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Range
- Class in
compbio.data.sequence
Range(int, int)
- Constructor for class compbio.data.sequence.
Range
Range(String[])
- Constructor for class compbio.data.sequence.
Range
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
readAAConResults(InputStream)
- Static method in class compbio.data.sequence.
SequenceUtil
Read AACon result with no alignment files.
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
readData(Timestamp, Timestamp, Services, Boolean)
- Method in class compbio.stat.collector.
StatDB
readDisembl(InputStream)
- Static method in class compbio.data.sequence.
SequenceUtil
> Foobar_dundeefriends # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 # REM465 355-368 # HOTLOOPS 190-204 # RESIDUE COILS REM465 HOTLOOPS M 0.86010 0.88512 0.37094 T 0.79983 0.85864 0.44331 >Next Sequence name
readFasta(InputStream)
- Static method in class compbio.data.sequence.
SequenceUtil
Reads fasta sequences from inStream into the list of FastaSequence objects
readGlobPlot(InputStream)
- Static method in class compbio.data.sequence.
SequenceUtil
> Foobar_dundeefriends # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 # REM465 355-368 # HOTLOOPS 190-204 # RESIDUE COILS REM465 HOTLOOPS M 0.86010 0.88512 0.37094 T 0.79983 0.85864 0.44331 >Next Sequence name
readIUPred(File)
- Static method in class compbio.data.sequence.
SequenceUtil
Read IUPred output
readJRonn(File)
- Static method in class compbio.data.sequence.
SequenceUtil
readJRonn(InputStream)
- Static method in class compbio.data.sequence.
SequenceUtil
Reader for JRonn horizontal file format
readJronnFile(String, String)
- Static method in class compbio.runner.
Util
RegistryWS
- Interface in
compbio.data.msa
JABAWS services registry
RegistryWS
- Class in
compbio.ws.server
JABAWS services registry
RegistryWS()
- Constructor for class compbio.ws.server.
RegistryWS
REM_EXPECTATION_THRESHOLD
- Variable in class compbio.runner.disorder.
Disembl
remove()
- Method in class compbio.data.sequence.
FastaReader
Not implemented
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 which can be a Parameter or an Option instance by the value in
element of the runner configuration descriptor.
removeJob(String)
- Method in class compbio.engine.cluster.drmaa.
ClusterSession
removeParam(String)
- Method in class compbio.engine.client.
CommandBuilder
removeRecordedJobs(Set<JobStat>)
- Method in class compbio.stat.collector.
StatDB
Removes the job if 1) It has already been recorded 2) It has not completed and did not timeout - this is to prevent recording the information on the incomplete jobs.
removeTask(ConfiguredExecutable<?>)
- Static method in class compbio.engine.
SubmissionManager
removeTask(String)
- Static method in class compbio.engine.
SubmissionManager
reportStat()
- Method in class compbio.stat.collector.
StatProcessor
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
run()
- Method in class compbio.engine.local.
StreamGobbler
run()
- Method in class compbio.stat.collector.
ExecutionStatCollector
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
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