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rconfigFile
- Static variable in class compbio.engine.client.
RunConfiguration
read(InputStream, Class<V>)
- Method in class compbio.engine.conf.
RunnerConfigMarshaller
read(InputStream, Class<V>, Class<?>...)
- Method in class compbio.engine.conf.
RunnerConfigMarshaller
readAndValidate(InputStream, Class<V>)
- Method in class compbio.engine.conf.
RunnerConfigMarshaller
readClustalFile(InputStream)
- Static method in class compbio.data.sequence.
ClustalAlignmentUtil
Read Clustal formatted alignment.
readClustalFile(File)
- Static method in class compbio.data.sequence.
ClustalAlignmentUtil
readClustalFile(String, String)
- Static method in class compbio.runner.
Util
readFasta(InputStream)
- Static method in class compbio.data.sequence.
SequenceUtil
Reads fasta sequences from inStream into the list of FastaSequence objects
removeArgument(String)
- Method in class compbio.metadata.
RunnerConfig
Removes the argument
Argument
if found.
removeArgumentByOptionName(String)
- Method in class compbio.metadata.
RunnerConfig
Removes the argument
removeJob(String)
- Method in class compbio.engine.cluster.drmaa.
ClusterSession
removeOutput(String)
- Method in class compbio.runner._impl.
BlastAll
removeOutput(String)
- Method in class compbio.runner._impl.
PSIBlast
removeParam(String)
- Method in class compbio.engine.client.
CommandBuilder
removeTask(ConfiguredExecutable<?>)
- Static method in class compbio.engine.
SubmissionManager
removeTask(String)
- Static method in class compbio.engine.
SubmissionManager
ResultNotAvailableException
- Exception in
compbio.metadata
ResultNotAvailableException is thrown wherever the results of the calculation cannot be obtained.
ResultNotAvailableException(String)
- Constructor for exception compbio.metadata.
ResultNotAvailableException
ResultNotAvailableException(Throwable)
- Constructor for exception compbio.metadata.
ResultNotAvailableException
ResultNotAvailableException(String, Throwable)
- Constructor for exception compbio.metadata.
ResultNotAvailableException
ResultNotAvailableExceptionBean
- Class in
compbio.data.msa.jaxws
This class was generated by the JAX-WS RI.
ResultNotAvailableExceptionBean()
- Constructor for class compbio.data.msa.jaxws.
ResultNotAvailableExceptionBean
Ronn
- Class in
compbio.runner._impl
Ronn(String)
- Constructor for class compbio.runner._impl.
Ronn
RPSBlast
- Class in
compbio.runner._impl
RPSBlast(String)
- Constructor for class compbio.runner._impl.
RPSBlast
run()
- Method in class compbio.engine.local.
StreamGobbler
RunConfiguration
- Class in
compbio.engine.client
Value class for persisting ConfExecutable instances
RunConfiguration()
- Constructor for class compbio.engine.client.
RunConfiguration
RunConfiguration(ConfExecutable<?>)
- Constructor for class compbio.engine.client.
RunConfiguration
RunnerConfig
<
T
> - Class in
compbio.metadata
The list of
Parameter
s and
Option
s supported by executable.
RunnerConfig()
- Constructor for class compbio.metadata.
RunnerConfig
RunnerConfigMarshaller
<
T
> - Class in
compbio.engine.conf
RunnerConfigMarshaller(Class<?>)
- Constructor for class compbio.engine.conf.
RunnerConfigMarshaller
RunnerConfigMarshaller(Class<?>, Class<?>...)
- Constructor for class compbio.engine.conf.
RunnerConfigMarshaller
Runners
- Class in
compbio.runner._impl
runPsiBlast()
- Method in class compbio.pipeline._jpred.
Jpred4
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