DatabaseDocument.java

  /**
   * Get the CDS FeatureLoc's associated with a give protein
   * @param peptideName
   * @return
   */
  public List getCdsFeatureLocsByPeptideName(final String peptideName)
  {
    Feature peptideFeature = getFeatureByUniquename(peptideName);
    Collection frs = peptideFeature.getFeatureRelationshipsForSubjectId();
    Iterator it = frs.iterator();
    Feature transcriptFeature = null;
    while(it.hasNext())
    {
      FeatureRelationship fr = (FeatureRelationship)it.next();
      if(fr.getCvTerm().getName().equalsIgnoreCase("derives_from"))
      {
        transcriptFeature = fr.getFeatureByObjectId();
        logger4j.debug("TRANSCRIPT :: "+transcriptFeature.getUniqueName());
        break;
      }
    }
    
    if(transcriptFeature == null)
      return null;
    return getCdsFeatureLocsByTranscriptName(transcriptFeature.getUniqueName());
  }
  
  /**
   * Get the CDS FeatureLoc's associated with a given transcript
   * @param transcriptName
   * @return
   */
  public List getCdsFeatureLocsByTranscriptName(final String transcriptName)
  {
    Feature transcriptFeature = getFeatureByUniquename(transcriptName);
    if(transcriptFeature == null)
      return null;
    
    Collection frs = transcriptFeature.getFeatureRelationshipsForObjectId();
    Iterator it = frs.iterator();
    List cdsFeatureLocs = new Vector();
    while(it.hasNext())
    {
      FeatureRelationship fr = (FeatureRelationship)it.next();
      org.gmod.schema.sequence.Feature child = fr.getFeatureBySubjectId();
      if(child.getCvTerm().getName().equals("exon") || 
         child.getCvTerm().getName().equals("pseudogenic_exon"))
      {
        Collection featureLocs = child.getFeatureLocsForFeatureId();

        Iterator it2 = featureLocs.iterator();
        while(it2.hasNext())
        {
          FeatureLoc featureLoc = (FeatureLoc) it2.next();
          cdsFeatureLocs.add(featureLoc);
        }
      }
    }

    Collections.sort(cdsFeatureLocs, new LocationComarator());
    return cdsFeatureLocs;
  }
  
  /**
   * Get the sequence for a feature.
   * @param uniqueName   the feature
   * @return      the resulting buffer
   */
  public PartialSequence getChadoSequence(final String uniqueName)
  {
    Feature feature = getDAOOnly().getResiduesByUniqueName(uniqueName);
    char[] c = getChars(feature.getResidues());
    
    PartialSequence ps = new PartialSequence(c, feature.getSeqLen(),
                                feature.getFeatureLoc().getFmin().intValue()+1,
                                feature.getFeatureLoc().getStrand(),
                                feature.getFeatureLoc().getPhase());
    return ps;
  }
  
  /**
   * Convert byte array to char array
   * @param b byte array
   * @return  char array
   */
  private char[] getChars(final byte b[])
  {
    char[] c = new char[b.length];

    for(int i = 0; i < b.length; i++)
      c[i] = (char)b[i];
    return c;
  }
  
  /**
   * Get the <code>List</code> of available schemas.
   * @return  the <code>List</code> of available schemas
   */
  public List getSchema()
  {
    return schema_list;
  }
  
  public Feature getFeatureByUniquename(final String uniqueName) 
  {
    GmodDAO dao = getDAOOnly();
    List features = dao.getFeaturesByUniqueName(uniqueName);
    if(features == null || features.size() < 1)
      return null;
      
    return (Feature)(dao.getFeaturesByUniqueName(uniqueName).get(0));
  }
  
  /**
   * Given a gene unique name return the poplypeptide chado features that belong
   * to that gene
   * @param geneName
   * @return
   */
  public Vector getPolypeptideFeatures(final String geneName)
  {
    Feature geneFeature =  getFeatureByUniquename(geneName);
    if(geneFeature == null)
      return null;
    
    Collection frs = geneFeature.getFeatureRelationshipsForObjectId();
    Iterator it = frs.iterator();
    List transcripts = new Vector(frs.size());
    while(it.hasNext())
    {
      FeatureRelationship fr = (FeatureRelationship)it.next();
      transcripts.add(fr.getFeatureBySubjectId());
    }
    
