/*
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published by
* the Free Software Foundation, either version 3 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see http://www.gnu.org/licenses/
*/
package org.phenotips.variantStoreIntegration.mocks;
import org.phenotips.variantstore.VariantStoreInterface;
import org.phenotips.variantstore.shared.VariantStoreException;
import java.nio.file.Path;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.Callable;
import java.util.concurrent.Future;
import java.util.concurrent.FutureTask;
import org.ga4gh.GAVariant;
/**
* A mock variant store.
*
* @version $Id: a877cacb6d061b2a0ed7ddff3e97b032c6090ff0 $
*/
public class MockVariantStore implements VariantStoreInterface
{
/**
* Start up the variant store.
*/
public void init()
{
}
@Override
public void init(Path path) throws VariantStoreException
{
}
/**
* Not used yet.
*/
@Override
public void stop()
{
};
/**
* @param id adsf
* @param isPublic asdfas
* @param file asdf
* @return Future sdf
*/
@Override
public Future<Boolean> addIndividual(String id, boolean isPublic, Path file)
{
Callable<Boolean> task = new MockProcessingTask();
return new FutureTask<Boolean>(task);
}
/**
* @param id w/e
* @return w/e
*/
@Override
public Future<Boolean> removeIndividual(String id)
{
Callable<Boolean> task = new MockProcessingTask();
return new FutureTask<Boolean>(task);
}
@Override
public List<GAVariant> getTopHarmfullVariants(String s, int i)
{
return null;
}
@Override
public List<String> getAllIndividuals()
{
return null;
}
/**
* Get a set of all known genes for an individual.
*
* @param id the individual's id
*
* @return the set of genes
*/
@Override
public Set<String> getAllGenesForIndividual(String id) {
return null;
}
/**
* Get the exomiser harmfulness score for a gene for an individual.
*
* @param id the individual's id
* @param gene the gene
*
* @return the exomiser harmfulness score for the gene for the individual.
*/
@Override
public Double getGeneScore(String id, String gene) {
return null;
}
/**
* Get a list of at most k variants with a known gene of an individual,
* sorted by harmfulness.
*
* @param id the individual
* @param gene the gene
* @param k the max number of variants to return
*
* @return the list of variants
*/
@Override
public List<GAVariant> getTopHarmfullVariantsForGene(String id, String gene, Integer k) {
return null;
}
/**
* Get a list of top k harmfull genes for an individual, sorted by
* harmfulness.
*
* @param id the individual's id
* @param k the max number of genes to return
*
* @return the list of genes
*/
@Override
public List<String> getTopGenesForIndividual(String id, Integer k) {
return null;
}
@Override
public Map<String, List<GAVariant>> getIndividualsWithGene(String geneSymbol, List<String> variantEffects,
Map<String, Double> alleleFrequencies)
{
// TODO Auto-generated method stub
return null;
}
@Override
public Map<String, List<GAVariant>> getIndividualsWithVariant(String chr, int pos, String ref, String alt)
{
// TODO Auto-generated method stub
return null;
}
}