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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.conservation;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.util.Arrays;
import java.util.List;
import org.apache.log4j.Logger;
import compbio.data.sequence.ScoreManager;
import compbio.data.sequence.SequenceUtil;
import compbio.engine.client.CommandBuilder;
import compbio.engine.client.Executable;
import compbio.engine.client.SkeletalExecutable;
import compbio.engine.client.EngineUtil;
import compbio.metadata.ResultNotAvailableException;
/**
* Command line
*
* java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
*
* @author pvtroshin
*
*/
public class AACon extends SkeletalExecutable<AACon> {
private static Logger log = Logger.getLogger(AACon.class);
/**
* Number of cores to use, defaults to 1 for local execution or the value of
* "jronn.cluster.cpunum" property for cluster execution
*/
private int ncoreNumber = 0;
private final String ncorePrm = "-t=";
public static final String KEY_VALUE_SEPARATOR = "=";
public static final String STAT_FILE = "stat.txt";
public AACon() {
addParameters(Arrays.asList("-jar", getLibPath(), "-d=" + STAT_FILE, "-f=RESULT_NO_ALIGNMENT"));
}
// HashMap<Method, float[]>
@Override
public ScoreManager getResults(String workDirectory) throws ResultNotAvailableException {
ScoreManager annotations = null;
try {
InputStream inStream = new FileInputStream(new File(workDirectory, getOutput()));
annotations = ScoreManager.newInstanceSingleSequence(SequenceUtil.readAAConResults(inStream));
inStream.close();
} 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 (NullPointerException e) {
log.error(e.getMessage(), e.getCause());
throw new ResultNotAvailableException(e);
}
return annotations;
}
private static String getLibPath() {
String settings = ph.getProperty("aacon.jar.file");
if (compbio.util.Util.isEmpty(settings)) {
throw new NullPointerException("Please define aacon.jar.file property in Executable.properties file "
+ "and initialize it with the location of aaconservation jar file");
}
if (new File(settings).isAbsolute()) {
// the jar can be found so no actions necessary
// no further actions is necessary
return settings;
}
return EngineUtil.convertToAbsolute(settings);
}
@Override
public List<String> getCreatedFiles() {
return Arrays.asList(getOutput(), getError());
}
@Override
public AACon setInput(String inFile) {
super.setInput(inFile);
cbuilder.setParam("-i=" + inFile);
return this;
}
@Override
public AACon setOutput(String outFile) {
super.setOutput(outFile);
cbuilder.setParam("-o=" + outFile);
return this;
}
@SuppressWarnings("unchecked")
@Override
public Class<AACon> getType() {
return (Class<AACon>) this.getClass();
}
public static String getStatFile() {
return STAT_FILE;
}
public void setNCore(int ncoreNumber) {
if (ncoreNumber < 1 || ncoreNumber > 100) {
throw new IndexOutOfBoundsException("Number of cores must be within 1 and 100 ");
}
this.ncoreNumber = ncoreNumber;
cbuilder.setParam(ncorePrm + Integer.toString(getNCore()));
}
int getNCore() {
return ncoreNumber;
}
@Override
public CommandBuilder<AACon> getParameters(ExecProvider provider) {
// If number of cores is provided, set it for the cluster execution
// only!
if (provider == Executable.ExecProvider.Cluster) {
int cpunum = SkeletalExecutable.getClusterCpuNum(getType());
cpunum = (cpunum == 0) ? 1 : cpunum;
setNCore(cpunum);
} else {
// Limit number of cores to 1 for ANY execution which does not set
// Ncores explicitly using setNCore method or is run on local VM
if (ncoreNumber == 0) {
setNCore(1);
}
}
return super.getParameters(provider);
}
}
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