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Packages that use Executable | |
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compbio.engine | |
compbio.engine.client | Classes and interfaces representing an input for engines. |
compbio.engine.conf | Classes commonly used by both engines. |
compbio.runner | Utilities commonly used by all runners. |
compbio.runner._impl | |
compbio.runner.msa | Wrappers for native executables for multiple sequence alignment (msa) |
compbio.runner.psiblast |
Uses of Executable in compbio.engine |
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Methods in compbio.engine with parameters of type Executable | ||
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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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static Executable.ExecProvider |
LoadBalancer.getEngine(Executable<?> executable)
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static
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LoadBalancer.getEngine(Executable<V> executable,
java.util.List<FastaSequence> dataSet)
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Uses of Executable in compbio.engine.client |
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Subinterfaces of Executable in compbio.engine.client | |
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interface |
ClusterNativeSpecExecutable<T>
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interface |
ConfiguredExecutable<T>
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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 | |
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class |
ConfExecutable<T>
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class |
SkeletalExecutable<T>
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Methods in compbio.engine.client that return Executable | |
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Executable<T> |
SkeletalExecutable.addParameters(java.util.List<java.lang.String> parameters)
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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.addParameters(java.util.List<java.lang.String> parameters)
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Executable<T> |
ConfiguredExecutable.getExecutable()
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Executable<T> |
ConfExecutable.getExecutable()
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Executable<?> |
SkeletalExecutable.loadRunConfiguration(RunConfiguration rconfig)
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Executable<?> |
Executable.loadRunConfiguration(RunConfiguration rconfig)
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Executable<T> |
SkeletalExecutable.setParameter(java.lang.String parameter)
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Methods in compbio.engine.client that return types with arguments of type Executable | |
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abstract java.lang.Class<? extends Executable<?>> |
SkeletalExecutable.getType()
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Methods in compbio.engine.client with parameters of type Executable | |
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static java.lang.String |
Util.getExecProperty(java.lang.String propertySpec,
Executable<?> exec)
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Method parameters in compbio.engine.client with type arguments of type Executable | ||
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static
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ConfExecutable.getRunnerLimits(java.lang.Class<? extends Executable<V>> clazz)
This method should be executed once and result of its execution reused. |
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static
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ConfExecutable.getRunnerOptions(java.lang.Class<? extends Executable<V>> clazz)
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static
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ConfExecutable.getRunnerPresets(java.lang.Class<? extends Executable<V>> clazz)
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Constructors in compbio.engine.client with parameters of type Executable | |
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ConfExecutable(Executable<T> executable,
java.lang.String taskDirectory)
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Uses of Executable in compbio.engine.conf |
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Methods in compbio.engine.conf that return types with arguments of type Executable | |
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static java.lang.Class<Executable<?>> |
DirectoryManager.getClass(java.lang.String taskId)
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Uses of Executable in compbio.runner |
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Classes in compbio.runner that implement Executable | |
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class |
_SkeletalCommandBuilder
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Methods in compbio.runner that return Executable | |
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Executable<?> |
_SkeletalCommandBuilder.loadRunConfiguration(RunConfiguration rconfig)
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Method parameters in compbio.runner with type arguments of type Executable | ||
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static java.util.List<java.lang.String> |
OptionCombinator.argumentsToCommandString(java.util.List<? extends Option<?>> arguments,
RunnerConfig<? extends Executable<?>> rconfig)
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static
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Util.getLimits(java.lang.Class<? extends Executable<T>> clazz)
For now just assume that all parameters which came in needs setting it will be a client responsibility to prepare RunnerConfig object then |
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static
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Util.getPresets(java.lang.Class<? extends Executable<T>> clazz)
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static
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Util.getSupportedOptions(java.lang.Class<? extends Executable<T>> clazz)
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Constructor parameters in compbio.runner with type arguments of type Executable | |
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OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig)
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Uses of Executable in compbio.runner._impl |
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Classes in compbio.runner._impl that implement Executable | |
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class |
BlastAll
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class |
Disembl
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class |
Mcl
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class |
NetNglyc
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class |
OB
TODO this needs fixing! Executable does not work |
class |
PSIBlast
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class |
Ronn
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class |
RPSBlast
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Methods in compbio.runner._impl that return Executable | |
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Executable<?> |
NetNglyc.loadRunConfiguration(RunConfiguration rconfig)
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Uses of Executable in compbio.runner.msa |
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Classes in compbio.runner.msa that implement Executable | |
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class |
ClustalW
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class |
Mafft
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class |
Muscle
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class |
Probcons
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class |
Tcoffee
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Methods in compbio.runner.msa that return types with arguments of type Executable | |
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java.lang.Class<? extends Executable<?>> |
Tcoffee.getType()
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java.lang.Class<? extends Executable<?>> |
ClustalW.getType()
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java.lang.Class<? extends Executable<?>> |
Probcons.getType()
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java.lang.Class<? extends Executable<?>> |
Muscle.getType()
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java.lang.Class<? extends Executable<?>> |
Mafft.getType()
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Uses of Executable in compbio.runner.psiblast |
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Classes in compbio.runner.psiblast that implement Executable | |
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class |
PsiBlast
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Methods in compbio.runner.psiblast that return types with arguments of type Executable | |
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java.lang.Class<? extends Executable<?>> |
PsiBlast.getType()
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