/*
* Copyright 2015 MiLaboratory.com
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package com.milaboratory.core.mutations.generator;
import org.apache.commons.math3.random.RandomGenerator;
import static com.milaboratory.core.mutations.generator.SubstitutionModels.getEmpiricalNucleotideSubstitutionModelWithNoise;
public class MutationModels {
public static NucleotideMutationModel getEmpiricalNucleotideMutationModel() {
return new GenericNucleotideMutationModel(
SubstitutionModels.getEmpiricalNucleotideSubstitutionModel(), 0.00522, 0.00198);
}
public static NucleotideMutationModel getEmpiricalNucleotideMutationModelWithNoise(
RandomGenerator rd, double minFactor, double maxFactor) {
double l = maxFactor - minFactor;
return new GenericNucleotideMutationModel(
getEmpiricalNucleotideSubstitutionModelWithNoise(rd, minFactor, maxFactor),
0.00522 * (minFactor + l * rd.nextDouble()),
0.00198 * (minFactor + l * rd.nextDouble()),
rd.nextLong());
}
}