compbio.runner.msa
Class Tcoffee

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

All Implemented Interfaces:

ClusterNativeSpecExecutable<Tcoffee>, Executable<Tcoffee>, PipedExecutable<Tcoffee>

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

Nested Class Summary

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

Executable.ExecProvider

Field Summary

static java.lang.String

KEY_VALUE_SEPARATOR

Constructor Summary

Tcoffee()

Method Summary

static int	getClusterCpuNum()
java.util.List<java.lang.String>	getCreatedFiles() This method cannot really tell whether the files has actually been created or not.
Limit<Tcoffee>	getLimit(java.lang.String presetName)
LimitsManager<Tcoffee>	getLimits()
java.lang.String	getNativeSpecs()
CommandBuilder<Tcoffee>	getParameters(Executable.ExecProvider provider)
Alignment	getResults(java.lang.String workDirectory)
java.lang.Class<? extends Executable<?>>	getType()
Tcoffee	setInput(java.lang.String inFile)
void	setNCore(int ncoreNumber)

Methods inherited from class compbio.engine.client.SkeletalExecutable

addParameters, equals, getClusterSettings, getError, getInput, getOutput, hashCode, loadRunConfiguration, setError, setOutput, setParameter, toString

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface compbio.engine.client.Executable

addParameters, getError, getInput, getOutput, loadRunConfiguration

Field Detail

KEY_VALUE_SEPARATOR

public static final java.lang.String KEY_VALUE_SEPARATOR

See Also:

Constant Field Values

Constructor Detail

Tcoffee

public Tcoffee()

Parameters:

workDirectory -

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)

getParameters

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

Specified by:

getParameters in interface Executable<Tcoffee>

Overrides:

getParameters in class SkeletalExecutable<Tcoffee>

getLimit

public Limit<Tcoffee> getLimit(java.lang.String presetName)

Specified by:

getLimit in interface Executable<Tcoffee>

getLimits

public LimitsManager<Tcoffee> getLimits()

Specified by:

getLimits in interface Executable<Tcoffee>

getNativeSpecs

public java.lang.String getNativeSpecs()

Specified by:

getNativeSpecs in interface ClusterNativeSpecExecutable<Tcoffee>

getClusterCpuNum

public static int getClusterCpuNum()

Returns:

number of cpus to use on the cluster or 0 if the value is undefined

getType

public java.lang.Class<? extends Executable<?>> getType()

Specified by:

getType in class SkeletalExecutable<Tcoffee>