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

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Here is the source code for bio.gcat.operation.analysis.BDAUsage.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 static bio.gcat.Help.*;
import static bio.gcat.nucleic.Tuple.*;
import java.util.Collection;
import java.util.HashMap;
import java.util.stream.Collectors;
import bio.gcat.geneticcode.dich.Codon;
import scala.collection.immutable.List;
import bio.gcat.Documented;
import bio.gcat.gui.AnalysisTool;
import bio.gcat.nucleic.Tuple;
import bio.gcat.operation.Cataloged;
import bio.gcat.operation.Named;
import com.google.common.collect.HashMultiset;
import com.google.common.collect.Multiset;
import com.google.common.collect.Multiset.Entry;

@Named(name = "BDA usage", icon = "bda")
@Cataloged(group = "Analyse Sequence")
@Documented(title = "BDA Usage", category = { OPERATIONS,
        ANALYSES }, resource = "help/operation/analysis/bda_usage.html")
public class BDAUsage implements Analysis {
    @Override
    public Result analyse(Collection<Tuple> tuples, Object... values) {
        if (condenseTuples(tuples).isEmpty())
            return new SimpleResult(this, "No tuples.");
        else if (Tuple.tuplesLength(tuples) != 3)
            return new SimpleResult(this, "Only sequences with codons (tuples of length 3) are allowed.");

        bio.gcat.geneticcode.dich.ct.ClassTable classTable = AnalysisTool.getBDATool().getClassTable();
        if (classTable == null)
            return new SimpleResult(this, "No Binary Dichotomic Algorithm. Use BDA Tool to open / create BDAs.");
        HashMap<Codon, List<Object>> codonToClass = classTable.codon2class();

        Multiset<List<Object>> classCount = HashMultiset.create(tuples.stream()
                .map(tuple -> codonToClass.get(new Codon(tuple.toString()))).collect(Collectors.toList()));

        StringBuilder builder = new StringBuilder();
        for (Entry<List<Object>> count : classCount.entrySet())
            builder.append(count.getElement().mkString("", "", "") + ": " + count.getCount() + "<br/>");
        return new SimpleResult(this, builder.toString());
    }
}