Uses of Interface
compbio.engine.client.Executable

Packages that use Executable

compbio.engine
compbio.engine.client	Classes and interfaces representing an input for engines.
compbio.engine.conf	Classes commonly used by both engines.
compbio.runner	Utilities commonly used by all runners.
compbio.runner._impl
compbio.runner.msa	Wrappers for native executables for multiple sequence alignment (msa)
compbio.runner.psiblast

Uses of Executable in compbio.engine

Methods in compbio.engine with parameters of type Executable

static <T> ConfiguredExecutable<T>	Configurator.configureExecutable(Executable<T> executable)
static <T> ConfiguredExecutable<T>	Configurator.configureExecutable(Executable<T> executable, Executable.ExecProvider provider)
static <T> ConfiguredExecutable<T>	Configurator.configureExecutable(Executable<T> executable, java.util.List<FastaSequence> dataSet)
static Executable.ExecProvider	LoadBalancer.getEngine(Executable<?> executable)
static <T,V> Executable.ExecProvider	LoadBalancer.getEngine(Executable<V> executable, java.util.List<FastaSequence> dataSet)

Uses of Executable in compbio.engine.client

Subinterfaces of Executable in compbio.engine.client

interface	ClusterNativeSpecExecutable<T>
interface	ConfiguredExecutable<T>
interface	PipedExecutable<T> This is a marker interface to indicate that the output of the process must be captured.

Classes in compbio.engine.client that implement Executable

class	ConfExecutable<T>
class	SkeletalExecutable<T>

Methods in compbio.engine.client that return Executable

Executable<T>	SkeletalExecutable.addParameters(java.util.List<java.lang.String> parameters)
Executable<T>	Executable.addParameters(java.util.List<java.lang.String> parameters) Adds parameter to the list of parameters for a native executable
Executable<T>	ConfExecutable.addParameters(java.util.List<java.lang.String> parameters)
Executable<T>	ConfiguredExecutable.getExecutable()
Executable<T>	ConfExecutable.getExecutable()
Executable<?>	SkeletalExecutable.loadRunConfiguration(RunConfiguration rconfig)
Executable<?>	Executable.loadRunConfiguration(RunConfiguration rconfig)
Executable<T>	SkeletalExecutable.setParameter(java.lang.String parameter)

Methods in compbio.engine.client that return types with arguments of type Executable

abstract java.lang.Class<? extends Executable<?>>

SkeletalExecutable.getType()

Methods in compbio.engine.client with parameters of type Executable

static java.lang.String

Util.getExecProperty(java.lang.String propertySpec, Executable<?> exec)

Method parameters in compbio.engine.client with type arguments of type Executable

static <V> LimitsManager<V>	ConfExecutable.getRunnerLimits(java.lang.Class<? extends Executable<V>> clazz) This method should be executed once and result of its execution reused.
static <V> RunnerConfig<V>	ConfExecutable.getRunnerOptions(java.lang.Class<? extends Executable<V>> clazz)
static <V> PresetManager<V>	ConfExecutable.getRunnerPresets(java.lang.Class<? extends Executable<V>> clazz)

Constructors in compbio.engine.client with parameters of type Executable

ConfExecutable(Executable<T> executable, java.lang.String taskDirectory)

Uses of Executable in compbio.engine.conf

Methods in compbio.engine.conf that return types with arguments of type Executable

static java.lang.Class<Executable<?>>

DirectoryManager.getClass(java.lang.String taskId)

Uses of Executable in compbio.runner

Classes in compbio.runner that implement Executable

class

_SkeletalCommandBuilder

Methods in compbio.runner that return Executable

Executable<?>

_SkeletalCommandBuilder.loadRunConfiguration(RunConfiguration rconfig)

Method parameters in compbio.runner with type arguments of type Executable

static java.util.List<java.lang.String>	OptionCombinator.argumentsToCommandString(java.util.List<? extends Option<?>> arguments, RunnerConfig<? extends Executable<?>> rconfig)
static <T> LimitsManager<T>	Util.getLimits(java.lang.Class<? extends Executable<T>> clazz) For now just assume that all parameters which came in needs setting it will be a client responsibility to prepare RunnerConfig object then
static <T> PresetManager<T>	Util.getPresets(java.lang.Class<? extends Executable<T>> clazz)
static <T> RunnerConfig<T>	Util.getSupportedOptions(java.lang.Class<? extends Executable<T>> clazz)

Constructor parameters in compbio.runner with type arguments of type Executable

OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig)

Uses of Executable in compbio.runner._impl

Classes in compbio.runner._impl that implement Executable

class	BlastAll
class	Disembl
class	Mcl
class	NetNglyc
class	OB TODO this needs fixing! Executable does not work
class	PSIBlast
class	Ronn
class	RPSBlast

Methods in compbio.runner._impl that return Executable

Executable<?>

NetNglyc.loadRunConfiguration(RunConfiguration rconfig)

Uses of Executable in compbio.runner.msa

Classes in compbio.runner.msa that implement Executable

class	ClustalW
class	Mafft
class	Muscle
class	Probcons
class	Tcoffee

Methods in compbio.runner.msa that return types with arguments of type Executable

java.lang.Class<? extends Executable<?>>	Tcoffee.getType()
java.lang.Class<? extends Executable<?>>	ClustalW.getType()
java.lang.Class<? extends Executable<?>>	Probcons.getType()
java.lang.Class<? extends Executable<?>>	Muscle.getType()
java.lang.Class<? extends Executable<?>>	Mafft.getType()

Uses of Executable in compbio.runner.psiblast

Classes in compbio.runner.psiblast that implement Executable

class

PsiBlast

Methods in compbio.runner.psiblast that return types with arguments of type Executable

java.lang.Class<? extends Executable<?>>

PsiBlast.getType()