/*
* Copyright © 2026 Dmitry Degrave
*
* 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 org.dnaerys.client;
import org.dnaerys.cluster.grpc.Chromosome;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import static java.util.Map.entry;
public class ContigsMapping {
static final Map<String, Chromosome> GRPC_CHR = Map.ofEntries(
entry("1", Chromosome.CHR_1),
entry("2", Chromosome.CHR_2),
entry("3", Chromosome.CHR_3),
entry("4", Chromosome.CHR_4),
entry("5", Chromosome.CHR_5),
entry("6", Chromosome.CHR_6),
entry("7", Chromosome.CHR_7),
entry("8", Chromosome.CHR_8),
entry("9", Chromosome.CHR_9),
entry("10", Chromosome.CHR_10),
entry("11", Chromosome.CHR_11),
entry("12", Chromosome.CHR_12),
entry("13", Chromosome.CHR_13),
entry("14", Chromosome.CHR_14),
entry("15", Chromosome.CHR_15),
entry("16", Chromosome.CHR_16),
entry("17", Chromosome.CHR_17),
entry("18", Chromosome.CHR_18),
entry("19", Chromosome.CHR_19),
entry("20", Chromosome.CHR_20),
entry("21", Chromosome.CHR_21),
entry("22", Chromosome.CHR_22),
entry("X", Chromosome.CHR_X),
entry("Y", Chromosome.CHR_Y),
entry("MT", Chromosome.CHR_MT)
);
static Chromosome contigName2GrpcChr(String contig) {
return GRPC_CHR.getOrDefault(contig, Chromosome.UNRECOGNIZED);
}
static List<Chromosome> contigName2GrpcChr(String[] contigs) {
ArrayList<Chromosome> res = new ArrayList<>(contigs.length);
for (String chr : contigs) {
res.add(contigName2GrpcChr(chr));
}
return res;
}
}
