FeaturesMapper.java

package org.genedb.crawl.mappers;

import java.util.Date;
import java.util.List;

import org.apache.ibatis.annotations.Param;

import org.genedb.crawl.model.BlastPair;
import org.genedb.crawl.model.Cvterm;
import org.genedb.crawl.model.Feature;
import org.genedb.crawl.model.LocatedFeature;
import org.genedb.crawl.model.HierarchyGeneFetchResult;
import org.genedb.crawl.model.HierarchyRelation;
import org.genedb.crawl.model.Statistic;

public interface FeaturesMapper {
	
	//int getFeatureID(String uniquename);
	
	List<HierarchyGeneFetchResult> getGeneForFeature(@Param("features") List<String> features );
	List<HierarchyRelation> getRelationshipsParents(@Param("feature") String feature, @Param("relationships") List<Cvterm> relationships );
	List<HierarchyRelation> getRelationshipsChildren(@Param("feature") String feature, @Param("relationships") List<Cvterm> relationships );
	
	
	
	List<Feature> coordinates(@Param("features") List<String> features, @Param("region") String region );
	List<Feature> synonyms(@Param("features") List<String> features, @Param("types") List<String> types );
	
	List<Feature> properties(@Param("features") List<String> features, @Param("types") List<String> types );
	
	List<Feature> pubs (@Param("features") List<String> features);
	List<Feature> dbxrefs (@Param("features") List<String> features);
	List<Feature> terms (@Param("features") List<String> features, @Param("cvs") List<String> cvs);
	List<Feature> orthologues(@Param("features") List<String> features);
	List<Feature> clusters(@Param("features") List<String> features);
	
	List<Feature> synonymsLike(
			@Param("term") String term, 
			@Param("regex") Boolean regex, 
			@Param("region") String region);
	
	List<Feature> featuresLike(
			@Param("term") String term, 
			@Param("regex") Boolean regex, 
			@Param("region") String region);
	
	List<Feature> withproperty(
			@Param("value") String value, 
			@Param("regex") Boolean regex, 
			@Param("region") String region,
			@Param("type") String type);
	
	List<Feature> withterm(
			@Param("cvterm") String cvterm,
			@Param("cv") String cv,
			@Param("regex") Boolean regex, 
			@Param("region") String region);
	
	List<Feature> timelastmodified(
			@Param("date") Date date, 
			@Param("organism_id") Integer organism_id, 
			@Param("types") List<String> types,
			@Param("exclude") boolean exclude);
	
	
	List<Feature> annotationModified(
			@Param("date") Date date, 
			@Param("organism_id") Integer organism_id, 
			@Param("region") String region);
	
	List<Statistic> annotationModifiedStatistics(@Param("date") Date date, @Param("organism_id") Integer organism_id, @Param("region") String region);
	
	List<BlastPair> blastPairs(
		@Param("f1") String f1, 
		@Param("start1") int start1, 
		@Param("end1") int end1, 
		@Param("f2") String f2, 
		@Param("start2") int start2, 
		@Param("end2") int end2, 
		@Param("length") Integer length, 
		@Param("normscore") Double normscore);
	
    // this method should return any features that are located on regular features
    // e.g. orthologues, but also domains...
    // TODO think about whether this is better implemented with a less chado-ish
	// interface - e.g. feature/domains
	// we already have features/orthologues done this way
	public List<LocatedFeature> locations(@Param("region") String region);
	
}