    Vector polypep = new Vector();
    for(int i=0; i<transcripts.size(); i++)
    {
      org.gmod.schema.sequence.Feature transcript = 
        (org.gmod.schema.sequence.Feature) transcripts.get(i);
      frs = transcript.getFeatureRelationshipsForObjectId();
      it = frs.iterator();
      while(it.hasNext())
      {
        FeatureRelationship fr = (FeatureRelationship)it.next();
        if(fr.getCvTerm().getName().equalsIgnoreCase("derives_from"))
          if(fr.getFeatureBySubjectId().getCvTerm().getName().equalsIgnoreCase("polypeptide"))
            polypep.add(fr.getFeatureBySubjectId());
      }
    }
    return polypep;
  }
  
  /**
   * Given a gene unique name return the poplypeptides that belong
   * to that gene
   * @param geneName
   * @return
   */
  /*public Vector getPolypeptideNames(final String geneName)
  {
    Vector polypeptides = getPolypeptideFeatures(geneName);
    Vector polypeptideNames = new Vector(polypeptides.size());
    for(int i=0; i<polypeptides.size(); i++)
    {
      Feature feature = (Feature)polypeptides.get(i);
      polypeptideNames.add(feature.getUniqueName());
    }
    return polypeptideNames;
  }*/
  
  public List getClustersByFeatureIds(final List featureIds)
  {
    GmodDAO dao = getDAOOnly();
    return dao.getClustersByFeatureIds(featureIds);
  }
  
  public List getParentFeaturesByChildFeatureIds(final List subjectIds)
  {
    GmodDAO dao = getDAOOnly();
    return dao.getParentFeaturesByChildFeatureIds(subjectIds);
  }
  
  public List getFeatureDbXRefsByFeatureId(final List featureIds)
  {
    GmodDAO dao = getDAOOnly();
    return dao.getFeatureDbXRefsByFeatureId(featureIds);
  }
  
  
  /**
   * Used by SimilarityLazyQualifierValue.bulkRetrieve() to get the match features
   * @param featureIds the <code>List</code> of feature_id's
   * @return  the corresponding features
   */
  public List getFeaturesByListOfIds(final List featureIds)
  {
    GmodDAO dao = getDAOOnly();
    return dao.getFeaturesByListOfIds(featureIds);
  }
  
  public List getFeaturePropByFeatureIds(final List featureIds)
  {
    GmodDAO dao = getDAOOnly();
    return dao.getFeaturePropByFeatureIds(featureIds);
  }
  
  public List getSimilarityMatches(List featureIds)
  {
    GmodDAO dao = getDAOOnly();
    if(featureIds == null)
      return dao.getSimilarityMatches(new Integer(srcFeatureId));
    else
      return dao.getSimilarityMatchesByFeatureIds(featureIds);
  }
  
  public List getFeatureLocsByListOfIds(List featureIds)
  {
    GmodDAO dao = getDAOOnly();
    return dao.getFeatureLocsByListOfIds(featureIds);
  }
  
  /**
   * 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 getDatabaseEntriesMultiSchema()
                   throws ConnectException, java.sql.SQLException
  {
    String schema = null;
    HashMap db    = null;
    try
    { 
      GmodDAO dao = getDAO();
      schema_list = dao.getSchema(); 
      
      Iterator it = schema_list.iterator();
        
      while(it.hasNext())
      {
        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(), gene_builder); 
          
            if(db == null)
              db = new HashMap();
            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;
  }
  
  
  /**
   * 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
  {

    HashMap db = null;
    try
    { 
      GmodDAO dao = getDAO();
      CvTermThread cvThread = new CvTermThread(dao);
      cvThread.start();
      
      schema_list = dao.getOrganisms();
      
      /*Organism org = new Organism();
      org.setCommonName("web");
      schema_list.add(org);*/
      
      final List pg_schemas = dao.getSchema();
      
