DatabaseDocument.java

    final ByteBuffer buff = new ByteBuffer();
    
    logger4j.debug("BUILD GENE GFF LINE");
    buildGffLineFromId(dao, chadoFeature.getFeatureId(), 
        id_store, parent.getUniqueName(), src_id, buff, chadoFeature);
    

    if(!readChildren)
    {
      logger4j.debug( new String(buff.getBytes()) );
      return buff;
    }
    
    // get children of gene
    List relations = new Vector(chadoFeature.getFeatureRelationshipsForObjectId());
    Set idsSeen = new HashSet();
    for(int i = 0; i < relations.size(); i++)
    {
      //Feature transcript = new Feature();
      int id = ((FeatureRelationship) relations.get(i)).getFeatureBySubjectId().getFeatureId();
      Integer idInt = new Integer(id);
      if(idsSeen.contains(idInt))
        continue;
      idsSeen.add(idInt);
      Feature transcript = buildGffLineFromId(dao, id, id_store, parent.getUniqueName(), 
                                              src_id, buff, null);

      if( transcript == null || transcript.getCvTerm() == null ||
          transcript.getCvTerm().getName() == null || 
         (transcript.getCvTerm().getName().indexOf("RNA") < 0 &&
          transcript.getCvTerm().getName().indexOf("transcript") < 0 ) )
        continue;
      // get children of transcript - exons and pp
      logger4j.debug("GET CHILDREN OF "+transcript.getName());
      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( "GFF:\n"+new String(buff.getBytes()) );

    // now wait for cvterm to be loaded
    if(cvThread != null)
    {
      while(cvThread.isAlive())
        try
        {
          Thread.sleep(10);
        }
        catch(InterruptedException e)
        {
          // TODO Auto-generated catch block
          e.printStackTrace();
        }
    }
    
    return buff;
  }
  
  
  /**
   * 
   * @param dao
   * @param featureId
   * @param id_store
   * @param parentName
   * @param srcFeatureId
   * @param this_buff
   * @param chadoFeature
   * @return
   */
  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);

    final FeatureLoc loc = getFeatureLoc(new Vector(
        chadoFeature.getFeatureLocsForFeatureId()), srcFeatureId);
    
    if(loc == null)
    {
      logger4j.debug("FEATURELOC NOT FOUND :: "+chadoFeature.getUniqueName());
      return null;
    }
    final Hashtable dbxrefs = IBatisDAO.mergeDbXRef(
        dao.getFeatureDbXRefsByFeatureUniquename(chadoFeature.getUniqueName()));
    
    final Hashtable synonym = getAllFeatureSynonyms( 
        dao.getFeatureSynonymsByFeatureUniquename(chadoFeature.getUniqueName()));
    
    final Hashtable featureCvTerms = getFeatureCvTermsByFeature(dao, 
                                  dao.getFeatureCvTermsByFeature(chadoFeature));
    
    final Hashtable featureCvTermDbXRefs = getFeatureCvTermDbXRef(dao, 
                             dao.getFeatureCvTermDbXRefByFeature(chadoFeature));
    
    Hashtable featureCvTermPubs = null;
    
    try
    {
      featureCvTermPubs = getFeatureCvTermPub(dao,
                          dao.getFeatureCvTermPubByFeature(chadoFeature));
    }
    catch(RuntimeException re){re.printStackTrace();}

    final Hashtable featurePubs = getFeaturePubs(dao,
        dao.getFeaturePubsByFeature(chadoFeature));
    List pubDbXRefs= new Vector(); //dao.getPubDbXRef();
    chadoToGFF(chadoFeature, parentName, dbxrefs, synonym, featureCvTerms,
        pubDbXRefs, featureCvTermDbXRefs, featureCvTermPubs, featurePubs, 
        id_store, dao, loc, this_buff, gene_builder);  
    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,
                                 final boolean gene_builder)
  {
    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, gene_builder);
    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 */
    
