/* Copyright (c) 2011 Peter Troshin * * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 * * This library is free software; you can redistribute it and/or modify it under the terms of the * Apache License version 2 as published by the Apache Software Foundation * * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache * License for more details. * * A copy of the license is in apache_license.txt. It is also available here: * @see: http://www.apache.org/licenses/LICENSE-2.0.txt * * Any republication or derived work distributed in source code form * must include this copyright and license notice. */ package compbio.runner.msa; import java.io.FileNotFoundException; import java.io.IOException; import java.util.Arrays; import java.util.List; import javax.xml.bind.annotation.XmlTransient; import org.apache.log4j.Logger; import compbio.data.sequence.Alignment; import compbio.data.sequence.UnknownFileFormatException; import compbio.engine.client.SkeletalExecutable; import compbio.metadata.ResultNotAvailableException; import compbio.runner.Util; public class Muscle extends SkeletalExecutable { /* * Tell JAXB to ignore this while marshalling */ @XmlTransient private static Logger log = Logger.getLogger(Muscle.class); private static final String EXEC_STAT_FILE = "stat.log"; public static final String KEY_VALUE_SEPARATOR = Util.SPACE; /** * Default options are * * -clwstrict - write output in clustal format * */ public Muscle() { /* * The –quiet command-line option disables writing progress messages to * standard error. If the –verbose command-line option is specified, a * progress message will be written to the log file when each iteration * completes. So –quiet and –verbose are not contradictory."-quiet", * "-verbose" */ addParameters(Arrays.asList("-clwstrict", "-quiet", "-verbose", "-nocore")); cbuilder.setParam("-log", EXEC_STAT_FILE); } @Override public Muscle setOutput(String outFile) { super.setOutput(outFile); cbuilder.setParam("-out", outFile); return this; } @Override public Muscle setInput(String inFile) { super.setInput(inFile); cbuilder.setParam("-in", inFile); return this; } @SuppressWarnings("unchecked") @Override public Alignment getResults(String workDirectory) throws ResultNotAvailableException { try { return Util.readClustalFile(workDirectory, getOutput()); } catch (FileNotFoundException e) { log.error(e.getMessage(), e.getCause()); throw new ResultNotAvailableException(e); } catch (IOException e) { log.error(e.getMessage(), e.getCause()); throw new ResultNotAvailableException(e); } catch (UnknownFileFormatException e) { log.error(e.getMessage(), e.getCause()); throw new ResultNotAvailableException(e); } catch (NullPointerException e) { log.error(e.getMessage(), e.getCause()); throw new ResultNotAvailableException(e); } } @Override public List getCreatedFiles() { return Arrays.asList(getOutput(), EXEC_STAT_FILE); } public static String getStatFile() { return EXEC_STAT_FILE; } @SuppressWarnings("unchecked") @Override public Class getType() { return (Class) this.getClass(); } }