      for(int j=0; j<dbxref.size(); j++)
      {
        if(((String)dbxref.get(j)).startsWith("GFF_source:"))
        {
          gff_source = ((String)dbxref.get(j)).substring(11);
          dbxref.removeElementAt(j);
        }
      }
    }

    this_buff.append(parentFeature + "\t"); // seqid
    
    if(gff_source != null)
      this_buff.append(gff_source+"\t");    // source
    else
      this_buff.append("chado\t");            
    this_buff.append(typeName + "\t");      // type
    this_buff.append(fmin + "\t");          // start
    this_buff.append(fmax + "\t");          // end
    this_buff.append(".\t");                // score
    if(strand.equals( new Short((short)-1)) )                        // strand
      this_buff.append("-\t");
    else if(strand.equals( new Short((short)1)) )
      this_buff.append("+\t");
    else
      this_buff.append(".\t");

    if(phase == null)
      this_buff.append(".\t");               // phase
    else
      this_buff.append(phase+"\t"); 

    this_buff.append("ID=" + name + ";");
    this_buff.append("feature_id=" + featureId.toString() + ";");

   
    if(parent_id != null && !parent_id.equals("0"))
    {
      if(parent_relationship.equals("derives_from"))
        this_buff.append("Derives_from=" + parent_id + ";");
      else
        this_buff.append("Parent=" + parent_id + ";");
    }

    this_buff.append("timelastmodified=" + timelastmodified + ";");
    
    // this is the chado feature_relationship.rank used
    // to order joined features e.g. exons
    if(rank > -1)
      this_buff.append("feature_relationship_rank="+rank+";"); 

    //this_buff.append("feature_id="+feature_id+";");
    
    // attributes
    if(feat.getFeatureProps() != null &&
       feat.getFeatureProps().size() > 0)
    {
      Collection featureprops = feat.getFeatureProps();
      Iterator it = featureprops.iterator();
      
      while(it.hasNext())
      {
        FeatureProp featprop = (FeatureProp)it.next();
        String qualifier_name = getCvtermName(featprop.getCvTerm().getCvTermId(), dao);
        if(qualifier_name == null)
          continue;
        if(featprop.getValue() != null)
          this_buff.append(qualifier_name+ "=" +
                           GFFStreamFeature.encode(featprop.getValue())+";");
      }
    }

    // append dbxrefs
    if(dbxref != null && dbxref.size() > 0)
    {
      this_buff.append("Dbxref=");
      for(int j=0; j<dbxref.size(); j++)
      {
        this_buff.append((String)dbxref.get(j));
        if(j<dbxref.size()-1)
          this_buff.append(",");
      }
      this_buff.append(";");
    }
    
    // append synonyms
    if(synonym != null &&
       synonym.containsKey(featureId))
    {   
      FeatureSynonym alias;
      Vector v_synonyms = (Vector)synonym.get(featureId);
      for(int j=0; j<v_synonyms.size(); j++)
      {
        alias = (FeatureSynonym)v_synonyms.get(j);
        
        this_buff.append( getCvtermName(alias.getSynonym().getCvTerm().getCvTermId(), dao) + "=" );
        //this_buff.append(alias.getSynonym().getCvterm().getName()+"=");
        this_buff.append(alias.getSynonym().getName());
        
        //if(j<v_synonyms.size()-1)
        this_buff.append(";");
      }
    }
    
    // /literature
    if(featurePubs != null &&
       featurePubs.containsKey(featureId))
    {
      FeaturePub featurePub;
      Vector v_featurePubs = (Vector)featurePubs.get(featureId);
      for(int j=0; j<v_featurePubs.size(); j++)
      {
        featurePub = (FeaturePub)v_featurePubs.get(j);
        this_buff.append( "literature=" );
        this_buff.append(featurePub.getPub().getUniqueName());
        this_buff.append(";");
      }
    }
    
    // GO, controlled_curation, product
    if(featureCvTerms != null && 
       featureCvTerms.containsKey(featureId))
    {
      FeatureCvTerm feature_cvterm;
      Vector v_feature_cvterms = (Vector)featureCvTerms.get(featureId);
      for(int j=0; j<v_feature_cvterms.size(); j++)
      {
        feature_cvterm = (FeatureCvTerm)v_feature_cvterms.get(j);
        
        Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() );
        
        List featureCvTermDbXRefList = null;
        
        if(featureCvTermDbXRefs != null)
          featureCvTermDbXRefList = (List)featureCvTermDbXRefs.get(featureCvTermId);
        
