com.salsaw.msalsa.clustal.ClustalOmegaManager.java Source code

Introduction

Here is the source code for com.salsaw.msalsa.clustal.ClustalOmegaManager.java

Source

/**
 * Copyright 2015 Alessandro Daniele, Fabio Cesarato, Andrea Giraldin
 * 
 * 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.salsaw.msalsa.clustal;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.nio.file.Path;
import java.nio.file.Paths;

import org.apache.commons.io.FilenameUtils;

import java.util.ArrayList;
import java.util.List;

import com.salsaw.msalsa.algorithm.exceptions.SALSAException;

public class ClustalOmegaManager extends ClustalManager {
    // CONSTANTS

    // keys of options
    private static final String INPUT_FILE = "infile";
    private static final String OUTPUT_FILE = "outfile";

    /**
     * MSA output file format (default: fasta)
     */
    private static final String OUTPUT_FORMAT = "outfmt";
    private static final String GUIDE_TREE_OUTPUT_FILE = "guidetree-out";

    // flag settings
    /**
     * Verbose output (increases if given multiple times)
     */
    private static final String VERBOSE = "verbose";
    /**
     * over-writing of already existing files
     */
    private static final String OVERWITE_OUTPUT_FILE = "force";

    // FILEDS
    private ClustalFileMapper clustalFileMapper;
    private ClustalOmegaOputputFormat clustalOmegaOputputFormat = ClustalOmegaOputputFormat.FASTA;

    // GET / SET
    public void setClustalFileMapper(ClustalFileMapper clustalFileMapper) {
        this.clustalFileMapper = clustalFileMapper;
    }

    // METHODS
    @Override
    protected String createBooleanParameterCommand(String value) {
        StringBuilder stringBuilder = new StringBuilder();
        stringBuilder.append(ARGUMENTS_START_SYMBOL);
        stringBuilder.append(ARGUMENTS_START_SYMBOL);
        stringBuilder.append(value);
        return stringBuilder.toString();
    }

    @Override
    protected String createParameterEqualsCommand(String key, String value) {
        StringBuilder stringBuilder = new StringBuilder();
        stringBuilder.append(ARGUMENTS_START_SYMBOL);
        stringBuilder.append(ARGUMENTS_START_SYMBOL);
        stringBuilder.append(key);
        stringBuilder.append(ARGUMENTS_ASSING_SYMBOL);
        stringBuilder.append(value);
        return stringBuilder.toString();
    }

    @Override
    public List<String> generateClustalArguments(List<String> commands) {
        if (clustalFileMapper == null) {
            throw new IllegalArgumentException("clustalFileMapper");
        }

        commands.add(
                createParameterEqualsCommand(INPUT_FILE, '"' + this.clustalFileMapper.getInputFilePath()) + '"');
        commands.add(createParameterEqualsCommand(OUTPUT_FILE, '"' + this.clustalFileMapper.getAlignmentFilePath())
                + '"');

        commands.add(createParameterEqualsCommand(GUIDE_TREE_OUTPUT_FILE,
                '"' + this.clustalFileMapper.getGuideTreeFilePath()) + '"');
        commands.add(createParameterEqualsCommand(OUTPUT_FORMAT, this.clustalOmegaOputputFormat.toString()));

        commands.add(createBooleanParameterCommand(VERBOSE));
        commands.add(createBooleanParameterCommand(OVERWITE_OUTPUT_FILE));

        return commands;
    }

    @Override
    public void callClustal(String clustalPath, ClustalFileMapper clustalFileMapper)
            throws IOException, InterruptedException, SALSAException {
        // Get program path to execute
        List<String> clustalProcessCommands = new ArrayList<String>();
        clustalProcessCommands.add(clustalPath);

        // Create the name of output files
        String inputFileName = FilenameUtils.getBaseName(clustalFileMapper.getInputFilePath());
        String inputFileFolderPath = FilenameUtils.getFullPath(clustalFileMapper.getInputFilePath());
        Path alignmentFilePath = Paths.get(inputFileFolderPath, inputFileName + "-aln.fasta");
        Path guideTreeFilePath = Paths.get(inputFileFolderPath, inputFileName + "-tree.dnd");

        // Set inside file mapper
        clustalFileMapper.setAlignmentFilePath(alignmentFilePath.toString());
        clustalFileMapper.setGuideTreeFilePath(guideTreeFilePath.toString());
        setClustalFileMapper(clustalFileMapper);

        // Create clustal omega data
        generateClustalArguments(clustalProcessCommands);

        // http://www.rgagnon.com/javadetails/java-0014.html
        ProcessBuilder builder = new ProcessBuilder(clustalProcessCommands);
        builder.redirectErrorStream(true);
        System.out.println(builder.command());
        final Process process = builder.start();
        InputStream is = process.getInputStream();
        InputStreamReader isr = new InputStreamReader(is);
        BufferedReader br = new BufferedReader(isr);

        String line;
        while ((line = br.readLine()) != null) {
            System.out.println(line);
        }
        process.waitFor();

        if (process.exitValue() != 0) {
            throw new SALSAException("Failed clustal omega call");
        }
    }
}