      // build a lookup hash of residue features in the
      // main schema
      Hashtable residueFeaturesLookup = new Hashtable();
      List list_residue_features = dao.getResidueFeatures();
      for(int i=0; i<list_residue_features.size(); i++)
      {
        Feature feature = (Feature)list_residue_features.get(i);
        Integer organismId = new Integer(feature.getOrganism().getOrganismId());
        List features;
        if(residueFeaturesLookup.containsKey(organismId))
          features= (List)residueFeaturesLookup.get(organismId);
        else
          features = new Vector();
        features.add(feature);
        residueFeaturesLookup.put(organismId, features);
      }
      
      // loop over organisms to identify those with features 
      // containing residues
      Iterator it = schema_list.iterator();
      while(it.hasNext())
      {
        final Organism organism = (Organism)it.next();
        String orgName = organism.getCommonName();
        
        if(orgName == null || orgName.equals(""))
        {
          orgName = organism.getGenus() + "." + organism.getSpecies();
          organism.setCommonName(orgName);
        }
        
        // search to see if this is in its own schema
        Iterator schemasIt = pg_schemas.iterator();
        while(schemasIt.hasNext())
        {
          schema = (String)schemasIt.next();         
          if( schema.equalsIgnoreCase(organism.getCommonName()) )
          {
            reset((String)getLocation(),  schema);
            dao = getDAO();
            orgName = schema;

            singleSchema = false;
            break;
          }
        }
        
        try
        {
          if(organism.getOrganismId() > 0)
          {
            Integer organismId = new Integer(organism.getOrganismId());
            
            if(residueFeaturesLookup.containsKey(organismId))
              list_residue_features = (List)residueFeaturesLookup.get(organismId);
            else if(singleSchema && residueFeaturesLookup.size()>0)
              continue;
            else
              list_residue_features = dao.getResidueFeatures(organismId);
          }
          else
            list_residue_features = 
              dao.getResidueFeaturesByOrganismCommonName(organism.getCommonName());
          
          Iterator it_residue_features = list_residue_features.iterator();
          while(it_residue_features.hasNext())
          {
            final Feature feature = (Feature)it_residue_features.next();
            final String typeName = feature.getCvTerm().getName();
                  
            if(db == null)
              db = new HashMap();
            if(organismNames == null)
              organismNames = new Vector();
            
            if(!organismNames.contains(orgName))
              organismNames.add(orgName);         
            
            db.put(orgName + " - " + typeName + " - " + feature.getUniqueName(),
                   Integer.toString(feature.getFeatureId())); 
          }
        }
        catch(RuntimeException e)
        {
          e.printStackTrace();
        }
      }
      
      residueFeaturesLookup.clear();
      list_residue_features.clear();
      
      // now wait for cvterm to be loaded
      while(cvThread.isAlive())
        Thread.sleep(10);
    }
    catch(RuntimeException sqlExp)
    {
      JOptionPane.showMessageDialog(null, "SQL Problems...\n"+
                                    getLocation()+"\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"+
                                    getLocation()+"\n"+
                                    sqlExp.getMessage(), 
                                    "SQL Error",
                                    JOptionPane.ERROR_MESSAGE);
      logger4j.debug(sqlExp.getMessage());
      throw sqlExp;
    }
    catch(InterruptedException e)
    {
      // TODO Auto-generated catch block
      e.printStackTrace();
    }
    
    return db;
  }
  
  /**
   * 
   */
  public void showCvTermLookUp()
  {
    try
    {
      new ChadoCvTermView( getDAO() );
    }
    catch(ConnectException e)
    {
      // TODO Auto-generated catch block
      e.printStackTrace();
    }
    catch(SQLException e)
    {
      // TODO Auto-generated catch block
      e.printStackTrace();
    }
  }
  
  /**
   * 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;
    }
  }
  
  /**
   * Get the username for this connection
   * @return
   */
  public String getUserName()
  {
    // "localhost:10001/backup?chado"
    
    String url = (String)getLocation();
    int index  = url.indexOf("?");
    
    String userName = url.substring(index+1).trim();
    if(userName.startsWith("user="))
      userName = userName.substring(5);
    
    return userName;
  }
  
  private GmodDAO getDAOOnly()
  {
    GmodDAO dao = null;
    try
    {
      dao = getDAO();
    }
    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 dao;
  }