        List featureCvTermPubList = null;
        
        if(featureCvTermPubs != null)
          featureCvTermPubList = (List)featureCvTermPubs.get(featureCvTermId);
          
        appendControlledVocabulary(this_buff, dao, feature_cvterm,
                                   featureCvTermDbXRefList,featureCvTermPubList, pubDbXRefs);
      }
      //System.out.println(new String(this_buff.getBytes()));
    }
      
    this_buff.append("\n");
  }
  
  /**
   * Appends controlled vocabulary terms to the buffer
   * @param attr_buff
   * @param dao
   * @param feature_cvterm
   * @param featureCvTermDbXRef
   */
  public static void appendControlledVocabulary(final ByteBuffer attr_buff,
                                          final GmodDAO dao,
                                          final FeatureCvTerm feature_cvterm,
                                          final List featureCvTermDbXRefs,
                                          final List featureCvTermPubs,
                                          final List pubDbXRefs)
  {
    CvTerm cvterm =  getCvTerm( feature_cvterm.getCvTerm().getCvTermId(), dao);
    DbXRef dbXRef = feature_cvterm.getCvTerm().getDbXRef();
    
    if(cvterm.getCv().getName().startsWith(DatabaseDocument.CONTROLLED_CURATION_TAG_CVNAME))
    {
      attr_buff.append("controlled_curation=");
      
      attr_buff.append("term="+
          GFFStreamFeature.encode(feature_cvterm.getCvTerm().getName())+"%3B");
      attr_buff.append("cv="+
          GFFStreamFeature.encode(feature_cvterm.getCvTerm().getCv().getName())+"%3B");   
      
      // N.B. the db_xref may be a FeatureCvTermDbXRef or a Pub for /controlled_curation
      int nfound_dbxref = 0;
      if(feature_cvterm.getPub().getUniqueName() != null &&
         !feature_cvterm.getPub().getUniqueName().equalsIgnoreCase("NULL"))
      {
        // PMID
        Pub pub = feature_cvterm.getPub();
        
        // internal check
        checkPubDbXRef(pubDbXRefs, pub.getPubId(), pub, feature_cvterm);
        
        attr_buff.append("db_xref="+ pub.getUniqueName());
        nfound_dbxref++;
      }
      
      if(featureCvTermDbXRefs != null &&
              featureCvTermDbXRefs.size() > 0)
      {
        for(int i=0; i<featureCvTermDbXRefs.size(); i++)
        {
          FeatureCvTermDbXRef featureCvTermDbXRef =
            (FeatureCvTermDbXRef)featureCvTermDbXRefs.get(i);
    
          if(feature_cvterm.getFeatureCvTermId() != 
            featureCvTermDbXRef.getFeatureCvTerm().getFeatureCvTermId())
            continue;
      
          if(nfound_dbxref == 0)
            attr_buff.append("db_xref=");
          else if(nfound_dbxref > 0)
            attr_buff.append("|");
          
          DbXRef fc_dbXRef = featureCvTermDbXRef.getDbXRef();
          attr_buff.append(fc_dbXRef.getDb().getName()+":");
          attr_buff.append(fc_dbXRef.getAccession());
          nfound_dbxref++;
        }
      }
      
      if(nfound_dbxref > 0)
        attr_buff.append("%3B");
      
      List feature_cvtermprops = (List) feature_cvterm.getFeatureCvTermProps();
      for(int i = 0; i < feature_cvtermprops.size(); i++)
      {
        FeatureCvTermProp feature_cvtermprop = 
          (FeatureCvTermProp)feature_cvtermprops.get(i);
        attr_buff.append(getCvtermName(feature_cvtermprop.getCvTerm()
            .getCvTermId(), dao));
        attr_buff.append("=");
        attr_buff.append(GFFStreamFeature.encode(feature_cvtermprop.getValue()));
        if(i < feature_cvtermprops.size()-1)
          attr_buff.append("%3B");
      }
      
      attr_buff.append(";");
    }
    else if(cvterm.getCv().getName().equals(DatabaseDocument.PRODUCTS_TAG_CVNAME))
    {
      attr_buff.append("product=");
      attr_buff.append(GFFStreamFeature.encode(feature_cvterm.getCvTerm().getName())+";");
    }
    else if(cvterm.getCv().getName().equals(DatabaseDocument.RILEY_TAG_CVNAME))
    {
      // class include the cvTermId as a convenience for looking up the term
      attr_buff.append("class=");
      attr_buff.append(dbXRef.getAccession()+"::"+
                      feature_cvterm.getCvTerm().getCvTermId()+";");
    }
    else
    {
      attr_buff.append("GO=");

