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/* 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.RunnerUtil;
public class Muscle extends SkeletalExecutable<Muscle> {
/*
* 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 = " ";
/**
* 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 RunnerUtil.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<String> getCreatedFiles() {
return Arrays.asList(getOutput(), EXEC_STAT_FILE);
}
public static String getStatFile() {
return EXEC_STAT_FILE;
}
@SuppressWarnings("unchecked")
@Override
public Class<Muscle> getType() {
return (Class<Muscle>) this.getClass();
}
}
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