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.InvalidRelationException;
import uk.ac.sanger.artemis.io.ReadFormatException;
import uk.ac.sanger.artemis.chado.*;
import uk.ac.sanger.artemis.components.DatabaseEntrySource;


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

  private String feature_id = "1";

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

  private static Hashtable cvterm;

  private InputStreamProgressListener progress_listener;

  private Hashtable db;

  /** 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;
  
  /**
   * 
   * 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(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 feature_id, String schema)
  {
    super(location);
    this.pfield = pfield;

    this.feature_id = feature_id;
    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 feature_id
   *          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 feature_id, String schema, boolean splitGFFEntry,
                          InputStreamProgressListener progress_listener)
  {
    super(location);
    this.pfield = pfield;
    this.feature_id = feature_id;
    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);
    
    /*
    if(!location.endsWith("="+schema))
    {
      int index = location.lastIndexOf('=');
      setLocation(location.substring(0,index+1) + schema);
      connIB  = null;
      jdbcDAO = null;
      System.setProperty("chado", (String)getLocation());
    }
    */
  }

  /**
   * Used by the gene builder to read a database entry
   * for a single gene.
   * @param location
   * @param pfield
   * @param feature_id
   * @param schema
   * @param gene_builder
   */
  public DatabaseDocument(String location, JPasswordField pfield,
          String feature_id, String schema, boolean gene_builder)
  {
    super(location);
    this.pfield = pfield;
    this.feature_id = feature_id;
    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 feature_id, String schema,
                          ByteBuffer gff_buff, String name)
  {
    super(location);
    this.pfield = pfield;
    this.feature_id = feature_id;
    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);
      connIB  = null;
      jdbcDAO = null;
      System.setProperty("chado", (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,
                                 feature_id, 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
    {
      ChadoDAO dao = getDAO();
      ByteBuffer entry = new ByteBuffer();
      
      try
      {
        if(dao instanceof IBatisDAO)
          ((IBatisDAO) dao).startTransaction();

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

        gff_buffer = getGff(dao, feature_id);

        
        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(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
   * @throws java.sql.SQLException
   */
  private ByteBuffer[] getGff(ChadoDAO dao, String parentFeatureID)
                       throws java.sql.SQLException
  {
    final int srcfeature_id = Integer.parseInt(parentFeatureID);
    
    // build srcfeature object
    ChadoFeatureLoc featureloc = new ChadoFeatureLoc();
    featureloc.setSrcfeature_id(srcfeature_id);
    ChadoFeature feature = new ChadoFeature();
    feature.setFeatureloc(featureloc);
    
    List featList = dao.getFeature(feature);

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

    final String parentFeature = dao.getFeatureName(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++)
    {
      ChadoFeature feat = (ChadoFeature)featList.get(i);
      String name       = feat.getUniquename();
      String feature_id = Integer.toString(feat.getId());

      id_store.put(feature_id, name);
    }
    
    // get all dbrefs & synonyms
    Hashtable dbxrefs = dao.getDbxref(null);
    Hashtable synonym = dao.getAlias(null);

    // create gff byte stream
    for(int i = 0; i < feature_size; i++)
    { 
      // select buffer based on feature type
      ChadoFeature feat = (ChadoFeature)featList.get(i);
      long 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,
                 dbxrefs, synonym,
                 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;
  }

  /**
   * 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,
                                    ChadoDAO dao) 
          throws SQLException, ReadFormatException, ConnectException
  {
    Hashtable id_store = new Hashtable();

    ChadoFeature feature = new ChadoFeature();
    feature.setUniquename(search_gene);

    reset((String)getLocation(), (String)schema_search.get(0));
    dao = getDAO();
    List featureList = dao.getLazyFeature(feature);
    
    ChadoCanonicalGene chado_gene = new ChadoCanonicalGene();

    if(featureList.size() > 1)
      System.err.println("More than one feature found!");

    feature = (ChadoFeature) featureList.get(0);
    id_store.put(Integer.toString(feature.getId()), feature.getUniquename());

    List featurelocs = feature.getFeaturelocsForFeatureId();
    ChadoFeatureLoc featureloc = (ChadoFeatureLoc) featurelocs.get(0);
    int src = featureloc.getSrcfeature_id();

    ChadoFeature parent = new ChadoFeature();
    parent.setId(src);

    List parentList = dao.getLazyFeature(parent);
    parent = (ChadoFeature) parentList.get(0);
    chado_gene.setSeqlen(parent.getLength());
    chado_gene.setSrcfeature_id(src);