      if(cvterm.getCv().getName().equals("molecular_function"))
        attr_buff.append("aspect=F%3B");
      else if(cvterm.getCv().getName().equals("cellular_component"))
        attr_buff.append("aspect=C%3B");
      else if(cvterm.getCv().getName().equals("biological_process"))
        attr_buff.append("aspect=P%3B");

      if(feature_cvterm.isNot())
        attr_buff.append("qualifier=NOT%3B");

      attr_buff.append("GOid="+dbXRef.getDb().getName() + ":"
          + dbXRef.getAccession() + "%3B");
      
      attr_buff.append("term="+
          GFFStreamFeature.encode(feature_cvterm.getCvTerm().getName())+"%3B");
      
      // PMID
      int nfound_pub = 0;
      if(feature_cvterm.getPub() != null &&
         feature_cvterm.getPub().getUniqueName() != null &&
         !feature_cvterm.getPub().getUniqueName().equalsIgnoreCase("NULL"))
      {
        Pub pub = feature_cvterm.getPub();
        attr_buff.append("db_xref="+
            pub.getUniqueName());
        nfound_pub++;
      }
      
      if(featureCvTermPubs != null &&
          featureCvTermPubs.size() > 0)
      {
        for(int i=0; i<featureCvTermPubs.size(); i++)
        {
          FeatureCvTermPub featureCvTermPub =
            (FeatureCvTermPub)featureCvTermPubs.get(i);
          
          if(feature_cvterm.getFeatureCvTermId() != 
            featureCvTermPub.getFeatureCvTerm().getFeatureCvTermId())
            continue;
          
          if(nfound_pub == 0)
            attr_buff.append("db_xref=");
          else if(nfound_pub > 0)
            attr_buff.append("|");

          attr_buff.append(featureCvTermPub.getPub().getUniqueName());
          nfound_pub++;
        }
      }
      
      if(nfound_pub > 0)
        attr_buff.append("%3B");
      
      if(featureCvTermDbXRefs != null &&
          featureCvTermDbXRefs.size() > 0 )
      {  
        int nfound = 0;
        for(int i=0; i<featureCvTermDbXRefs.size(); i++)
        {
          FeatureCvTermDbXRef featureCvTermDbXRef =
            (FeatureCvTermDbXRef)featureCvTermDbXRefs.get(i);
          
          
          if(feature_cvterm.getFeatureCvTermId() != 
            featureCvTermDbXRef.getFeatureCvTerm().getFeatureCvTermId())
          {
            continue;
          }
          
          if(nfound == 0)
            attr_buff.append("with=");
          else if(nfound > 1)
            attr_buff.append("|");
          
          DbXRef fc_dbXRef = featureCvTermDbXRef.getDbXRef();
          attr_buff.append(fc_dbXRef.getDb().getName()+":");
          attr_buff.append(fc_dbXRef.getAccession());
          nfound++;
        }
        
        if(nfound > 0)
          attr_buff.append("%3B");
      }
      
      List feature_cvtermprops = (List)feature_cvterm
          .getFeatureCvTermProps();
      for(int i = 0; i < feature_cvtermprops.size(); i++)
      {
        FeatureCvTermProp feature_cvtermprop = 
          (FeatureCvTermProp)feature_cvtermprops.get(i);
        
        if(feature_cvtermprop.getValue() == null)
          continue;
        
        attr_buff.append(getCvtermName(feature_cvtermprop.getCvTerm()
            .getCvTermId(), dao));
        attr_buff.append("=");
        attr_buff.append(GFFStreamFeature.encode(feature_cvtermprop.getValue()));
        if(i < feature_cvtermprops.size()-1)
          attr_buff.append("%3B");
      }
      
