FeatureMapper.java

package org.genedb.crawl.mappers;

import java.util.List;

import org.apache.ibatis.annotations.Param;
import org.genedb.crawl.model.Coordinates;
import org.genedb.crawl.model.Cvterm;
import org.genedb.crawl.model.Dbxref;
import org.genedb.crawl.model.Feature;
import org.genedb.crawl.model.FeatureRelationship;
import org.genedb.crawl.model.Orthologue;
import org.genedb.crawl.model.Property;
import org.genedb.crawl.model.Gene;
import org.genedb.crawl.model.LocatedFeature;
import org.genedb.crawl.model.Pub;
import org.genedb.crawl.model.Synonym;
import org.genedb.crawl.model.Transcript;

public interface FeatureMapper {

	Feature get(
		@Param("uniqueName") String uniqueName,
		@Param("name") String name,
		@Param("organism_id") Integer organism_id,
		@Param("type") String type);

	Feature getWithSynonym(
		@Param("uniqueName") String uniqueName,
		@Param("name") String name,
		@Param("organism_id") Integer organism_id,
		@Param("type") String type);

	List<Property> properties(Feature feature);

	List<Cvterm> terms (Feature feature);

	List<Coordinates> coordinates(Feature feature);

	List<Synonym> synonyms(Feature feature);
	List<Pub> pubs (Feature feature);

	List<LocatedFeature> domains (Feature feature);
	List<Dbxref> dbxrefs (Feature feature);
	List<Orthologue> orthologues (Feature feature);

	void delete(Feature feature);

//	LocatedFeature getOfType(
//			@Param("uniqueName") String uniqueName,
//			@Param("organism_id") Integer organism_id,
//			@Param("name") String name,
//			@Param("type") String type);

	List<Transcript> transcripts(@Param("gene") Gene gene, @Param("exons") boolean exons);

	List<Feature> parents(@Param("feature") Feature feature, @Param("relationships") List<Cvterm> relationships);
	List<Feature> children(@Param("feature") Feature feature, @Param("relationships") List<Cvterm> relationships );

}