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

static java.lang.String

KEY_VALUE_SEPARATOR

Fields inherited from class compbio.engine.client.SkeletalExecutable

ERROR, INPUT, OUTPUT

Constructor Summary

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

Method Summary

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, loadRunConfiguration, setError, setParameter, toString

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Field Detail

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