      attr_buff.append(";");
    }
  }
  
  /**
   * Check the PubDbXref contains the Pub in FeatureCvTerm
   * @param pubDbXRefs
   * @param pubId
   * @param pub
   * @param feature_cvterm
   */
  private static void checkPubDbXRef(final List pubDbXRefs, final int pubId,
                                     final Pub pub, final FeatureCvTerm feature_cvterm)
  {
    PubDbXRef pubDbXRef = null;
    for(int i = 0; i < pubDbXRefs.size(); i++)
    {
      pubDbXRef = (PubDbXRef) pubDbXRefs.get(i);
      if(pubDbXRef.getPub().getPubId() == pubId)
      {
        DbXRef dbxref = pubDbXRef.getDbXRef();
        Splash.logger4j.debug("Checking PubDbXRef and found Pub "+dbxref.getDb().getName()+
                              ":"+dbxref.getAccession());
        break;
      }
    }
    
    if(pubDbXRef == null || 
        !pub.getUniqueName().endsWith(pubDbXRef.getDbXRef().getAccession()))
     {
       Splash.logger4j.debug("Checking PubDbXRef and not found Pub "+
                           feature_cvterm.getPub().getUniqueName());
      
       JOptionPane.showMessageDialog(null, "Cannot find pub_dbxref for:\n"+
           feature_cvterm.getPub().getUniqueName(), 
           "Database Error",
           JOptionPane.ERROR_MESSAGE);
     }
  }
  
  /**
   * Look up the cvterm_id for a controlled vocabulary name.
   * @param name  
   * @return
   */
  public static Integer getCvtermID(String name)
  {
    Enumeration enum_cvterm = cvterms.keys();
    while(enum_cvterm.hasMoreElements())
    {
      Integer key = (Integer)enum_cvterm.nextElement();
      if(name.equals( ((CvTerm)cvterms.get(key)).getName() ))
        return key;
    }
    return null;
  }

  /**
   * Look up a cvterm name from the collection of cvterms.
   * @param id  a cvterm_id  
   * @return    the cvterm name
   */
  private static String getCvtermName(int id, GmodDAO dao)
  {
    return getCvTerm(id, dao).getName();
  }
  
  private static CvTerm getCvTerm(int id, GmodDAO dao)
  {
    if(cvterms == null)
      getCvterms(dao);

    return (CvTerm)cvterms.get(new Integer(id));
  }
  
  /**
   * Use the CvTerm name to return a CvTerm.
   * @param cvTermId
   * @return
   */
  public static CvTerm getCvTermByCvTermName(String cvterm_name)
  {
    Enumeration enum_cvterm = cvterms.elements();
    while(enum_cvterm.hasMoreElements())
    {
      CvTerm cvterm = (CvTerm)enum_cvterm.nextElement();
      if(cvterm_name.equals( cvterm.getName() ))
        return cvterm;
    }
    
    return null;
  }
  
  /**
   * Use the CvTermId to return a CvTerm.
   * @param cvTermId
   * @return
   */
  public static CvTerm getCvTermByCvTermId(final int cvTermId)
  {
    Enumeration enum_cvterm = cvterms.elements();
    while(enum_cvterm.hasMoreElements())
    {
      CvTerm cvterm = (CvTerm)enum_cvterm.nextElement();
      if(cvterm.getCvTermId() == cvTermId)
        return cvterm;
    }
    
    return null;
  }
  
  /**
   * Use the Cv name and CvTerm name to return a CvTerm.
   * @param cvterm_name
   * @param cvName
   * @return
   */
  public static CvTerm getCvTermByCvAndCvTerm(final String cvterm_name,
                                              final String cvName)
  {
    Enumeration enum_cvterm = cvterms.elements();
    while(enum_cvterm.hasMoreElements())
    {
      CvTerm cvterm = (CvTerm)enum_cvterm.nextElement();
      if(cvName.equals( cvterm.getCv().getName() ) &&
         cvterm_name.equals( cvterm.getName() ))
        return cvterm;
    }
    return null;
  }

  /**
   * This is different from getCvTermByCvAndCvTerm as it makes sure
   * the Cv name part matches the name supplied to the function, i.e.
   * by matching just the start.
   * @param cvterm_name
   * @param cvName
   * @return
   */
  public static CvTerm getCvTermByCvPartAndCvTerm(final String cvterm_name,
                                              final String cvName)
  {
    Enumeration enum_cvterm = cvterms.elements();
    while(enum_cvterm.hasMoreElements())
    {
      CvTerm cvterm = (CvTerm)enum_cvterm.nextElement();
      if(cvterm.getCv().getName().startsWith( cvName ) &&
         cvterm_name.equals( cvterm.getName() ))
        return cvterm;
    }
    return null;
  }
  /**
   * Look up cvterms names and id and return in a hashtable.
   * @param dao the data access object
   * @return    the cvterm <code>Hashtable</code>
   */
  private static Hashtable getCvterms(GmodDAO dao)
  {
    cvterms = new Hashtable();

