Uses of Interface
compbio.engine.client.ConfiguredExecutable

Packages that use ConfiguredExecutable

Package	Description
compbio.engine
compbio.engine.client
compbio.engine.cluster.drmaa
compbio.engine.local
compbio.runner	Utilities commonly used by all runners.
compbio.ws.server

Uses of ConfiguredExecutable in compbio.engine

Fields in compbio.engine declared as ConfiguredExecutable

Modifier and Type	Field and Description
private ConfiguredExecutable<?>	Job.cexecutable

Fields in compbio.engine with type parameters of type ConfiguredExecutable

Modifier and Type	Field and Description
(package private) static java.util.Map<java.lang.String,java.util.concurrent.Future<ConfiguredExecutable<?>>>	SubmissionManager.submittedTasks

Methods in compbio.engine that return ConfiguredExecutable

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)
ConfiguredExecutable<?>	Job.getConfExecutable()
ConfiguredExecutable<?>	AsyncExecutor.getResults(java.lang.String jobId) Retrieve the results of the job.
ConfiguredExecutable<?>	SyncExecutor.waitForResult() Call to this method block for as long as it is required for an executable to finish its job.

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

Modifier and Type	Method and Description
static java.util.concurrent.Future<ConfiguredExecutable<?>>	SubmissionManager.getTask(java.lang.String taskId)

Methods in compbio.engine with parameters of type ConfiguredExecutable

Modifier and Type	Method and Description
static void	SubmissionManager.addTask(ConfiguredExecutable<?> executable, java.util.concurrent.Future<ConfiguredExecutable<?>> future)
static boolean	Cleaner.deleteFiles(ConfiguredExecutable<?> exec) This method returns true if all files specified by List files were successfully removed or there was no files to remove (files list was empty)
static AsyncExecutor	Configurator.getAsyncEngine(ConfiguredExecutable<?> executable)
static AsyncExecutor	Configurator.getAsyncEngine(ConfiguredExecutable<?> executable, Executable.ExecProvider provider)
(package private) static Executable.ExecProvider	Configurator.getExecProvider(ConfiguredExecutable<?> executable, java.util.List<FastaSequence> dataSet) Depending on the values defined in the properties (engine.cluster.enable=true and engine.local.enable=true) return either Cluster job submission engine #JobRunner or local job submission engine #LocalRunner If both engines enabled than ask LoadBalancer for an engine.
static SyncExecutor	Configurator.getSyncEngine(ConfiguredExecutable<?> executable)
static SyncExecutor	Configurator.getSyncEngine(ConfiguredExecutable<?> executable, Executable.ExecProvider provider)
(package private) static boolean	Configurator.isTargetedForLocalExecution(ConfiguredExecutable<?> executable)
static void	SubmissionManager.removeTask(ConfiguredExecutable<?> executable)
java.lang.String	AsyncExecutor.submitJob(ConfiguredExecutable<?> executable) Submits job for the execution Immediate execution is not guaranteed, this method puts the job in the queue.

Method parameters in compbio.engine with type arguments of type ConfiguredExecutable

Modifier and Type	Method and Description
static void	SubmissionManager.addTask(ConfiguredExecutable<?> executable, java.util.concurrent.Future<ConfiguredExecutable<?>> future)

Constructors in compbio.engine with parameters of type ConfiguredExecutable

Constructor and Description
Job(java.lang.String taskId, java.lang.String jobId, ConfiguredExecutable<?> cexecutable)

Uses of ConfiguredExecutable in compbio.engine.client

Classes in compbio.engine.client that implement ConfiguredExecutable

Modifier and Type	Class and Description
class	ConfExecutable<T>

Methods in compbio.engine.client that return ConfiguredExecutable

Modifier and Type	Method and Description
static ConfiguredExecutable<?>	EngineUtil.loadExecutable(java.lang.String taskId)
static ConfiguredExecutable<?>	Util.loadExecutable(java.lang.String taskId)
ConfiguredExecutable<?>	ConfExecutable.loadRunConfiguration(java.io.InputStream input)
ConfiguredExecutable<?>	ConfiguredExecutable.loadRunConfiguration(java.io.InputStream input)
ConfiguredExecutable<?>	ConfExecutable.loadRunConfiguration(RunConfiguration rconf)
static ConfiguredExecutable<?>	ConfExecutable.newConfExecutable(RunConfiguration rconf)

Uses of ConfiguredExecutable in compbio.engine.cluster.drmaa

Fields in compbio.engine.cluster.drmaa declared as ConfiguredExecutable

Modifier and Type	Field and Description
(package private) ConfiguredExecutable<?>	JobRunner.confExecutable
(package private) ConfiguredExecutable<?>	ClusterRunner.confExecutable

Methods in compbio.engine.cluster.drmaa that return ConfiguredExecutable

Modifier and Type	Method and Description
ConfiguredExecutable<?>	ClusterSession.getResults(java.lang.String taskId)
ConfiguredExecutable<?>	AsyncJobRunner.getResults(java.lang.String jobId)
ConfiguredExecutable<?>	AsyncClusterRunner.getResults(java.lang.String jobId)
ConfiguredExecutable<?>	JobRunner.waitForResult()
ConfiguredExecutable<?>	ClusterRunner.waitForResult()

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

Modifier and Type	Method and Description
(package private) void	ClusterSession.addJob(java.lang.String jobId, ConfiguredExecutable<?> executable)
static JobRunner	JobRunner.getInstance(ConfiguredExecutable<?> executable)
static ClusterRunner	ClusterRunner.getInstance(ConfiguredExecutable<?> executable)
(package private) void	JobRunner.setPipes(ConfiguredExecutable<?> executable)
(package private) void	ClusterRunner.setPipes(ConfiguredExecutable<?> executable)
java.lang.String	AsyncJobRunner.submitJob(ConfiguredExecutable<?> executable)
java.lang.String	AsyncClusterRunner.submitJob(ConfiguredExecutable<?> executable)