  /**
   * 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(final Vector sql,
                    final boolean force)
  {
    GmodDAO dao = null;
    int ncommit = -1;
    final Hashtable featureIdStore = new Hashtable();
    boolean useTransactions = false;

    try
    {
      dao = getDAO();
      
      if(!force && dao instanceof IBatisDAO)
        useTransactions = true;
      
      if(useTransactions)
      {
        ((IBatisDAO) dao).startTransaction();
        logger4j.debug("START TRANSACTION");
      }
      boolean unchanged;
      
      //
      // check feature timestamps have not changed
      Vector names_checked = new Vector();
      
      for(int i = 0; i < sql.size(); i++)
      {
        final ChadoTransaction tsn = (ChadoTransaction)sql.get(i);
        final Object uniquenames[] = getUniqueNames(tsn);
        
        if(uniquenames == null)
          continue;
        
        for(int j=0; j<uniquenames.length; j++)
        {
          final String uniquename = (String) uniquenames[j];
          
          if(uniquename == null || names_checked.contains(uniquename))
            continue;

          names_checked.add(uniquename);
          final String keyName = tsn.getFeatureKey();

          unchanged = checkFeatureTimestamp(schema, uniquename, 
              dao, keyName, featureIdStore, tsn);
          if(!unchanged)
          {
            if(useTransactions)
              ((IBatisDAO) dao).endTransaction();
            return 0;
          }
        }
      }  
      
      final Timestamp ts = new Timestamp(new java.util.Date().getTime());
      //
      // commit to database
      for(ncommit = 0; ncommit < sql.size(); ncommit++)
      {
        try
        {
          ChadoTransaction tsn = (ChadoTransaction) sql.get(ncommit);
          commitChadoTransaction(tsn, dao, ts);
        }
        catch (RuntimeException re)
        {
          if(!force)
            throw re;
          logger4j.warn(constructExceptionMessage(re, sql, ncommit));
          logger4j.warn("NOW TRYING TO CONTINUE TO COMMIT");
        }
      }

      //
      // update timelastmodified timestamp
      names_checked = new Vector();
      for(int i = 0; i < sql.size(); i++)
      {
        final ChadoTransaction tsn = (ChadoTransaction) sql.get(i);
        final Object uniquenames[] = getUniqueNames(tsn);
             
        if(uniquenames == null)
          continue;
        
        if(tsn.getType() == ChadoTransaction.UPDATE &&
           tsn.getFeatureObject() instanceof Feature)
        {
          for(int j=0; j<uniquenames.length; j++)
            names_checked.add((String) uniquenames[j]);
          continue;  
        }
        
        for(int j=0; j<uniquenames.length; j++)
        {
          final String uniquename = (String) uniquenames[j];
          if(uniquename == null || names_checked.contains(uniquename))
            continue;

          names_checked.add(uniquename);

          final Feature feature;

          // retieve from featureId store
          if(featureIdStore != null && featureIdStore.containsKey(uniquename))
          {
            Feature f = (Feature) featureIdStore.get(uniquename);

            feature = new Feature();
            feature.setFeatureId(f.getFeatureId());
            feature.setUniqueName(uniquename);
            feature.setObsolete(f.isObsolete());
          }
          else
            feature = dao.getFeatureByUniqueName(uniquename, 
                                       tsn.getFeatureKey());

          if(feature != null)
          {
            feature.setTimeLastModified(ts);
            feature.setName("0");  // do not change name
            dao.merge(feature);
          }
        }

        GFFStreamFeature gff_feature = (GFFStreamFeature) tsn.getGff_feature();
        gff_feature.setLastModified(ts);
      }