    try
    {
      List cvterm_list = dao.getCvTerms();
      Iterator it = cvterm_list.iterator();

      while(it.hasNext())
      {
        CvTerm cvterm = (CvTerm)it.next();
        cvterms.put(new Integer(cvterm.getCvTermId()), cvterm);
      }
    }
    catch(RuntimeException sqle)
    {
      System.err.println("SQLException retrieving CvTerms");
      System.err.println(sqle);
    }

    return cvterms;
  }
  
  public List getDatabaseNames()
  {
    try
    {
      GmodDAO dao = getDAO();
      List dbs = dao.getDbs();
      List names = new Vector();
      Iterator it = dbs.iterator();
      while(it.hasNext())
      {
        Db db = (Db)it.next();
        names.add(db.getName());
      }
      return names;
    }
    catch(ConnectException e)
    {
      // TODO Auto-generated catch block
      e.printStackTrace();
    }
    catch(SQLException e)
    {
      // TODO Auto-generated catch block
      e.printStackTrace();
    }
    return null;
  }
  
  public static Vector getCvterms(final String search_str, final String cv_name)
  {
    final Vector cvterm_match = new Vector();
    
    Enumeration enum_cvterm = cvterms.keys();
    while(enum_cvterm.hasMoreElements())
    {
      Integer key = (Integer)enum_cvterm.nextElement();
      CvTerm cvterm = (CvTerm)cvterms.get(key);
      
      if(cvterm.getCv().getName().startsWith(cv_name))
      {
        if(cvterm.getName().indexOf(search_str) > -1)
          cvterm_match.add(cvterm);
      }
    }
    
    return cvterm_match;
  }

  /**
   * Look up synonym type names e.g. synonym, systematic_id.
   * @return    the synonym tag names
   */
  public static String[] getSynonymTypeNames(String cv_name)
  {
    Vector synonym_names = new Vector();
    Enumeration cvterm_enum = cvterms.elements();
    while(cvterm_enum.hasMoreElements())
    {
      CvTerm cvterm = (CvTerm)cvterm_enum.nextElement();
      if(cvterm.getCv().getName().equals(cv_name))
        synonym_names.add(cvterm.getName());
    }
    
    return (String[])synonym_names.toArray(
                       new String[synonym_names.size()]);
  }
  
  
  /**
   * Get the sequence for a feature.
   * @param dao   the data access object
   * @param buff  the buffer to add the sequence to
   * @return      the resulting buffer
   * @throws java.sql.SQLException
   */
  private ByteBuffer getChadoSequence(GmodDAO dao, ByteBuffer buff)
  {
    Feature feature = dao.getFeatureById(Integer.parseInt(srcFeatureId));
 
    buff.append("##FASTA\n>");
    buff.append(feature.getUniqueName());
    buff.append("\n");
    buff.append(feature.getResidues());
    return buff;
  }

  /**
   * Get the <code>List</code> of available schemas.
   * @return  the <code>List</code> of available schemas
   */
  public List getSchema()
  {
    return schema_list;
  }
  
  public List getSimilarityMatches()
  {
    try
    {
      GmodDAO dao = getDAO();
      return dao.getSimilarityMatches(new Integer(srcFeatureId));
    }
    catch(RuntimeException sqlExp)
    {
      JOptionPane.showMessageDialog(null, "SQL Problems...\n"+
                                    sqlExp.getMessage(), 
                                    "SQL Error",
                                    JOptionPane.ERROR_MESSAGE);
    }
    catch(ConnectException exp)
    {
      JOptionPane.showMessageDialog(null, "Connection Problems...\n"+
            exp.getMessage(), 
            "Connection Error",
            JOptionPane.ERROR_MESSAGE);
    }
    catch(java.sql.SQLException sqlExp)
    {
      JOptionPane.showMessageDialog(null, "SQL Problems....\n"+
                                    sqlExp.getMessage(), 
                                    "SQL Error",
                                    JOptionPane.ERROR_MESSAGE);
    }
    return null;
  }
  
