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

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Here is the source code for bio.gcat.operation.analysis.TupleUsage.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.ANALYSES;
import static bio.gcat.Help.OPERATIONS;
import static bio.gcat.Utilities.containsOnly;
import static bio.gcat.nucleic.Tuple.normalizeTuples;
import static bio.gcat.nucleic.Tuple.splitTuples;
import static bio.gcat.nucleic.Tuple.tupleString;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.Collection;

import com.google.common.collect.HashMultiset;
import com.google.common.collect.Multiset;

import bio.gcat.Documented;
import bio.gcat.Parameter;
import bio.gcat.Parameter.Type;
import bio.gcat.log.Logger;
import bio.gcat.nucleic.Acid;
import bio.gcat.nucleic.Tuple;
import bio.gcat.operation.Cataloged;
import bio.gcat.operation.Named;

@Named(name = "tuple usage", icon = "report")
@Cataloged(group = "Analyse Sequence")
@Parameter.Annotation(key = "file", label = "File", type = Type.FILE)
@Documented(title = "Tuple Usage", category = { OPERATIONS,
        ANALYSES }, resource = "help/operation/analysis/tuple_usage.html")
public class TupleUsage implements Analysis {
    private static final String DELIMITER = ", ", TIMES = "x ";
    private static final Tuple EMPTY_TUPLE = new Tuple();

    @Override
    public Result analyse(Collection<Tuple> tuples, Object... values) {
        Logger logger = getLogger();

        if (values[0] == null) {
            logger.log("Choose an existing file to count tuple usage in.");
            return null;
        }

        Acid acid;
        if ((acid = Tuple.tuplesAcid(tuples)) == null) {
            logger.log("Tuples with variable acids, can't analyse tuple usage.");
            return null; //tuples not all in same acid
        }

        Multiset<Tuple> tupleCount = HashMultiset.create();
        try (BufferedReader reader = new BufferedReader(new InputStreamReader((InputStream) values[0]))) {
            String line;
            while ((line = reader.readLine()) != null)
                tupleCount.addAll(normalizeTuples(splitTuples(tupleString(line).trim()), acid));
        } catch (IOException e) {
            logger.log("Error while reading file.", e);
            return null;
        }

        StringBuilder builder = new StringBuilder();
        for (Tuple tuple : (!tuples.isEmpty() && !containsOnly(tuples, EMPTY_TUPLE) ? normalizeTuples(tuples, acid)
                : tupleCount.elementSet()))
            builder.append(DELIMITER).append(tupleCount.count(tuple)).append(TIMES).append(tuple);
        return new SimpleResult(this,
                builder.length() != 0 ? builder.substring(DELIMITER.length()).toString() : "no tuples");
    }
}