Uses of Interface
compbio.engine.client.Executable

Packages that use Executable

compbio.engine
compbio.engine.client
compbio.engine.conf
compbio.runner	Utilities commonly used by all runners.
compbio.runner._impl
compbio.runner.conservation
compbio.runner.disorder
compbio.runner.msa	Wrappers for native executables for multiple sequence alignment (msa)
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

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, List<FastaSequence> dataSet)
static Executable.ExecProvider	LoadBalancer.getEngine(Executable<?> executable)
static <T,V> Executable.ExecProvider	LoadBalancer.getEngine(Executable<V> executable, List<FastaSequence> dataSet)

Uses of Executable in compbio.engine.client

Subinterfaces of Executable in compbio.engine.client

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

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

static String

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

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

static int	SkeletalExecutable.getClusterCpuNum(Class<? extends Executable<?>> type)
static <V> RunnerConfig<V>	ConfExecutable.getRunnerOptions(Class<? extends Executable<V>> clazz)
static <V> PresetManager<V>	ConfExecutable.getRunnerPresets(Class<? extends Executable<V>> clazz)

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

ConfExecutable(Executable<T> executable, String taskDirectory)

Uses of Executable in compbio.engine.conf

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

static Class<Executable<?>>

DirectoryManager.getClass(String taskId)

Uses of Executable in compbio.runner

Classes in compbio.runner that implement Executable

class

_SkeletalCommandBuilder Deprecated.

Methods in compbio.runner that return Executable

Executable<?>

_SkeletalCommandBuilder.loadRunConfiguration(RunConfiguration rconfig) Deprecated.

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

static List<String>	OptionCombinator.argumentsToCommandString(List<? extends Option<?>> arguments, RunnerConfig<? extends Executable<?>> rconfig)
static <T> PresetManager<T>	Util.getPresets(Class<? extends Executable<T>> clazz)
static <T> RunnerConfig<T>	Util.getSupportedOptions(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	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.conservation

Classes in compbio.runner.conservation that implement Executable

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

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

class	ClustalO
class	ClustalW
class	Mafft
class	Muscle
class	Probcons
class	Tcoffee

Uses of Executable in compbio.ws.client

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

static Class<? extends Executable<?>>	ServicesUtil.getRunnerByJobDirectory(File jobdir)
static Class<? extends Executable<?>>	ServicesUtil.getServiceImpl(Services service)

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

static Services

ServicesUtil.getServiceByRunner(Class<Executable<?>> runnerClassName)