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*
* 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.ReadFormatException;
import uk.ac.sanger.artemis.chado.IBatisDAO;
import uk.ac.sanger.artemis.chado.JdbcDAO;
import uk.ac.sanger.artemis.chado.GmodDAO;
import uk.ac.sanger.artemis.chado.ChadoTransaction;
import uk.ac.sanger.artemis.components.database.DatabaseEntrySource;
import org.gmod.schema.sequence.Feature;
import org.gmod.schema.sequence.FeatureProp;
import org.gmod.schema.sequence.FeatureLoc;
import org.gmod.schema.sequence.FeatureRelationship;
import org.gmod.schema.sequence.FeatureSynonym;
import org.gmod.schema.sequence.FeatureCvTerm;
import org.gmod.schema.sequence.FeatureCvTermProp;
import org.gmod.schema.general.DbXRef;
import org.gmod.schema.pub.PubDbXRef;
import org.gmod.schema.pub.Pub;
* Objects of this class are Documents created from a relational database.
*
*/
/** source feature_id */
private String srcFeatureId = "1";
/** database schema */
private String schema = "public";
private static Hashtable cvterms;
private InputStreamProgressListener progress_listener;
/** JDBC DAO */
private JdbcDAO jdbcDAO = null;
/** iBatis DAO */
private IBatisDAO connIB = null;
private String[] types = { "exon", "gene", "CDS", "transcript" };
private List schema_list;
private boolean gene_builder;
// controlled vocabulary
/** controlled_curation controlled vocabulary */
*
* 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)
if(location.indexOf('=') > -1)
this.schema = location.substring( location.indexOf('=')+ 1);
*
* Create a new Document from a database.
*
* @param location
* This should be a URL string giving:
* @param feature_id
* ID of a feature to be extracted.
*
*/
public DatabaseDocument(String location, JPasswordField pfield,
String srcFeatureId, String schema)
this.srcFeatureId = srcFeatureId;
*
* Create a new Document from a database.
*
* @param location
* This should be a URL string giving:
* jdbc:postgresql://host:port/datbase_name?user=username
* @param srcFeatureId
* ID of a feature to be extracted.
* @param splitGFFEntry
* split into separate entries based on feature types.
* @param progress_listener
* input stream progress listener
*
*/
public DatabaseDocument(String location, JPasswordField pfield,
String srcFeatureId, String schema, boolean splitGFFEntry,
InputStreamProgressListener progress_listener)
{
super(location);
this.srcFeatureId = srcFeatureId;
this.progress_listener = progress_listener;
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