- rand - Static variable in class compbio.runner.OptionCombinator
-
- Range - Class in compbio.data.sequence
-
- Range() - Constructor for class compbio.data.sequence.Range
-
- Range(int, int) - Constructor for class compbio.data.sequence.Range
-
- Range(String[]) - Constructor for class compbio.data.sequence.Range
-
- ranges - Variable in class compbio.data.sequence.Score
-
- rconfig - Variable in class compbio.runner.OptionCombinator
-
- 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.RunnerUtil
-
- 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
- readIUPred(InputStream, IUPredResult) - Static method in class compbio.data.sequence.SequenceUtil
-
## Long Disorder
# P53_HUMAN
1 M 0.9943
2 E 0.9917
3 E 0.9879
(every line)
- 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.RunnerUtil
-
- readJronnFile(String, String) - Static method in class compbio.runner.Util
-
- readRNAStruct(String, String) - Static method in class compbio.runner.RunnerUtil
-
- readRNAStructStream(InputStream) - Static method in class compbio.data.sequence.RNAStructReader
-
- readRNAStructStream(InputStream, InputStream) - Static method in class compbio.data.sequence.RNAStructReader
-
- reference - Variable in class compbio.stat.servlet.ServiceTestResult
-
- reference - Variable in class compbio.ws.client.Services.ServiceInfo
-
- regex - Variable in enum compbio.data.sequence.RNAStructReader.AlifoldLine
-
- 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
-
- 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.
- removeFile(String) - Static method in class compbio.engine.Cleaner
-
- removeInvalidXMLCharacters(String) - Static method in class compbio.engine.FilePuller
-
This method ensures that the output String has only valid XML unicode
characters as specified by the XML 1.0 standard.
- removeJob(String) - Method in class compbio.engine.cluster.drmaa.ClusterSession
-
- removeJobFromListbyTaskId(String) - Static 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
-
- reportException(Exception) - Method in class compbio.ws.client.WSTester
-
- reportResults(Services, boolean) - Method in class compbio.ws.client.WSTester
-
- reportStat() - Method in class compbio.stat.collector.StatProcessor
-
- reportUsage(Services) - Static method in class compbio.ws.server.GAUtils
-
- reportUsage(Services, String) - Static method in class compbio.ws.server.GAUtils
-
- reportUsage(ConfiguredExecutable<T>, Logger) - Static method in class compbio.ws.server.WSUtil
-
- 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
-
- RESULTSIZE - Static variable in class compbio.stat.collector.JobStat
-
- resultSize - Variable in class compbio.stat.collector.JobStat
-
- RNAalifold - Class in compbio.runner.structure
-
- RNAalifold() - Constructor for class compbio.runner.structure.RNAalifold
-
- RNAALIFOLD_INFO - Static variable in enum compbio.ws.client.Services
-
- RNAalifoldWS - Class in compbio.ws.server
-
- RNAalifoldWS() - Constructor for class compbio.ws.server.RNAalifoldWS
-
- RNAOut() - Constructor for enum compbio.data.sequence.RNAStructReader.RNAOut
-
- RNAStructReader - Class in compbio.data.sequence
-
- RNAStructReader() - Constructor for class compbio.data.sequence.RNAStructReader
-
- RNAStructReader.AlifoldLine - Enum in compbio.data.sequence
-
- RNAStructReader.AlifoldResult - Enum in compbio.data.sequence
-
- RNAStructReader.RNAOut - Enum in compbio.data.sequence
-
- RNAStructScoreManager - Class in compbio.data.sequence
-
- RNAStructScoreManager() - Constructor for class compbio.data.sequence.RNAStructScoreManager
-
- RNAStructScoreManager(List<String>, List<TreeSet<Score>>) - Constructor for class compbio.data.sequence.RNAStructScoreManager
-
- ru_stime - Variable in class compbio.engine.cluster.drmaa.StatisticManager
-
- ru_utime - Variable in class compbio.engine.cluster.drmaa.StatisticManager
-
- ru_wallclock - Variable in class compbio.engine.cluster.drmaa.StatisticManager
-
- run() - Method in class compbio.engine.local.StreamGobbler
-
- run() - Method in class compbio.stat.collector.DirCleaner
-
- 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
-
- runnerClassName - Variable in class compbio.engine.client.RunConfiguration
-
Runner class name
- runnerClassName - Variable in class compbio.metadata.LimitsManager
-
- runnerClassName - Variable in class compbio.metadata.PresetManager
-
- runnerClassName - Variable in class compbio.metadata.RunnerConfig
-
The class name of a runnable e.g.
- RunnerConfig<T> - Class in compbio.metadata
-
- 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
-
- RunnerConfigMarshaller.MySchemaOutputResolver - Class in compbio.engine.conf
-
- RunnerUtil - Class in compbio.runner
-
- RunnerUtil() - Constructor for class compbio.runner.RunnerUtil
-
- RUNTIME - Static variable in class compbio.stat.collector.JobStat
-