compbio.runner.msa

Class Muscle

java.lang.Object

compbio.engine.client.SkeletalExecutable<Muscle>

compbio.runner.msa.Muscle

All Implemented Interfaces:

Executable<Muscle>

public class Muscle
extends SkeletalExecutable<Muscle>

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	EXEC_STAT_FILE
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
Muscle() Default options are -clwstrict - write output in clustal format

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)
static java.lang.String	getStatFile()
java.lang.Class<Muscle>	getType()
Muscle	setInput(java.lang.String inFile)
Muscle	setOutput(java.lang.String outFile)

Methods inherited from class compbio.engine.client.SkeletalExecutable

addParameters, equals, getClusterCpuNum, getClusterJobSettings, 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

Field Detail

log

private static org.apache.log4j.Logger log

EXEC_STAT_FILE

private static final java.lang.String EXEC_STAT_FILE

See Also:

Constant Field Values

KEY_VALUE_SEPARATOR

public static final java.lang.String KEY_VALUE_SEPARATOR

See Also:

Constant Field Values

Constructor Detail

Muscle

public Muscle()

Default options are -clwstrict - write output in clustal format

Method Detail

setOutput

public Muscle setOutput(java.lang.String outFile)

Overrides:

setOutput in class SkeletalExecutable<Muscle>

setInput

public Muscle setInput(java.lang.String inFile)

Overrides:

setInput in class SkeletalExecutable<Muscle>

getResults

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

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<Muscle>

Overrides:

getCreatedFiles in class SkeletalExecutable<Muscle>

See Also:

Executable.getCreatedFiles()

getStatFile

public static java.lang.String getStatFile()

getType

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

Specified by:

getType in class SkeletalExecutable<Muscle>

Returns:

subclasses must return their type