Uses of Interface
compbio.engine.client.Executable

Packages that use Executable

Package	Description
compbio.engine
compbio.engine.client
compbio.engine.cluster.drmaa
compbio.engine.conf
compbio.runner	Utilities commonly used by all runners.
compbio.runner.conservation
compbio.runner.disorder
compbio.runner.msa	Wrappers for native executables for multiple sequence alignment (msa)
compbio.runner.structure
compbio.ws.client	A command line client and web services testing client for JAva Bioinformatics Analysis Web Services.

Uses of Executable in compbio.engine

Methods in compbio.engine with parameters of type Executable

Modifier and Type	Method and Description
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

Modifier and Type	Interface and Description
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

Modifier and Type	Class and Description
class	ConfExecutable<T>
class	SkeletalExecutable<T>

Fields in compbio.engine.client declared as Executable

Modifier and Type	Field and Description
private Executable<T>	ConfExecutable.exec

Methods in compbio.engine.client that return Executable

Modifier and Type	Method and Description
Executable<T>	SkeletalExecutable.addParameters(java.util.List<java.lang.String> parameters)
Executable<T>	ConfExecutable.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.getExecutable()
Executable<T>	ConfiguredExecutable.getExecutable()
Executable<?>	SkeletalExecutable.loadRunConfiguration(RunConfiguration rconfig)
Executable<?>	Executable.loadRunConfiguration(RunConfiguration rconfig)
Executable<T>	SkeletalExecutable.setParameter(java.lang.String parameter)

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

Modifier and Type	Method and Description
static java.lang.String	EngineUtil.getExecProperty(java.lang.String propertySpec, Executable<?> exec)
static java.lang.String	Util.getExecProperty(java.lang.String propertySpec, Executable<?> exec)

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

Modifier and Type	Method and Description
static int	SkeletalExecutable.getClusterCpuNum(java.lang.Class<? extends Executable<?>> type)
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

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

Uses of Executable in compbio.engine.cluster.drmaa

Methods in compbio.engine.cluster.drmaa with parameters of type Executable

Modifier and Type	Method and Description
(package private) void	JobRunner.setNativeSpecs(Executable<?> executable)
(package private) void	ClusterRunner.setNativeSpecs(Executable<?> executable)

Uses of Executable in compbio.engine.conf

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

Modifier and Type	Method and Description
static java.lang.Class<Executable<?>>	DirectoryManager.getClass(java.lang.String taskId)

Uses of Executable in compbio.runner

Fields in compbio.runner with type parameters of type Executable

Modifier and Type	Field and Description
private RunnerConfig<? extends Executable<?>>	OptionCombinator.rconfig

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

Modifier and Type	Method and Description
static java.util.List<java.lang.String>	OptionCombinator.argumentsToCommandString(java.util.List<? extends Option<?>> arguments, RunnerConfig<? extends Executable<?>> rconfig)
static <T> PresetManager<T>	Util.getPresets(java.lang.Class<? extends Executable<T>> clazz)
static <T> PresetManager<T>	RunnerUtil.getPresets(java.lang.Class<? extends Executable<T>> clazz)
static <T> RunnerConfig<T>	Util.getSupportedOptions(java.lang.Class<? extends Executable<T>> clazz)
static <T> RunnerConfig<T>	RunnerUtil.getSupportedOptions(java.lang.Class<? extends Executable<T>> clazz)

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

Constructor and Description
OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig)

Uses of Executable in compbio.runner.conservation

Classes in compbio.runner.conservation that implement Executable

Modifier and Type	Class and Description
class	AACon Command line java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out

Uses of Executable in compbio.runner.disorder

Classes in compbio.runner.disorder that implement Executable

Modifier and Type	Class and Description
class	Disembl DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops fold_rem465 sequence_file print 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' This version of DisEMBL is 1.4 (latest available for download in Feb 2011) capable of outputting raw values The values of the parameters are hard coded in DisEMBL.py script.
class	GlobPlot ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file' Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file' Hard-coded values are 10 15 74 4 5.
class	IUPred iupred sequenceFile Maximum sequence length is 40000 chars.
class	Jronn Command line java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out

Uses of Executable in compbio.runner.msa

Classes in compbio.runner.msa that implement Executable

Modifier and Type	Class and Description
class	ClustalO
class	ClustalW
class	GLprobs
class	Mafft
class	MSAprobs
class	Muscle
class	Probcons
class	Tcoffee

Uses of Executable in compbio.runner.structure

Classes in compbio.runner.structure that implement Executable

Modifier and Type	Class and Description
class	RNAalifold

Uses of Executable in compbio.ws.client

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

Modifier and Type	Method and Description
static java.lang.Class<? extends Executable<?>>	ServicesUtil.getRunnerByJobDirectory(java.io.File jobdir)
private static java.lang.Class<? extends Executable<?>>	ServicesUtil.getServiceImpl(Services service)

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

Modifier and Type	Method and Description
static Services	ServicesUtil.getServiceByRunner(java.lang.Class<? extends Executable> class1)