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Packages that use ConfiguredExecutable | |
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compbio.engine | |
compbio.engine.client | Classes and interfaces representing an input for engines. |
compbio.engine.cluster.drmaa | An cluster engine classes responsible for execution of Executables on the clusters. |
compbio.engine.local | An local engine classes responsible for execution of Executables on the local computer (the same machine as JVM running these classes). |
compbio.runner | Utilities commonly used by all runners. |
compbio.ws.server |
Uses of ConfiguredExecutable in compbio.engine |
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Methods in compbio.engine that return ConfiguredExecutable | ||
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static
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Configurator.configureExecutable(Executable<T> executable)
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static
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Configurator.configureExecutable(Executable<T> executable,
Executable.ExecProvider provider)
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static
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Configurator.configureExecutable(Executable<T> executable,
java.util.List<FastaSequence> dataSet)
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ConfiguredExecutable<?> |
Job.getConfExecutable()
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ConfiguredExecutable<?> |
AsyncExecutor.getResults(java.lang.String jobId)
Retrieve the results of the job. |
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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 | |
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static java.util.concurrent.Future<ConfiguredExecutable<?>> |
SubmissionManager.getTask(java.lang.String taskId)
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Methods in compbio.engine with parameters of type ConfiguredExecutable | |
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static void |
SubmissionManager.addTask(ConfiguredExecutable<?> executable,
java.util.concurrent.Future<ConfiguredExecutable<?>> future)
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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)
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static AsyncExecutor |
Configurator.getAsyncEngine(ConfiguredExecutable<?> executable,
Executable.ExecProvider provider)
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static SyncExecutor |
Configurator.getSyncEngine(ConfiguredExecutable<?> executable)
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static SyncExecutor |
Configurator.getSyncEngine(ConfiguredExecutable<?> executable,
Executable.ExecProvider provider)
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static void |
SubmissionManager.removeTask(ConfiguredExecutable<?> executable)
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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 | |
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static void |
SubmissionManager.addTask(ConfiguredExecutable<?> executable,
java.util.concurrent.Future<ConfiguredExecutable<?>> future)
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Constructors in compbio.engine with parameters of type ConfiguredExecutable | |
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Job(java.lang.String taskId,
java.lang.String jobId,
ConfiguredExecutable<?> cexecutable)
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Uses of ConfiguredExecutable in compbio.engine.client |
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Classes in compbio.engine.client that implement ConfiguredExecutable | |
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class |
ConfExecutable<T>
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Methods in compbio.engine.client that return ConfiguredExecutable | |
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static ConfiguredExecutable<?> |
Util.loadExecutable(java.lang.String taskId)
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ConfiguredExecutable<?> |
ConfiguredExecutable.loadRunConfiguration(java.io.InputStream input)
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ConfiguredExecutable<?> |
ConfExecutable.loadRunConfiguration(java.io.InputStream input)
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ConfiguredExecutable<?> |
ConfExecutable.loadRunConfiguration(RunConfiguration rconf)
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static ConfiguredExecutable<?> |
ConfExecutable.newConfExecutable(RunConfiguration rconf)
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Uses of ConfiguredExecutable in compbio.engine.cluster.drmaa |
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Methods in compbio.engine.cluster.drmaa that return ConfiguredExecutable | |
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ConfiguredExecutable<?> |
ClusterSession.getResults(java.lang.String taskId)
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ConfiguredExecutable<?> |
AsyncJobRunner.getResults(java.lang.String jobId)
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ConfiguredExecutable<?> |
JobRunner.waitForResult()
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Methods in compbio.engine.cluster.drmaa with parameters of type ConfiguredExecutable | |
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static JobRunner |
JobRunner.getInstance(ConfiguredExecutable<?> executable)
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java.lang.String |
AsyncJobRunner.submitJob(ConfiguredExecutable<?> executable)
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Constructors in compbio.engine.cluster.drmaa with parameters of type ConfiguredExecutable | |
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JobRunner(ConfiguredExecutable<?> confExec)
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Uses of ConfiguredExecutable in compbio.engine.local |
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Methods in compbio.engine.local that return ConfiguredExecutable | |
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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)
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ConfiguredExecutable<?> |
AsyncLocalRunner.getResults(java.lang.String taskId)
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ConfiguredExecutable<?> |
LocalRunner.waitForResult()
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Methods in compbio.engine.local with parameters of type ConfiguredExecutable | |
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static boolean |
LocalEngineUtil.cleanup(ConfiguredExecutable<?> confExecutable)
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java.lang.String |
AsyncLocalRunner.submitJob(ConfiguredExecutable<?> executable)
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Method parameters in compbio.engine.local with type arguments of type ConfiguredExecutable | |
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static boolean |
LocalEngineUtil.cancelJob(java.util.concurrent.Future<ConfiguredExecutable<?>> future,
java.lang.String workDirectory)
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static JobStatus |
LocalEngineUtil.getJobStatus(java.util.concurrent.Future<ConfiguredExecutable<?>> future)
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static ConfiguredExecutable<?> |
LocalEngineUtil.getResults(java.util.concurrent.Future<ConfiguredExecutable<?>> future,
java.lang.String taskId)
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Constructors in compbio.engine.local with parameters of type ConfiguredExecutable | |
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ExecutableWrapper(ConfiguredExecutable<?> executable,
java.lang.String workDirectory)
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LocalRunner(ConfiguredExecutable<?> executable)
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Uses of ConfiguredExecutable in compbio.runner |
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Methods in compbio.runner with parameters of type ConfiguredExecutable | |
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static void |
Util.writeInput(java.util.List<FastaSequence> sequences,
ConfiguredExecutable<?> exec)
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Uses of ConfiguredExecutable in compbio.ws.server |
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Methods in compbio.ws.server with parameters of type ConfiguredExecutable | ||
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static
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WSUtil.align(java.util.List<FastaSequence> sequences,
ConfiguredExecutable<T> confExec,
org.apache.log4j.Logger statLog,
javax.xml.ws.WebServiceContext wsContext,
java.lang.String callingMethod,
Limit<T> limit)
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static AsyncExecutor |
WSUtil.getEngine(ConfiguredExecutable<?> confClustal)
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