  /**
   * Create a hashtable of the available entries with residues.
   * @return a <code>Hashtable</code> of the <code>String</code>
   *          representation (schema-type-feature_name) and the
   *          corresponding feature_id
   * @throws ConnectException
   * @throws java.sql.SQLException
   */
  public HashMap getDatabaseEntries()
                   throws ConnectException, java.sql.SQLException
  {
    String schema = null;
    HashMap db = new HashMap();
    try
    { 
      GmodDAO dao = getDAO();
      schema_list = dao.getSchema();  //.getOrganisms();
      
      Iterator it = schema_list.iterator();
        
      while(it.hasNext())
      {
        //Organism organism = (Organism)it.next();
        //schema = organism.getCommonName();
        schema = (String)it.next();
        
        reset((String)getLocation(),  schema);

        try
        {
          dao = getDAO();
          List list_residue_features = dao.getResidueFeatures();
          
          Iterator it_residue_features = list_residue_features.iterator();
          while(it_residue_features.hasNext())
          {
            Feature feature = (Feature)it_residue_features.next();
            String typeName = getCvtermName(feature.getCvTerm().getCvTermId(), getDAO()); 
          
            db.put(schema + " - " + typeName + " - " + feature.getUniqueName(),
                   Integer.toString(feature.getFeatureId()));
          }
        }
        catch(RuntimeException e){}
        catch(java.sql.SQLException sqlExp){}
      }
      
    }
    catch(RuntimeException sqlExp)
    {
      JOptionPane.showMessageDialog(null, "SQL Problems...\n"+
                                    sqlExp.getMessage(), 
                                    "SQL Error",
                                    JOptionPane.ERROR_MESSAGE);
      
      logger4j.debug(sqlExp.getMessage());
      //sqlExp.printStackTrace();
    }
    catch(ConnectException exp)
    {
      JOptionPane.showMessageDialog(null, "Connection Problems...\n"+
            exp.getMessage(), 
            "Connection Error",
            JOptionPane.ERROR_MESSAGE);
      logger4j.debug(exp.getMessage());
      throw exp;
    }
    catch(java.sql.SQLException sqlExp)
    {
      JOptionPane.showMessageDialog(null, "SQL Problems....\n"+
                                    sqlExp.getMessage(), 
                                    "SQL Error",
                                    JOptionPane.ERROR_MESSAGE);
      logger4j.debug(sqlExp.getMessage());
      throw sqlExp;
    }
    
    return db;
  }
  
  
  /**
   * Get the data access object (DAO).
   * @return data access object
   */
  private GmodDAO getDAO()
     throws java.net.ConnectException, SQLException
  { 
    if(!iBatis)
    {
      if(jdbcDAO == null)
       jdbcDAO = new JdbcDAO((String)getLocation(), pfield); 
      return jdbcDAO;
    }
    else
    {   
      if(connIB == null)
      {
        System.setProperty("chado", (String)getLocation());
        connIB = new IBatisDAO(pfield);
      }
      return connIB;
    }
  }


  /**
   * Create a new OutputStream object from this Document. The contents of the
   * Document can be written from the stream.
   * 
   * @exception IOException
   *              Thrown if the Document can't be written.
   */
  public OutputStream getOutputStream() throws IOException
  {
    final File write_file = new File(System.getProperty("user.dir")+
                                     System.getProperty("file.separator")+
                                     getName());

    final FileOutputStream file_output_stream =
      new FileOutputStream(write_file);

    if(write_file.getName().endsWith(".gz")) 
    {
      // assume this file should be gzipped
      return new java.util.zip.GZIPOutputStream (file_output_stream);
    } 
    else 
      return file_output_stream;
  }

  /**
   * Commit the <code>ChadoTransaction</code> SQL back to the
   * database.
   * @param sql the collection of <code>ChadoTransaction</code> objects
   * @return
   */
  public int commit(Vector sql)
  {
    int i = 0;

    try
    {
      
      GmodDAO dao = getDAO();
      if(dao instanceof IBatisDAO)
        ((IBatisDAO) dao).startTransaction();
      boolean unchanged;
      
      //
      // check feature timestamps have not changed
      Vector names_checked = new Vector();
      for(i = 0; i < sql.size(); i++)
      {
        ChadoTransaction tsn = (ChadoTransaction)sql.get(i);
        if( (tsn.getType() == ChadoTransaction.INSERT ||
             tsn.getType() == ChadoTransaction.DELETE) && 
             tsn.getFeatureObject() instanceof Feature )
          continue;
            
        final String uniquename = tsn.getUniquename();
        
        if(uniquename == null)
          continue;
        
        if(names_checked.contains(uniquename))
          continue;

        names_checked.add(uniquename);
        