    ByteBuffer clusterOrthoParalog = null;
    if(feat.getFeatureRelationshipsForSubjectId() != null)
    {
      Collection relations = feat.getFeatureRelationshipsForSubjectId();
      Iterator it = relations.iterator();
      Set featureRelationshipIds = new HashSet();
      //Set duplicates = new HashSet();
      
      while(it.hasNext())
      {
        final FeatureRelationship fr = 
                            (FeatureRelationship)it.next();
        final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() );

        if(featureRelationshipIds.contains( featureRelationShipId ))
          continue;
        
        featureRelationshipIds.add(featureRelationShipId);
        final String cvTermName;
        if( fr.getCvTerm().getName() == null )
        {
          int parent_type_id = fr.getCvTerm().getCvTermId();
          cvTermName = getCvtermName(parent_type_id, dao, gene_builder);
        }
        else
          cvTermName = fr.getCvTerm().getName();
      
        if(cvTermName.equals("derives_from") || cvTermName.equals("part_of") ||
           cvTermName.equals("proper_part_of") || 
           cvTermName.equals("partof") || cvTermName.equals("producedby")) // flybase
        {
          parent_relationship = cvTermName;
          parent_id = Integer.toString(fr.getFeatureByObjectId().getFeatureId());
          rank      = fr.getRank();
        }
        else
        {
          if(clusterOrthoParalog == null)
            clusterOrthoParalog = new ByteBuffer();
          // ortholog/paralog/cluster data
          int orthologueFeature = fr.getFeatureByObjectId().getFeatureId();
          clusterOrthoParalog.append(cvTermName+"="+
              GFFStreamFeature.encode("object_id="+orthologueFeature+"; rank="+fr.getRank())+";");
        }
      }
    }

    // look up parent name
    if(parent_id != null && id_store != null &&  id_store.containsKey(parent_id))
      parent_id = ((Feature)id_store.get(parent_id)).getUniqueName();
 
    // 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");
    
    if(typeName.equals("exon"))
      this_buff.append(EXONMODEL + "\t");   // type
    else
      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(feat.getName() != null)
      this_buff.append("Name=" + feat.getName() + ";");
   
    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_buff.append("isObsolete=" + Boolean.toString(feat.isObsolete()) + ";");
    
    // 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, gene_builder);
        if(qualifier_name == null)
          continue;
        if(featprop.getValue() != null)
          this_buff.append(GFFStreamFeature.encode(qualifier_name)+ "=" +
                           GFFStreamFeature.encode(featprop.getValue())+";");
      }
    }

    if(clusterOrthoParalog != null)
      this_buff.append(clusterOrthoParalog);
    
    // append dbxrefs
    boolean foundPrimaryDbXRef = false;
    if(feat.getDbXRef() != null)
    {
      this_buff.append("Dbxref=");
      this_buff.append(GFFStreamFeature.encode(
          feat.getDbXRef().getDb().getName()+":"+feat.getDbXRef().getAccession()));
      foundPrimaryDbXRef = true;
      if(dbxref == null || dbxref.size() == 0)
        this_buff.append(";");
    }
    
    if(dbxref != null && dbxref.size() > 0)
    {
      if(foundPrimaryDbXRef)
        this_buff.append(",");
      else
        this_buff.append("Dbxref=");
      for(int j=0; j<dbxref.size(); j++)
      {
        this_buff.append(GFFStreamFeature.encode((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, gene_builder) + "=" );
        //this_buff.append(alias.getSynonym().getCvterm().getName()+"=");
        this_buff.append(alias.getSynonym().getName());
        
        if(!alias.isCurrent())
          this_buff.append(GFFStreamFeature.encode(";current=false"));
        
        //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, gene_builder);
      }
      //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,
                                          final boolean gene_builder)
  {
    CvTerm cvterm =  getCvTerm( feature_cvterm.getCvTerm().getCvTermId(), dao, gene_builder);
    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, gene_builder));
        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, gene_builder));
        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(final String name)
  {
    Enumeration enum_cvterm = cvterms.keys();
    while(enum_cvterm.hasMoreElements())
    {
      Integer key = (Integer)enum_cvterm.nextElement();
      if(name.equalsIgnoreCase( ((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(final int id, 
                                      final GmodDAO dao,
                                      final boolean gene_builder)
  {
    if(gene_builder)
      return dao.getCvTermById(id).getName();
    
    return getCvTerm(id, dao, gene_builder).getName();
  }
  
  private static CvTerm getCvTerm(final int id, 
                                  final GmodDAO dao,
                                  final boolean gene_builder)
  {
    if(gene_builder)
      return dao.getCvTermById(id);
    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(final String cvterm_name)
  {
    Enumeration enum_cvterm = cvterms.elements();
    while(enum_cvterm.hasMoreElements())
    {
      CvTerm cvterm = (CvTerm)enum_cvterm.nextElement();
      if(cvterm_name.equalsIgnoreCase( cvterm.getName() ))
        return cvterm;
    }
    
    return null;
  }
  
  /**
   * Use the CvTermId to return a CvTerm.
   * @param cvTermId
   * @return
   */
  public static CvTerm getCvTermByCvTermId(final int cvTermId,
                                           final uk.ac.sanger.artemis.io.Feature feature)
  {
    if(cvterms == null)
    {
      try
      {
        DatabaseDocument doc =
          (DatabaseDocument) ((DocumentEntry)feature.getEntry()).getDocument();
        return doc.getDAO().getCvTermById(cvTermId);
      }
      catch(ConnectException e)
      { 
        logger4j.warn(e.getMessage()); 
      }
      catch(SQLException e) 
      { 
        logger4j.warn(e.getMessage()); 
      }
    }
    
