compbio.runner.msa
Class ClustalO

java.lang.Object
  compbio.engine.client.SkeletalExecutable<ClustalO>
      compbio.runner.msa.ClustalO

All Implemented Interfaces:

Executable<ClustalO>

public class ClustalO
extends SkeletalExecutable<ClustalO>

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

ClustalO()
--threads= Number of processors to use -l, --log= Log all non-essential output to this file

Method Summary

CommandBuilder<ClustalO>	getParameters(Executable.ExecProvider provider)
Alignment	getResults(java.lang.String workDirectory)
static java.lang.String	getStatFile()
java.lang.Class<ClustalO>	getType()
ClustalO	setInput(java.lang.String inFile)
void	setNCore(int ncoreNumber)
ClustalO	setOutput(java.lang.String outFile)

Methods inherited from class compbio.engine.client.SkeletalExecutable

addParameters, equals, getClusterCpuNum, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, 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

ClustalO

public ClustalO()

--threads= Number of processors to use -l, --log= Log all non-essential output to this file

Method Detail

setOutput

public ClustalO setOutput(java.lang.String outFile)

Overrides:

setOutput in class SkeletalExecutable<ClustalO>

setInput

public ClustalO setInput(java.lang.String inFile)

Overrides:

setInput in class SkeletalExecutable<ClustalO>

getResults

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

Throws:

ResultNotAvailableException

getStatFile

public static java.lang.String getStatFile()

getType

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

Specified by:

getType in class SkeletalExecutable<ClustalO>

Returns:

subclasses must return their type

getParameters

public CommandBuilder<ClustalO> getParameters(Executable.ExecProvider provider)

Specified by:

getParameters in interface Executable<ClustalO>

Overrides:

getParameters in class SkeletalExecutable<ClustalO>

setNCore

public void setNCore(int ncoreNumber)