    ByteBuffer buff = new ByteBuffer();
    
    chadoToGFF(feature, null, null, null, null, dao,
               featureloc, buff);

    // get children of gene
    List relations = feature.getFeatureRelationshipsForObjectId();
    
    for(int i = 0; i < relations.size(); i++)
    {
      ChadoFeature transcript = new ChadoFeature();
      transcript.setId(((ChadoFeatureRelationship) relations.get(i))
          .getSubject_id());
      featureList = dao.getLazyFeature(transcript);

      transcript = (ChadoFeature) featureList.get(0);
      id_store.put(Integer.toString(transcript.getId()), transcript
          .getUniquename());

      ChadoFeatureLoc loc = ChadoFeature.getFeatureLoc(transcript
          .getFeaturelocsForFeatureId(), src);
      chadoToGFF(transcript, feature.getUniquename(), null,
          null, id_store, dao, loc, buff);

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

      for(int j = 0; j < transcipt_relations.size(); j++)
      {
        ChadoFeature child = new ChadoFeature();
        child.setId(((ChadoFeatureRelationship) transcipt_relations.get(j))
            .getSubject_id());
        featureList = dao.getLazyFeature(child);

        child = (ChadoFeature) featureList.get(0);
        id_store.put(Integer.toString(child.getId()), child.getUniquename());

        loc = ChadoFeature.getFeatureLoc(child.getFeaturelocsForFeatureId(),src);
        chadoToGFF(child, transcript.getUniquename(), null,
                   null, id_store, dao, loc, buff);
      }
    }

    return buff;
  }
  
  /**
   * 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 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 ChadoFeature feat,
                                 final String parentFeature,
                                 final Hashtable dbxrefs,
                                 final Hashtable synonym,
                                 final Hashtable id_store,
                                 final ChadoDAO dao,
                                 final ChadoFeatureLoc featureloc,
                                 final ByteBuffer this_buff)
  {
    String gff_source = null;
    
    int fmin          = featureloc.getFmin() + 1;
    int fmax          = featureloc.getFmax();
    long type_id      = feat.getCvterm().getCvtermId();
    int strand        = featureloc.getStrand();
    int phase         = featureloc.getPhase();
    String name       = feat.getUniquename();
    String typeName   = getCvtermName(type_id, dao);

    String timelastmodified = Long.toString(feat.getTimelastmodified().getTime());
    Integer feature_id      = new Integer(feat.getId());

    String parent_id = null;
    String parent_relationship = null;
    int rank = -1;
    if(feat.getFeature_relationship() != null)
    {
      ChadoFeatureRelationship feat_relationship = feat.getFeature_relationship();
      parent_id = Integer.toString(feat_relationship.getObject_id());
      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 = feat.getFeatureRelationshipsForSubjectId();
      for(int i=0; i<relations.size(); i++)
      {
        ChadoFeatureRelationship feat_relationship = 
                            (ChadoFeatureRelationship)relations.get(i);
        parent_id = Integer.toString(feat_relationship.getObject_id());
        System.out.println("HERE   "+i+" "+feat_relationship.getCvterm().getName()+ " "+
            feat_relationship.getObject_id()+" "+feat_relationship.getSubject_id()+ " parent_id="+ parent_id);
        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(feature_id))
    {
      dbxref = (Vector)dbxrefs.get(feature_id);
      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 == -1)                        // strand
      this_buff.append("-\t");
    else if(strand == 1)
      this_buff.append("+\t");
    else
      this_buff.append(".\t");

    if(phase > 3)
      this_buff.append(".\t");               // phase
    else
      this_buff.append(phase+"\t"); 

    this_buff.append("ID=" + name + ";");

   
    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 features e.g. exons
    if(rank > -1)
      this_buff.append("feature_relationship_rank="+rank+";");

    //this_buff.append("feature_id="+feature_id+";");
    
    // attributes
    Hashtable qualifiers = feat.getQualifiers();
    
    if(qualifiers != null && qualifiers.size() > 0)
    {
      Enumeration e_qualifiers = qualifiers.keys();
      while(e_qualifiers.hasMoreElements())
      {
        Long qualifier_type_id = (Long)e_qualifiers.nextElement();
        String qualifier_name = getCvtermName(qualifier_type_id.longValue(), dao);
        if(qualifier_name == null)
          continue;
        
