compbio.runner.msa

Class MSAprobs

java.lang.Object

compbio.engine.client.SkeletalExecutable<MSAprobs>

compbio.runner.msa.MSAprobs

All Implemented Interfaces:

Executable<MSAprobs>, PipedExecutable<MSAprobs>

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

Nested Class Summary

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

Executable.ExecProvider

Field Summary

Fields

Modifier and Type	Field and Description
private static java.lang.String	ANNOTATION
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
MSAprobs()

Method Summary

Modifier and Type	Method and Description
java.util.List<java.lang.String>	getCreatedFiles() This method cannot really tell whether the files has actually been created or not.
Alignment	getResults(java.lang.String workDirectory)
java.lang.Class<MSAprobs>	getType()
MSAprobs	setInput(java.lang.String inFile)

Methods inherited from class compbio.engine.client.SkeletalExecutable

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

Field Detail

log

private static org.apache.log4j.Logger log

ANNOTATION

private static final java.lang.String ANNOTATION

See Also:

Constant Field Values

KEY_VALUE_SEPARATOR

public static final java.lang.String KEY_VALUE_SEPARATOR

See Also:

Constant Field Values

Constructor Detail

MSAprobs

public MSAprobs()

Method Detail

getResults

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

Specified by:

getResults in interface Executable<MSAprobs>

Throws:

ResultNotAvailableException

getCreatedFiles

public java.util.List<java.lang.String> getCreatedFiles()

Description copied from class: SkeletalExecutable

This method cannot really tell whether the files has actually been created or not. It must be overridden as required.

Specified by:

getCreatedFiles in interface Executable<MSAprobs>

Overrides:

getCreatedFiles in class SkeletalExecutable<MSAprobs>

See Also:

Executable.getCreatedFiles()

setInput

public MSAprobs setInput(java.lang.String inFile)

Overrides:

setInput in class SkeletalExecutable<MSAprobs>

getType

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

Specified by:

getType in class SkeletalExecutable<MSAprobs>

Returns:

subclasses must return their type