    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)
  {
    final Enumeration enum_cvterm = cvterms.elements();
    while(enum_cvterm.hasMoreElements())
    {
      final 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(final GmodDAO dao)
  {
    try
    {
      final List cvterm_list = dao.getCvTerms();
      final Iterator it = cvterm_list.iterator();
      cvterms = new Hashtable(cvterm_list.size());

      while(it.hasNext())
      {
        final 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);
    }
    logger4j.debug("LOADED CvTerms");
    
    return cvterms;
  }
  
  /**
   * Get CvTerm's in a given CV
   * @param cvName
   * @return
   */
  public Vector getCvTermsByCvName(final String cvName)
  {
    if(cvterms == null)
    {
      logger4j.debug("getCvTermsByCvName LOADING CVTERMS");
      getCvterms(getDAOOnly());
    }
    
    return getCvterms("", cvName);
  }
  
  public List getDatabaseNames()
  {
    GmodDAO dao = getDAOOnly();
    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;
  }
  
  public List getOrganismNames()
  {
    if(organismNames != null && organismNames.size() > 0)
      return organismNames;
    
    GmodDAO dao = getDAOOnly();
    List organisms = dao.getOrganisms();
    organismNames = new Vector();
    Iterator it = organisms.iterator();
    while(it.hasNext())
    {
      Organism organism = (Organism)it.next();
      organismNames.add(organism.getCommonName());
    }
    return organismNames;
  }
  
  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;
  }
  
  /**
   * Get a list of the CV names
   * @return
   */
  public static List getCvControledCurationNames()
  {
    if(cvControledCuratioNames != null)
      return cvControledCuratioNames;
    cvControledCuratioNames = new Vector();
    final Enumeration enum_cvterm = cvterms.elements();
    while(enum_cvterm.hasMoreElements())
    {
      final CvTerm cvTerm = (CvTerm)enum_cvterm.nextElement();
      final String cvNameStr = cvTerm.getCv().getName();
      
      if(cvNameStr.startsWith(DatabaseDocument.CONTROLLED_CURATION_TAG_CVNAME) && 
         !cvControledCuratioNames.contains(cvNameStr))
        cvControledCuratioNames.add(cvNameStr);
    }
    
    return cvControledCuratioNames;
  }

  /**
   * Look up synonym type names e.g. synonym, systematic_id.
   * @return    the synonym tag names
   */
  public static String[] getSynonymTypeNames(final String cv_name, 
                                             final GFFStreamFeature feature)
  {
    if(cvterms == null)
    {
      DatabaseDocument doc = (DatabaseDocument)feature.getDocumentEntry().getDocument();
      try
      {
        Cv cv = new Cv();
        cv.setName(cv_name);
        List synonymCvTerms = doc.getDAO().getCvTermByNameInCv(null, cv);
        String synonymNames[] = new String[synonymCvTerms.size()];
        for(int i=0; i<synonymCvTerms.size(); i++)
          synonymNames[i] = ((CvTerm) synonymCvTerms.get(i)).getName();

        return synonymNames;
      }
      catch(ConnectException e){}
      catch(SQLException e){}   
    }
    
    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()]);
  }
  
  public void insertCvTerm(CvTerm cvTerm)
  {
    final GmodDAO dao = getDAOOnly();
    dao.persist(cvTerm);
    cvTerm = dao.getCvTermByNameAndCvName(cvTerm.getName(), cvTerm.getCv().getName());
    cvterms.put(new Integer(cvTerm.getCvTermId()), 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 Feature getChadoSequence(GmodDAO dao, ByteBuffer buff)
  {
    Feature feature = dao.getFeatureById(Integer.parseInt(srcFeatureId));
    getChadoSequence(feature, buff);
    return feature;
  }
  
  
  /**
   * 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 void getChadoSequence(final Feature feature, ByteBuffer buff)
  {
    buff.append("##FASTA\n>");
    buff.append(feature.getUniqueName());
    buff.append("\n");
    buff.append(feature.getResidues());
  }