      final String nocommit = System.getProperty("nocommit");
      if( useTransactions && 
          (nocommit == null || nocommit.equals("false")))
      {
        ((IBatisDAO) dao).commitTransaction();
        logger4j.debug("TRANSACTION COMPLETE");
      }
      else if(useTransactions && 
          (nocommit != null && nocommit.equals("true")))
        logger4j.debug("TRANSACTION NOT COMMITTED : nocommit property set to true");
    }
    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();
    }
    catch (RuntimeException re)
    {
      final String msg = constructExceptionMessage(re, sql, ncommit);
      JOptionPane.showMessageDialog(null, msg,
          "Problems Writing to Database ",
          JOptionPane.ERROR_MESSAGE);
      logger4j.error(msg);
      //re.printStackTrace();
    }
    finally
    {
      if(useTransactions)
        try
        {
          ((IBatisDAO) dao).endTransaction();
          logger4j.debug("END TRANSACTION");
        }
        catch(SQLException e){ e.printStackTrace(); }
    }
    
    if(featureIdStore != null)
      featureIdStore.clear();
        
    return ncommit;
  }
  
  /**
   * Get the uniquenames involved in a transaction
   * @param tsn
   * @return
   */
  private Object[] getUniqueNames(final ChadoTransaction tsn)
  {
    if(tsn.getGff_feature() == null)
      return null;
    if(tsn.getGff_feature().getSegmentRangeStore() == null ||
       tsn.getGff_feature().getSegmentRangeStore().size() < 2 ||
       tsn.getFeatureObject() instanceof FeatureProp)
      return new Object[]{ tsn.getUniquename() };
    else 
      return tsn.getGff_feature().getSegmentRangeStore().keySet().toArray();
  }
  
  /**
   * Construct an exeption message from the ChadoTransaction
   * @param re
   * @param sql
   * @param ncommit
   * @return
   */
  private String constructExceptionMessage(final RuntimeException re,
                                           final Vector sql,
                                           final int ncommit)
  {
    String msg = "";
    if(ncommit > -1 && ncommit < sql.size())
    {
      final ChadoTransaction t_failed = (ChadoTransaction)sql.get(ncommit);
      
      if(t_failed.getType() == ChadoTransaction.DELETE)
        msg = "DELETE failed ";
      else if(t_failed.getType() == ChadoTransaction.INSERT)
        msg = "INSERT failed ";
      else if(t_failed.getType() == ChadoTransaction.UPDATE)
        msg = "UPDATE failed ";
        
      if(t_failed.getUniquename() != null)
        msg = msg + "for " + t_failed.getUniquename()+":";
      else if(t_failed.getFeatureObject() != null &&
              t_failed.getFeatureObject() instanceof Feature)
      {
        final Feature chadoFeature = (Feature)t_failed.getFeatureObject();
        if(chadoFeature.getUniqueName() != null)
          msg = msg + "for " + chadoFeature.getUniqueName() +":";
      }
        
      msg = msg+"\n";
    }
    
    return msg + re.getMessage();  
  }
  
  /**
   * Commit a single chado transaction
   * @param tsn
   * @param dao
   */
  private void commitChadoTransaction(final ChadoTransaction tsn,
                                      final GmodDAO dao,
                                      final Timestamp ts)
  {
    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());
        }
        feature.setTimeLastModified(ts);
      }
      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 &&
            ((Feature) tsn.getFeatureObject()).getFeatureLoc() != null)
        {
          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());
    }
  }
  
  /**
   * 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 GmodDAO dao,
                                       final String keyName,
                                       final Hashtable featureIdStore,
                                       final ChadoTransaction tsn)
  {
    final Timestamp timestamp  = tsn.getLastModified();
    final Object featureObject = tsn.getFeatureObject();
    
    final Feature feature = dao.getFeatureByUniqueName(uniquename, keyName);
    if(feature == null)
      return true;
    
    featureIdStore.put(uniquename, feature);
    
    if(featureObject instanceof FeatureProp)
      ((FeatureProp)featureObject).setFeature(feature);
    else if(featureObject instanceof FeatureLoc)
    {
      if(((FeatureLoc)featureObject).getFeatureByFeatureId().getUniqueName().equals(uniquename))
      {
        logger4j.debug("Setting featureId for:"  + uniquename );
        ((FeatureLoc)featureObject).setFeatureByFeatureId(feature);
      }
    }
    
    final Timestamp now = feature.getTimeLastModified();
    
    if(now != null && timestamp != null)
    {
      now.setNanos(0);
      timestamp.setNanos(0);
      
      if(now.compareTo(timestamp) != 0)
      {
        final 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()+