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

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
private int	ncoreNumber Number of cores to use, defaults to 1 for local execution or the value of "tcoffee.cluster.cpunum" property for cluster execution
private static java.lang.String	ncorePrm Number of cores parameter name

Fields inherited from class compbio.engine.client.SkeletalExecutable

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

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
(package private) int	getNCore()
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, 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

ncorePrm

private static final java.lang.String ncorePrm

Number of cores parameter name

See Also:

Constant Field Values

ncoreNumber

private int ncoreNumber

Number of cores to use, defaults to 1 for local execution or the value of "tcoffee.cluster.cpunum" property for cluster execution

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)

getNCore

int getNCore()