Uses of Interface
compbio.engine.client.ConfiguredExecutable

Packages that use ConfiguredExecutable

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

Methods in compbio.engine that return ConfiguredExecutable

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)
ConfiguredExecutable<?>	Job.getConfExecutable()
ConfiguredExecutable<?>	AsyncExecutor.getResults(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

static Future<ConfiguredExecutable<?>>

SubmissionManager.getTask(String taskId)

Methods in compbio.engine with parameters of type ConfiguredExecutable

static void	SubmissionManager.addTask(ConfiguredExecutable<?> executable, Future<ConfiguredExecutable<?>> future)
static boolean	Cleaner.deleteFiles(ConfiguredExecutable<?> exec) Deprecated. 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)
static SyncExecutor	Configurator.getSyncEngine(ConfiguredExecutable<?> executable)
static SyncExecutor	Configurator.getSyncEngine(ConfiguredExecutable<?> executable, Executable.ExecProvider provider)
static void	SubmissionManager.removeTask(ConfiguredExecutable<?> executable)
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

static void

SubmissionManager.addTask(ConfiguredExecutable<?> executable, Future<ConfiguredExecutable<?>> future)

Constructors in compbio.engine with parameters of type ConfiguredExecutable

Job(String taskId, String jobId, ConfiguredExecutable<?> cexecutable)

Uses of ConfiguredExecutable in compbio.engine.client

Classes in compbio.engine.client that implement ConfiguredExecutable

class

ConfExecutable<T>

Methods in compbio.engine.client that return ConfiguredExecutable

static ConfiguredExecutable<?>	Util.loadExecutable(String taskId)
ConfiguredExecutable<?>	ConfiguredExecutable.loadRunConfiguration(InputStream input)
ConfiguredExecutable<?>	ConfExecutable.loadRunConfiguration(InputStream input)
ConfiguredExecutable<?>	ConfExecutable.loadRunConfiguration(RunConfiguration rconf)
static ConfiguredExecutable<?>	ConfExecutable.newConfExecutable(RunConfiguration rconf)

Uses of ConfiguredExecutable in compbio.engine.cluster.drmaa

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

ConfiguredExecutable<?>	ClusterSession.getResults(String taskId)
ConfiguredExecutable<?>	AsyncJobRunner.getResults(String jobId)
ConfiguredExecutable<?>	JobRunner.waitForResult()

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

static JobRunner	JobRunner.getInstance(ConfiguredExecutable<?> executable)
String	AsyncJobRunner.submitJob(ConfiguredExecutable<?> executable)

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

JobRunner(ConfiguredExecutable<?> confExec)

Uses of ConfiguredExecutable in compbio.engine.local

Methods in compbio.engine.local that return ConfiguredExecutable

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

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

static boolean	LocalEngineUtil.cleanup(ConfiguredExecutable<?> confExecutable)
String	AsyncLocalRunner.submitJob(ConfiguredExecutable<?> executable)

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

static boolean	LocalEngineUtil.cancelJob(Future<ConfiguredExecutable<?>> future, String workDirectory)
static JobStatus	LocalEngineUtil.getJobStatus(Future<ConfiguredExecutable<?>> future)
static ConfiguredExecutable<?>	LocalEngineUtil.getResults(Future<ConfiguredExecutable<?>> future, String taskId)

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

ExecutableWrapper(ConfiguredExecutable<?> executable, String workDirectory)

LocalRunner(ConfiguredExecutable<?> executable)

Uses of ConfiguredExecutable in compbio.runner

Methods in compbio.runner with parameters of type ConfiguredExecutable

static void

Util.writeInput(List<FastaSequence> sequences, ConfiguredExecutable<?> exec)

Uses of ConfiguredExecutable in compbio.ws.server

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

static <T> String	WSUtil.align(List<FastaSequence> sequences, ConfiguredExecutable<T> confExec, org.apache.log4j.Logger logger, String callingMethod, Limit<T> limit)
static <T> String	WSUtil.analize(List<FastaSequence> sequences, ConfiguredExecutable<T> confExec, org.apache.log4j.Logger log, String method, Limit<T> limit)
static AsyncExecutor	WSUtil.getEngine(ConfiguredExecutable<?> confClustal)