compbio.runner.structure

Class RNAalifold

java.lang.Object

compbio.engine.client.SkeletalExecutable<RNAalifold>

compbio.runner.structure.RNAalifold

All Implemented Interfaces:

Executable<RNAalifold>, PipedExecutable<RNAalifold>

public class RNAalifold
extends SkeletalExecutable<RNAalifold>
implements PipedExecutable<RNAalifold>

Nested Class Summary

Nested classes/interfaces inherited from interface compbio.engine.client.Executable

Executable.ExecProvider

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	KEY_VALUE_SEPARATOR
private static org.apache.log4j.Logger	log

Fields inherited from class compbio.engine.client.SkeletalExecutable

cbuilder, ERROR, errorFile, INPUT, inputFile, OUTPUT, outputFile, ph

Constructor Summary

Constructors

Constructor and Description
RNAalifold()

Method Summary

Modifier and Type	Method and Description
RNAStructScoreManager	getResults(java.lang.String workDirectory)
java.lang.Class<RNAalifold>	getType()
RNAalifold	setInput(java.lang.String inFile)
RNAalifold	setOutput(java.lang.String outFile)

Methods inherited from class compbio.engine.client.SkeletalExecutable

addParameters, equals, getClusterCpuNum, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, hashCode, isErrorSet, isInputSet, isOutputSet, loadRunConfiguration, setError, setParameter, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface compbio.engine.client.Executable

addParameters, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, loadRunConfiguration

Field Detail

log

private static org.apache.log4j.Logger log

KEY_VALUE_SEPARATOR

public static final java.lang.String KEY_VALUE_SEPARATOR

See Also:

Constant Field Values

Constructor Detail

RNAalifold

public RNAalifold()

Method Detail

setOutput

public RNAalifold setOutput(java.lang.String outFile)

Overrides:

setOutput in class SkeletalExecutable<RNAalifold>

setInput

public RNAalifold setInput(java.lang.String inFile)

Overrides:

setInput in class SkeletalExecutable<RNAalifold>

getType

public java.lang.Class<RNAalifold> getType()

Specified by:

getType in class SkeletalExecutable<RNAalifold>

Returns:

subclasses must return their type

getResults

public RNAStructScoreManager getResults(java.lang.String workDirectory)
                                 throws ResultNotAvailableException

Specified by:

getResults in interface Executable<RNAalifold>

Throws:

ResultNotAvailableException