Constructors in compbio.engine.cluster.drmaa with parameters of type ConfiguredExecutable

Constructor and Description
ClusterRunner(ConfiguredExecutable<?> confExec)
JobRunner(ConfiguredExecutable<?> confExec)

Uses of ConfiguredExecutable in compbio.engine.local

Fields in compbio.engine.local declared as ConfiguredExecutable

Modifier and Type	Field and Description
private ConfiguredExecutable<?>	ExecutableWrapper.confExec
private ConfiguredExecutable<?>	LocalRunner.executable

Fields in compbio.engine.local with type parameters of type ConfiguredExecutable

Modifier and Type	Field and Description
private java.util.concurrent.Future<ConfiguredExecutable<?>>	LocalRunner.future

Methods in compbio.engine.local that return ConfiguredExecutable

Modifier and Type	Method and Description
ConfiguredExecutable<?>	ExecutableWrapper.call() It is vital that output and error streams are captured immediately for this call() to succeed.
static ConfiguredExecutable<?>	LocalEngineUtil.getResults(java.util.concurrent.Future<ConfiguredExecutable<?>> future, java.lang.String taskId)
ConfiguredExecutable<?>	AsyncLocalRunner.getResults(java.lang.String taskId)
ConfiguredExecutable<?>	LocalRunner.waitForResult()

Methods in compbio.engine.local that return types with arguments of type ConfiguredExecutable

Modifier and Type	Method and Description
(package private) java.util.concurrent.Future<ConfiguredExecutable<?>>	LocalRunner.getFuture()

Methods in compbio.engine.local with parameters of type ConfiguredExecutable

Modifier and Type	Method and Description
static boolean	LocalEngineUtil.cleanup(ConfiguredExecutable<?> confExecutable)
java.lang.String	AsyncLocalRunner.submitJob(ConfiguredExecutable<?> executable)

Method parameters in compbio.engine.local with type arguments of type ConfiguredExecutable

Modifier and Type	Method and Description
static boolean	LocalEngineUtil.cancelJob(java.util.concurrent.Future<ConfiguredExecutable<?>> future, java.lang.String workDirectory)
static JobStatus	LocalEngineUtil.getJobStatus(java.util.concurrent.Future<ConfiguredExecutable<?>> future)
static ConfiguredExecutable<?>	LocalEngineUtil.getResults(java.util.concurrent.Future<ConfiguredExecutable<?>> future, java.lang.String taskId)

Constructors in compbio.engine.local with parameters of type ConfiguredExecutable

Constructor and Description
ExecutableWrapper(ConfiguredExecutable<?> executable, java.lang.String workDirectory)
LocalRunner(ConfiguredExecutable<?> executable)

Uses of ConfiguredExecutable in compbio.runner

Methods in compbio.runner with parameters of type ConfiguredExecutable

Modifier and Type	Method and Description
static void	RunnerUtil.writeClustalInput(java.util.List<FastaSequence> sequences, ConfiguredExecutable<?> exec, char gapChar)
static void	Util.writeInput(java.util.List<FastaSequence> sequences, ConfiguredExecutable<?> exec)
static void	RunnerUtil.writeInput(java.util.List<FastaSequence> sequences, ConfiguredExecutable<?> exec)

Uses of ConfiguredExecutable in compbio.ws.server

Methods in compbio.ws.server that return ConfiguredExecutable

Modifier and Type	Method and Description
(package private) ConfiguredExecutable<T>	GenericMetadataService.init(java.util.List<FastaSequence> sequences)
(package private) ConfiguredExecutable<GLprobs>	GLprobsWS.init(java.util.List<FastaSequence> dataSet)
(package private) ConfiguredExecutable<Mafft>	MafftWS.init(java.util.List<FastaSequence> dataSet)
(package private) ConfiguredExecutable<ClustalO>	ClustalOWS.init(java.util.List<FastaSequence> dataSet)
(package private) ConfiguredExecutable<MSAprobs>	MSAprobsWS.init(java.util.List<FastaSequence> dataSet)
(package private) ConfiguredExecutable<Muscle>	MuscleWS.init(java.util.List<FastaSequence> sequences)
(package private) ConfiguredExecutable<ClustalW>	ClustalWS.init(java.util.List<FastaSequence> dataSet)
(package private) ConfiguredExecutable<Tcoffee>	TcoffeeWS.init(java.util.List<FastaSequence> sequences)
(package private) ConfiguredExecutable<Probcons>	ProbconsWS.init(java.util.List<FastaSequence> dataSet)

Methods in compbio.ws.server with parameters of type ConfiguredExecutable

Modifier and Type	Method and Description
static <T> java.lang.String	WSUtil.align(java.util.List<FastaSequence> sequences, ConfiguredExecutable<T> confExec, org.apache.log4j.Logger logger, java.lang.String callingMethod, Limit<T> limit)
static <T> java.lang.String	WSUtil.analize(java.util.List<FastaSequence> sequences, ConfiguredExecutable<T> confExec, org.apache.log4j.Logger log, java.lang.String method, Limit<T> limit)
static <T> java.lang.String	WSUtil.fold(java.util.List<FastaSequence> sequences, ConfiguredExecutable<T> confExec, org.apache.log4j.Logger log, java.lang.String method, Limit<T> limit)
static AsyncExecutor	WSUtil.getEngine(ConfiguredExecutable<?> confClustal)
(package private) static <T> void	WSUtil.reportUsage(ConfiguredExecutable<T> confExec, org.apache.log4j.Logger logger)