compbio.runner.msa

Class Tcoffee

java.lang.Object

compbio.engine.client.SkeletalExecutable<Tcoffee>

compbio.runner.msa.Tcoffee

All Implemented Interfaces:

Executable<Tcoffee>, PipedExecutable<Tcoffee>

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

Nested Class Summary

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

Executable.ExecProvider

Field Summary

Fields

Modifier and Type	Field and Description
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
private static compbio.util.PropertyHelper	ph

Fields inherited from class compbio.engine.client.SkeletalExecutable

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

Constructor Summary

Constructors

Constructor and Description
Tcoffee()

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.
(package private) int	getNCore()
CommandBuilder<Tcoffee>	getParameters(Executable.ExecProvider provider)
Alignment	getResults(java.lang.String workDirectory)
java.lang.Class<Tcoffee>	getType()
Tcoffee	setInput(java.lang.String inFile)
void	setNCore(int ncoreNumber)

Methods inherited from class compbio.engine.client.SkeletalExecutable

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

Field Detail

log

private static org.apache.log4j.Logger log

ph

private static compbio.util.PropertyHelper ph

KEY_VALUE_SEPARATOR

public static final java.lang.String KEY_VALUE_SEPARATOR

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

ncorePrm

private static final java.lang.String ncorePrm

See Also:

Constant Field Values

Constructor Detail

Tcoffee

public Tcoffee()

Method Detail

setInput

public Tcoffee setInput(java.lang.String inFile)

Overrides:

setInput in class SkeletalExecutable<Tcoffee>

getResults

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

Specified by:

getResults in interface Executable<Tcoffee>

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<Tcoffee>

Overrides:

getCreatedFiles in class SkeletalExecutable<Tcoffee>

See Also:

Executable.getCreatedFiles()

setNCore

public void setNCore(int ncoreNumber)

getNCore

int getNCore()

getParameters

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

Specified by:

getParameters in interface Executable<Tcoffee>

Overrides:

getParameters in class SkeletalExecutable<Tcoffee>

getType

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

Specified by:

getType in class SkeletalExecutable<Tcoffee>

Returns:

subclasses must return their type