compbio.engine.client
Class SkeletalExecutable<T>

java.lang.Object
  compbio.engine.client.SkeletalExecutable<T>

All Implemented Interfaces:

Executable<T>

Direct Known Subclasses:

AACon, ClustalO, ClustalW, Disembl, GlobPlot, IUPred, Jronn, Mafft, Muscle, Probcons, Tcoffee

public abstract class SkeletalExecutable<T>
extends java.lang.Object
implements Executable<T>

Nested Class Summary

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

Executable.ExecProvider

Field Summary

static java.lang.String	ERROR
static java.lang.String	INPUT
static java.lang.String	OUTPUT

Constructor Summary

SkeletalExecutable()

SkeletalExecutable(java.lang.String parameterKeyValueDelimiter)

Method Summary

Executable<T>	addParameters(java.util.List<java.lang.String> parameters) Adds parameter to the list of parameters for a native executable
boolean	equals(java.lang.Object obj)
static int	getClusterCpuNum(java.lang.Class<? extends Executable<?>> type)
java.lang.String	getClusterJobSettings()
java.util.List<java.lang.String>	getCreatedFiles() This method cannot really tell whether the files has actually been created or not.
java.lang.String	getError()
java.lang.String	getInput()
Limit<T>	getLimit(java.lang.String presetName)
LimitsManager<T>	getLimits()
java.lang.String	getOutput()
CommandBuilder<T>	getParameters(Executable.ExecProvider provider)
abstract java.lang.Class<T>	getType()
int	hashCode()
Executable<?>	loadRunConfiguration(RunConfiguration rconfig)
SkeletalExecutable<T>	setError(java.lang.String errFile)
SkeletalExecutable<T>	setInput(java.lang.String inFile)
SkeletalExecutable<T>	setOutput(java.lang.String outFile)
Executable<T>	setParameter(java.lang.String parameter)
java.lang.String	toString()

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface compbio.engine.client.Executable

getResults

Field Detail

INPUT

public static final java.lang.String INPUT

See Also:

Constant Field Values

OUTPUT

public static final java.lang.String OUTPUT

See Also:

Constant Field Values

ERROR

public static final java.lang.String ERROR

See Also:

Constant Field Values

Constructor Detail

SkeletalExecutable

public SkeletalExecutable()

SkeletalExecutable

public SkeletalExecutable(java.lang.String parameterKeyValueDelimiter)

Method Detail

setInput

public SkeletalExecutable<T> setInput(java.lang.String inFile)

setOutput

public SkeletalExecutable<T> setOutput(java.lang.String outFile)

setError

public SkeletalExecutable<T> setError(java.lang.String errFile)

getParameters

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

Specified by:

getParameters in interface Executable<T>

addParameters

public Executable<T> addParameters(java.util.List<java.lang.String> parameters)

Description copied from interface: Executable

Adds parameter to the list of parameters for a native executable

Specified by:

addParameters in interface Executable<T>

Returns:

this Executable

setParameter

public Executable<T> setParameter(java.lang.String parameter)

getCreatedFiles

public java.util.List<java.lang.String> getCreatedFiles()

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<T>

See Also:

Executable.getCreatedFiles()

getInput

public java.lang.String getInput()

Specified by:

getInput in interface Executable<T>

getOutput

public java.lang.String getOutput()

Specified by:

getOutput in interface Executable<T>

getError

public java.lang.String getError()

Specified by:

getError in interface Executable<T>

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

loadRunConfiguration

public Executable<?> loadRunConfiguration(RunConfiguration rconfig)

Specified by:

loadRunConfiguration in interface Executable<T>

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

getClusterJobSettings

public java.lang.String getClusterJobSettings()

Specified by:

getClusterJobSettings in interface Executable<T>

getClusterCpuNum

public static int getClusterCpuNum(java.lang.Class<? extends Executable<?>> type)

Returns:

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

getLimit

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

Specified by:

getLimit in interface Executable<T>

getLimits

public LimitsManager<T> getLimits()

Specified by:

getLimits in interface Executable<T>

getType

public abstract java.lang.Class<T> getType()

Returns:

subclasses must return their type