        String keyName = tsn.getFeatureKey();
        unchanged = checkFeatureTimestamp(schema, 
                         uniquename, 
                         tsn.getLastModified(), dao, 
                         keyName, tsn.getFeatureObject());
        if(!unchanged)
          return 0;
      }  
      
      try
      {
        //
        // commit to database
        for(i = 0; i < sql.size(); i++)
        {
          ChadoTransaction tsn = (ChadoTransaction) sql.get(i);

          if(tsn.getType() == ChadoTransaction.UPDATE)
          {
            if(tsn.getFeatureObject() instanceof Feature)
            {
              Feature feature = (Feature)tsn.getFeatureObject();
              
              if(feature.getUniqueName() != null)
              {
                final String uniquename;
                if(tsn.getOldUniquename() != null)
                  uniquename = (String)tsn.getOldUniquename();
                else
                  uniquename = feature.getUniqueName();
                
                Feature old_feature
                    = dao.getFeatureByUniqueName(uniquename, tsn.getFeatureKey());
                
                if(old_feature != null)
                  feature.setFeatureId( old_feature.getFeatureId() );
                
                tsn.setOldUniquename(feature.getUniqueName());
              }
            }
            dao.merge(tsn.getFeatureObject());
            //dao.updateAttributes(tsn);
          }
          else if(tsn.getType() == ChadoTransaction.INSERT)
          {
            if(tsn.getFeatureObject() instanceof FeatureCvTerm)
              ArtemisUtils.inserFeatureCvTerm(dao, (FeatureCvTerm)tsn.getFeatureObject());
            else
            {
              // set srcfeature_id
              if(tsn.getFeatureObject() instanceof Feature)
              {
                FeatureLoc featureloc = ((Feature) tsn.getFeatureObject()).getFeatureLoc();
                Feature featureBySrcFeatureId = new Feature();
                featureBySrcFeatureId.setFeatureId(Integer.parseInt(srcFeatureId));
                featureloc.setFeatureBySrcFeatureId(featureBySrcFeatureId);
              }
              dao.persist(tsn.getFeatureObject());
            }
            
          }
          else if(tsn.getType() == ChadoTransaction.DELETE)
          {
            if(tsn.getFeatureObject() instanceof FeatureCvTerm)
              ArtemisUtils.deleteFeatureCvTerm(dao, (FeatureCvTerm)tsn.getFeatureObject());
            else
              dao.delete(tsn.getFeatureObject());
          }
        }

        //
        // update timelastmodified timestamp
        Timestamp ts = new Timestamp(new java.util.Date().getTime());
        names_checked = new Vector();
        for(int j = 0; j < sql.size(); j++)
        {
          ChadoTransaction tsn = (ChadoTransaction)sql.get(j);
          
          if( (tsn.getType() == ChadoTransaction.INSERT ||
              tsn.getType() == ChadoTransaction.DELETE) && 
              tsn.getFeatureObject() instanceof Feature )
           continue;
          
          final String uniquename = tsn.getUniquename();
          if(uniquename == null)
            continue;
            
          if(names_checked.contains(uniquename))
            continue;

          names_checked.add(uniquename);

          Feature feature = dao.getFeatureByUniqueName(uniquename, tsn.getFeatureKey());
          if(feature != null)
          {
            feature.setTimeLastModified(ts);
            dao.merge(feature);
          }

          GFFStreamFeature gff_feature = (GFFStreamFeature) tsn
              .getGff_feature();
          gff_feature.setLastModified(ts);
        }
        
        if(dao instanceof IBatisDAO && 
           System.getProperty("nocommit") == null)
           ((IBatisDAO) dao).commitTransaction();
      }
      finally
      {
        if(dao instanceof IBatisDAO)
          ((IBatisDAO) dao).endTransaction();
      }
    }
    catch (java.sql.SQLException sqlExp)
    {
      JOptionPane.showMessageDialog(null, "Problems Writing...\n" +
                                    sqlExp.getMessage(),
                                    "Problems Writing to Database ",
                                    JOptionPane.ERROR_MESSAGE);
      sqlExp.printStackTrace();
    }
    catch (java.net.ConnectException conn_ex)
    {
      JOptionPane.showMessageDialog(null, "Problems connecting..."+
                                    conn_ex.getMessage(),
                                    "Database Connection Error - Check Server",
                                    JOptionPane.ERROR_MESSAGE);
      conn_ex.printStackTrace();
    }

