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call()
- Method in class compbio.engine.local.
ExecutableWrapper
It is vital that output and error streams are captured immediately for this call() to succeed.
canAcceptMoreWork()
- Method in class compbio.engine.local.
LocalExecutorService
If the Executor queue is empty
CancelJob
- Class in
compbio.data.msa.jaxws
CancelJob()
- Constructor for class compbio.data.msa.jaxws.
CancelJob
cancelJob(String)
- Method in interface compbio.data.msa.
MsaWS
Stop running job but leave its output untouched
cancelJob(String)
- Method in interface compbio.engine.
AsyncExecutor
Stop running job.
cancelJob(String)
- Method in class compbio.engine.cluster.drmaa.
AsyncJobRunner
cancelJob(String, ClusterSession)
- Static method in class compbio.engine.cluster.drmaa.
ClusterUtil
cancelJob()
- Method in class compbio.engine.cluster.drmaa.
JobRunner
cancelJob(String)
- Method in class compbio.engine.local.
AsyncLocalRunner
cancelJob(Future<ConfiguredExecutable<?>>, String)
- Static method in class compbio.engine.local.
LocalEngineUtil
cancelJob()
- Method in class compbio.engine.local.
LocalRunner
cancelJob()
- Method in interface compbio.engine.
SyncExecutor
Stops running job.
cancelJob(String)
- Method in class compbio.ws.server.
ClustalWS
cancelJob(String)
- Method in class compbio.ws.server.
MafftWS
cancelJob(String)
- Method in class compbio.ws.server.
MuscleWS
cancelJob(String)
- Method in class compbio.ws.server.
ProbconsWS
cancelJob(String)
- Method in class compbio.ws.server.
TcoffeeWS
cancelJob(String)
- Static method in class compbio.ws.server.
WSUtil
CancelJobResponse
- Class in
compbio.data.msa.jaxws
CancelJobResponse()
- Constructor for class compbio.data.msa.jaxws.
CancelJobResponse
ChunkHolder
- Class in
compbio.metadata
Represents a chunk of string data together with the position in a file from where corresponding to of the data.
ChunkHolder(String, long)
- Constructor for class compbio.metadata.
ChunkHolder
Cleaner
- Class in
compbio.engine
Cleaner()
- Constructor for class compbio.engine.
Cleaner
cleanSequence(String)
- Static method in class compbio.data.sequence.
SequenceUtil
Removes all whitespace chars in the sequence string
cleanup(String)
- Method in interface compbio.engine.
AsyncExecutor
Remove all files and a job directory for a jobid.
cleanup(String)
- Method in class compbio.engine.cluster.drmaa.
AsyncJobRunner
cleanup()
- Method in class compbio.engine.cluster.drmaa.
JobRunner
cleanup(String)
- Method in class compbio.engine.local.
AsyncLocalRunner
cleanup(ConfiguredExecutable<?>)
- Static method in class compbio.engine.local.
LocalEngineUtil
cleanup()
- Method in class compbio.engine.local.
LocalRunner
cleanup()
- Method in interface compbio.engine.
SyncExecutor
Clean up after the job
close()
- Method in class compbio.engine.cluster.drmaa.
ClusterSession
ClustalAlignmentUtil
- Class in
compbio.data.sequence
Tools to read and write clustal formated files
ClustalAlignmentUtil()
- Constructor for class compbio.data.sequence.
ClustalAlignmentUtil
ClustalW
- Class in
compbio.runner.msa
ClustalW()
- Constructor for class compbio.runner.msa.
ClustalW
ClustalWS
- Class in
compbio.ws.server
ClustalWS()
- Constructor for class compbio.ws.server.
ClustalWS
CLUSTER_STAT_IN_SEC
- Static variable in class compbio.engine.cluster.drmaa.
ClusterUtil
CLUSTER_TASK_ID_PREFIX
- Static variable in class compbio.engine.client.
ConfExecutable
CLUSTER_WORK_DIRECTORY
- Static variable in class compbio.engine.
Configurator
ClusterJobId
- Class in
compbio.engine
ClusterJobId(String)
- Constructor for class compbio.engine.
ClusterJobId
ClusterNativeSpecExecutable
<
T
> - Interface in
compbio.engine.client
ClusterSession
- Class in
compbio.engine.cluster.drmaa
ClusterUtil
- Class in
compbio.engine.cluster.drmaa
ClusterUtil()
- Constructor for class compbio.engine.cluster.drmaa.
ClusterUtil
CommandBuilder
<
T
> - Class in
compbio.engine.client
CommandBuilder(String)
- Constructor for class compbio.engine.client.
CommandBuilder
compareTo(Delayed)
- Method in class compbio.engine.
FilePuller
compbio.data._structure
- package compbio.data._structure
compbio.data.msa
- package compbio.data.msa
compbio.data.msa.jaxws
- package compbio.data.msa.jaxws
compbio.pipeline._jpred
- package compbio.pipeline._jpred
compbio.runner._jpred
- package compbio.runner._jpred
compbio.runner.psiblast
- package compbio.runner.psiblast
compbio.ws.client
- package compbio.ws.client
compbio.ws.server
- package compbio.ws.server
confDir
- Static variable in class compbio.engine.conf.
PropertyHelperManager
ConfExecutable
<
T
> - Class in
compbio.engine.client
ConfExecutable(Executable<T>, String)
- Constructor for class compbio.engine.client.
ConfExecutable
Configurator
- Class in
compbio.engine
Configurator()
- Constructor for class compbio.engine.
Configurator
ConfiguredExecutable
<
T
> - Interface in
compbio.engine.client
configureExecutable(Executable<T>)
- Static method in class compbio.engine.
Configurator
configureExecutable(Executable<T>, List<FastaSequence>)
- Static method in class compbio.engine.
Configurator
configureExecutable(Executable<T>, Executable.ExecProvider)
- Static method in class compbio.engine.
Configurator
connect(String, Jws2Client.Services)
- Static method in class compbio.ws.client.
Jws2Client
Connects to a web service by the host and the service name
convertToAbsolute(String)
- Static method in class compbio.engine.client.
Util
copyAndValidateRConfig(RunnerConfig<?>)
- Method in class compbio.metadata.
RunnerConfig
countMatchesInSequence(String, String)
- Static method in class compbio.data.sequence.
FastaSequence
CustomAlign
- Class in
compbio.data.msa.jaxws
CustomAlign()
- Constructor for class compbio.data.msa.jaxws.
CustomAlign
customAlign(List<FastaSequence>, List<Option<T>>)
- Method in interface compbio.data.msa.
MsaWS
Align a list of sequences with options.
customAlign(List<FastaSequence>, List<Option<ClustalW>>)
- Method in class compbio.ws.server.
ClustalWS
customAlign(List<FastaSequence>, List<Option<Mafft>>)
- Method in class compbio.ws.server.
MafftWS
customAlign(List<FastaSequence>, List<Option<Muscle>>)
- Method in class compbio.ws.server.
MuscleWS
customAlign(List<FastaSequence>, List<Option<Probcons>>)
- Method in class compbio.ws.server.
ProbconsWS
customAlign(List<FastaSequence>, List<Option<Tcoffee>>)
- Method in class compbio.ws.server.
TcoffeeWS
CustomAlignResponse
- Class in
compbio.data.msa.jaxws
CustomAlignResponse()
- Constructor for class compbio.data.msa.jaxws.
CustomAlignResponse
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