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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 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 ClustalW extends SkeletalExecutable<ClustalW> {
private static Logger log = Logger.getLogger(ClustalW.class);
private static final String EXEC_STAT_FILE = "stat.log";
private static final String TREE_FILE_EXT = ".dnd";
public static final String KEY_VALUE_SEPARATOR = "=";
public ClustalW() {
super(KEY_VALUE_SEPARATOR);
addParameters(Arrays.asList("-OUTORDER=ALIGNED", "-QUIET", "-STATS="
+ EXEC_STAT_FILE));
// set default in, outs and err files
this.setInput(super.inputFile);
this.setOutput(super.outputFile);
this.setError(super.errorFile);
}
@Override
public ClustalW setOutput(String outFile) {
super.setOutput(outFile);
cbuilder.setParam("-OUTFILE=" + outFile);
return this;
}
@Override
public ClustalW setInput(String inFile) {
super.setInput(inFile);
cbuilder.setParam("-INFILE=" + inFile);
return this;
}
@SuppressWarnings("unchecked")
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,
convertInputNameToTreeName());
}
/**
* Clustal output tree with same name as input file but .dnd extension e.g.
* this methods do similar conversion TO122.fasta -> TO122.dnd or
* TO122.fasta.in -> TO122.fasta.dnd It does not seems that there is any
* limits on the name length
*
* @return
*/
private String convertInputNameToTreeName() {
assert super.getInput() != null;
int dotIdx = getInput().lastIndexOf(".");
String treeFileName = "";
if (dotIdx > 0) {
treeFileName = getInput().substring(0, dotIdx);
}
return treeFileName + TREE_FILE_EXT;
}
public static String getStatFile() {
return EXEC_STAT_FILE;
}
@SuppressWarnings("unchecked")
@Override
public Class<ClustalW> getType() {
return (Class<ClustalW>) this.getClass();
}
}
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