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package compbio.runner.structure;
import java.io.FileNotFoundException;
import java.io.IOException;
import org.apache.log4j.Logger;
import compbio.data.sequence.RNAStructScoreManager;
import compbio.engine.client.PipedExecutable;
import compbio.engine.client.SkeletalExecutable;
import compbio.metadata.ResultNotAvailableException;
import compbio.runner.RunnerUtil;
public class RNAalifold extends SkeletalExecutable<RNAalifold>
implements PipedExecutable<RNAalifold> {
private static Logger log = Logger.getLogger(RNAalifold.class);
// May not be necessary as defult is "<space>" but still dont know
// How to deal with different key value separators for different params
public static final String KEY_VALUE_SEPARATOR = " ";
public RNAalifold() {
super(KEY_VALUE_SEPARATOR);
}
@Override
public RNAalifold setOutput(String outFile) {
super.setOutput(outFile);
return this;
}
@Override
public RNAalifold setInput(String inFile) {
cbuilder.setLast(inFile);
super.setInput(inFile);
return this;
}
@SuppressWarnings("unchecked")
@Override
public Class<RNAalifold> getType() {
return (Class<RNAalifold>) this.getClass();
}
@SuppressWarnings("unchecked")
@Override
public RNAStructScoreManager getResults(String workDirectory)
throws ResultNotAvailableException {
try {
return RunnerUtil.readRNAStruct(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);
}
}
}
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