bio.gcat.operation.analysis.AminoAcids.java Source code

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Here is the source code for bio.gcat.operation.analysis.AminoAcids.java

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/*
 * Copyright [2016] [Mannheim University of Applied Sciences]
 * 
 * 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 bio.gcat.operation.analysis;

import java.util.Collection;
import java.util.Optional;
import bio.gcat.Documented;
import bio.gcat.nucleic.Compound;
import bio.gcat.nucleic.Tuple;
import bio.gcat.operation.Cataloged;
import bio.gcat.operation.Named;
import com.google.common.collect.EnumMultiset;
import com.google.common.collect.Multiset;
import com.google.common.collect.Multiset.Entry;
import static bio.gcat.Help.*;

@Named(name = "amino acids", icon = "bricks")
@Cataloged(group = "Analyse Sequence")
@Documented(title = "Amino Acids", category = { OPERATIONS,
        ANALYSES }, resource = "help/operation/analysis/amino_acids.html")
public class AminoAcids implements Analysis {
    private static final String DELIMITER = ", ", TIMES = "x ";

    @Override
    public Result analyse(Collection<Tuple> tuples, Object... values) {
        Multiset<Compound> compounds = EnumMultiset.create(Compound.class);
        for (Tuple tuple : tuples)
            compounds.add(Compound.isStop(tuple) ? Compound.STOP
                    : Optional.ofNullable(tuple.getCompound()).orElse(Compound.UNKNOWN));

        StringBuilder builder = new StringBuilder();
        for (Entry<Compound> compound : compounds.entrySet())
            builder.append(DELIMITER).append(compound.getCount()).append(TIMES).append(compound.getElement());

        return new SimpleResult(this, builder.substring(DELIMITER.length()).toString());
    }
}