        Vector qualifier_value = (Vector)qualifiers.get(qualifier_type_id);
        for(int j=0; j<qualifier_value.size(); j++)
        {
          ChadoFeatureProp featprop = (ChadoFeatureProp)qualifier_value.get(j);
         
          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(feature_id))
    {   
      ChadoFeatureSynonym alias;
      Vector v_synonyms = (Vector)synonym.get(feature_id);
      for(int j=0; j<v_synonyms.size(); j++)
      {
        alias = (ChadoFeatureSynonym)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(";");
      }
    }
    
    this_buff.append("\n");
  }
  
  
  /**
   * Look up the cvterm_id for a controlled vocabulary name.
   * @param name  
   * @return
   */
  public static Long getCvtermID(String name)
  {
    Enumeration enum_cvterm = cvterm.keys();
    while(enum_cvterm.hasMoreElements())
    {
      Long key = (Long)enum_cvterm.nextElement();
      if(name.equals(cvterm.get(key)))
        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(long id, ChadoDAO dao)
  {
    if(cvterm == null)
      getCvterm(dao);

    return (String)cvterm.get(new Long(id));
  }

  /**
   * 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 getCvterm(ChadoDAO dao)
  {
    cvterm = new Hashtable();

    try
    {
      List cvtem_list = dao.getCvterm();
      Iterator it = cvtem_list.iterator();

      while(it.hasNext())
      {
        ChadoCvterm cv = (ChadoCvterm)it.next();
        cvterm.put(new Long(cv.getCvtermId()), cv.getName());
      }
    }
    catch(SQLException sqle)
    {
      System.err.println("SQLException retrieving CvTerms");
      System.err.println(sqle);
    }

    return cvterm;
  }

  /**
   * 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(ChadoDAO dao, ByteBuffer buff)
                     throws java.sql.SQLException
  {
    ChadoFeature feature = dao.getSequence(Integer.parseInt(feature_id));

    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;
  }

  /**
   * 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 Hashtable getDatabaseEntries()
                   throws ConnectException, java.sql.SQLException
  {
    db = new Hashtable();
 
    ChadoDAO dao = null;
    
    try
    {
      dao = getDAO();
    }
    catch(ConnectException exp)
    {
      JOptionPane.showMessageDialog(null, "Connection Problems...\n"+
            exp.getMessage(), 
            "Connection Error",
            JOptionPane.ERROR_MESSAGE);
      throw exp;
    }
    catch(java.sql.SQLException sqlExp)
    {
      JOptionPane.showMessageDialog(null, "SQL Problems...\n"+
                                    sqlExp.getMessage(), 
                                    "SQL Error",
                                    JOptionPane.ERROR_MESSAGE);
      throw sqlExp;
    }
      
    try
    {
      if(dao instanceof IBatisDAO)
        ((IBatisDAO) dao).startTransaction();
      
      schema_list = dao.getSchema();
      Iterator it      = schema_list.iterator();

      while(it.hasNext())
      {
        String schema = (String)it.next();
  
        List list = dao.getResidueType(schema);
         
        if(list.size() == 0)  // no residues for this organism
          continue;

        List list_residue_features = dao.getResidueFeatures(list, schema);
        Iterator it_residue_features = list_residue_features.iterator();
        while(it_residue_features.hasNext())
        {
          ChadoFeature feature = (ChadoFeature)it_residue_features.next();
          String typeName = getCvtermName(feature.getCvterm().getCvtermId(), getDAO()); 
          
          db.put(schema + " - " + typeName + " - " + feature.getUniquename(),
                 Integer.toString(feature.getId()));
        }
      }
      
      if(dao instanceof IBatisDAO)
        ((IBatisDAO) dao).commitTransaction();
      
    }
    catch(java.sql.SQLException sqlExp)
    {
      JOptionPane.showMessageDialog(null, "SQL Problems...\n"+
                                    sqlExp.getMessage(), 
                                    "SQL Error",
                                    JOptionPane.ERROR_MESSAGE);
      sqlExp.printStackTrace();
    }
    finally
    {
      if(dao instanceof IBatisDAO)
        ((IBatisDAO) dao).endTransaction();
    }
    
    return db;
  }
  
  
  /**
   * Get the data access object (DAO).
   * @return data access object
   */
  private ChadoDAO getDAO()
     throws java.net.ConnectException, SQLException
  {
    if(!iBatis)
    {
      if(jdbcDAO == null)
       jdbcDAO = new JdbcDAO((String)getLocation(), pfield); 
      return jdbcDAO;
    }
    else
    {
      if(connIB == null)
        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)