      
    return i;
  }
  
  /**
   * Check the <code>Timestamp</code> on a feature (for versioning).
   * @param schema      the schema
   * @param uniquename  the feature uniquename
   * @param timestamp   the last read feature timestamp
   */
  public boolean checkFeatureTimestamp(final String schema,
                                       final String uniquename,
                                       final Timestamp timestamp,
                                       final GmodDAO dao,
                                       final String keyName,
                                       final Object featureObject)
  {
    Feature feature = dao.getFeatureByUniqueName(uniquename, keyName);
    if(feature == null)
      return true;
    
    if(featureObject instanceof FeatureProp)
      ((FeatureProp)featureObject).setFeature(feature);
    else if(featureObject instanceof FeatureLoc)
      ((FeatureLoc)featureObject).setFeatureByFeatureId(feature);
      
    Timestamp now = feature.getTimeLastModified();
    
    if(now != null && timestamp != null)
    {
      now.setNanos(0);
      timestamp.setNanos(0);
      
      if(now.compareTo(timestamp) != 0)
      {
        SimpleDateFormat date_format = 
                   new SimpleDateFormat("dd.MM.yyyy hh:mm:ss z");
        
        //System.out.println(date_format.format(now)+"   "+
        //                   date_format.format(timestamp));
        int select = JOptionPane.showConfirmDialog(null, uniquename +
                                      " has been altered at :\n"+
                                      date_format.format(now)+"\nOverwite?", 
                                      "Feature Changed", 
                                      JOptionPane.OK_CANCEL_OPTION);
        if(select == JOptionPane.OK_OPTION)
          return true;
        else
          return false;
      }
    }
    return true;
  }

  
  public static void main(String args[])
  {
    try
    {
      GmodDAO dao;
      DatabaseEntrySource src = new DatabaseEntrySource();
      src.setLocation(true);
      
      if(System.getProperty("ibatis") == null)
        dao = new JdbcDAO(src.getLocation(), src.getPfield()); 
      else
        dao = new IBatisDAO(src.getPfield());
      
      Feature feature = new Feature();
      feature.setUniqueName(args[0]);
      List schemas = new Vector();
      schemas.add(args[1]);
      List featureList = new Vector();
      featureList.add(dao.getFeatureByUniqueName(args[0], "polypeptide")); 
      System.out.println("FINISHED getFeature()");
      for(int i = 0; i < featureList.size(); i++)
      {
        feature = (Feature)featureList.get(i);
        
        String abb  = feature.getOrganism().getAbbreviation();
        String type = feature.getCvTerm().getName();
        int fmin    = feature.getFeatureLoc().getFmin().intValue() + 1;
        int fmax    = feature.getFeatureLoc().getFmax().intValue();
        String featprop = 
          ((FeatureProp)(new Vector(feature.getFeatureProps()).get(0))).getCvTerm().getName();
        
        System.out.print(fmin+".."+fmax);
        System.out.print(" "+type);
        System.out.print(" "+featprop);
        System.out.print(" "+feature.getFeatureLoc().getStrand());
        System.out.print(" "+feature.getUniqueName());
        System.out.print(" "+abb);
        System.out.println(" "+Integer.toString(feature.getFeatureId()));
        
/*      Hashtable synonyms = getAllFeatureSynonyms(dao, null);
        Vector syns = (Vector)synonyms.get(new Integer(feature.getId()));
        for(int j=0; j<syns.size(); j++)
        {
          FeatureSynonym alias = (FeatureSynonym)syns.get(j);
          System.out.print(" "+alias.getSynonym().getCvterm().getName()+
                           "="+alias.getSynonym().getName());
        }*/
        
        System.out.println(" "); 
      }
    }
    catch(SQLException sqle)
    {
      sqle.printStackTrace();
    }
    catch(RuntimeException re)
    {
      re.printStackTrace();
    }
    catch(ConnectException e)
    {
      e.printStackTrace();
    }
  }

  public Document getParent()
  {
    return null;
  }
  
  public static FeatureLoc getFeatureLoc(List locs, int srcfeature_id)
  {
    for(int i=0; i<locs.size(); i++)
    {
      FeatureLoc loc = (FeatureLoc)locs.get(i);
      if(loc.getFeatureBySrcFeatureId().getFeatureId() == srcfeature_id)
        return loc;
    }
    return null;
  }


  public String getSrcFeatureId()
  {
    return srcFeatureId;
  }
}