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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.ws.server;
import java.util.List;
import org.apache.log4j.Logger;
import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.ScoreManager;
import compbio.engine.client.ConfiguredExecutable;
import compbio.engine.client.SkeletalExecutable;
import compbio.metadata.JobSubmissionException;
import compbio.metadata.Limit;
import compbio.metadata.LimitExceededException;
import compbio.metadata.Option;
import compbio.metadata.Preset;
import compbio.metadata.ResultNotAvailableException;
import compbio.metadata.UnsupportedRuntimeException;
import compbio.metadata.WrongParameterException;
import compbio.runner.conservation.AACon;
/**
* Common methods for all SequenceAnnotation web services
*
* @author pvtroshin
*
* @param <T>
*
* @version 1.0 June 2011
* @since 2.0
*/
public abstract class SequenceAnnotationService<T> extends GenericMetadataService {
/*
* FIXME - instances of the Runner (?) and their types should be defined in
* Executable IF
*/
SequenceAnnotationService(SkeletalExecutable<T> exec, Logger log) {
super(exec, log);
}
public ScoreManager getAnnotation(String jobId)
throws ResultNotAvailableException {
return WSUtil.getAnnotation(jobId, log);
}
@SuppressWarnings("unchecked")
public String analize(List<FastaSequence> sequences)
throws UnsupportedRuntimeException, LimitExceededException, JobSubmissionException {
WSUtil.validateFastaInput(sequences);
ConfiguredExecutable<T> confIUPred = init(sequences);
return WSUtil.analize(sequences, confIUPred, log, "analize", getLimit(""));
}
@SuppressWarnings("unchecked")
public String customAnalize(List<FastaSequence> sequences,
List<Option<T>> options) throws UnsupportedRuntimeException,
LimitExceededException, JobSubmissionException,
WrongParameterException {
WSUtil.validateFastaInput(sequences);
ConfiguredExecutable<T> confAACon = init(sequences);
// Could not do that! Space separated values
// will all be treated as keys! thus duplicates removed
// String params = cbuilder.getCommand();
List<String> params = WSUtil.getCommands(options,
AACon.KEY_VALUE_SEPARATOR);
confAACon.addParameters(params);
return WSUtil.analize(sequences, confAACon, log, "customAnalize", getLimit(""));
}
public String presetAnalize(List<FastaSequence> sequences, Preset<T> preset)
throws UnsupportedRuntimeException, LimitExceededException, JobSubmissionException, WrongParameterException {
WSUtil.validateAAConInput(sequences);
if (preset == null) {
throw new WrongParameterException("Preset must be provided!");
}
@SuppressWarnings("unchecked")
ConfiguredExecutable<T> confAAcon = init(sequences);
confAAcon.addParameters(preset.getOptions());
@SuppressWarnings("unchecked")
Limit<T> limit = getLimit(preset.getName());
return WSUtil.analize(sequences, confAAcon, log, "presetAnalize", limit);
}
}
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