-C-Index -

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-C

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.JManagement -: Stop running the job jobId 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.ClustalOWS -: -
cancelJob(String) - -Method in class compbio.ws.server.ClustalWS -: -
cancelJob(String) - -Method in class compbio.ws.server.GenericMetadataService -: -
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 -: -
checkService(Services) - -Method in class compbio.ws.client.WSTester -: Test JABA web service -
ChunkHolder - Class in compbio.metadata: Represents a chunk of a string data together with the position in a file for - the next read operation.
ChunkHolder(String, long) - -Constructor for class compbio.metadata.ChunkHolder -: -
Cleaner - Class in compbio.engine: Deprecated.
Cleaner() - -Constructor for class compbio.engine.Cleaner -: Deprecated. -
cleanProteinSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -: Remove all non AA chars from the sequence -
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.data.sequence.FastaReader -: Call this method to close the connection to the input file if you want to - free up the resources. -
close() - -Method in class compbio.engine.cluster.drmaa.ClusterSession -: -
closeSilently(Logger, Closeable) - -Static method in class compbio.data.sequence.SequenceUtil -: Closes the Closable and logs the exception if any -
ClustalAlignmentUtil - Class in compbio.data.sequence: Tools to read and write clustal formated files
ClustalAlignmentUtil() - -Constructor for class compbio.data.sequence.ClustalAlignmentUtil -: -
ClustalO - Class in compbio.runner.msa
ClustalO() - -Constructor for class compbio.runner.msa.ClustalO -: --threads= Number of processors to use - - -l, --log= Log all non-essential output to this file -
ClustalOWS - Class in compbio.ws.server
ClustalOWS() - -Constructor for class compbio.ws.server.ClustalOWS -: -
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 -: -
ClusterSession - Class in compbio.engine.cluster.drmaa
ClusterUtil - Class in compbio.engine.cluster.drmaa
ClusterUtil() - -Constructor for class compbio.engine.cluster.drmaa.ClusterUtil -: -
COILS_EXPECTATION_THRESHOLD - -Variable in class compbio.runner.disorder.Disembl -: For the region to be considered disordered the values must exceed these -
CommandBuilder<T> - Class in compbio.engine.client
CommandBuilder(String) - -Constructor for class compbio.engine.client.CommandBuilder -: -
compare(Hit, Hit) - -Method in class compbio.pipeline._jpred.Hit.EvalueComporator -: -
compare(Hit, Hit) - -Method in class compbio.pipeline._jpred.Hit.NumberComporator -: -
compareTo(Range) - -Method in class compbio.data.sequence.Range -: -
compareTo(Score) - -Method in class compbio.data.sequence.Score -: -
compareTo(Delayed) - -Method in class compbio.engine.FilePuller -: -
compbio.data._structure - package compbio.data._structure
compbio.data.msa - package compbio.data.msa: Web Service interfaces for JAva Bioinformatics Analysis Web Services.
compbio.data.msa.jaxws - package compbio.data.msa.jaxws
compbio.pipeline._jpred - package compbio.pipeline._jpred
compbio.runner._jpred - package compbio.runner._jpred
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() - -Static method in class compbio.ws.client.AAConClient -: Connects to a AACon web service by the host and the service name -
connect(String, Services) - -Static method in class compbio.ws.client.Jws2Client -: Connects to a web service by the host and the service name web service - type -
connectToRegistry(String) - -Static method in class compbio.ws.client.Jws2Client -: Get a connection of JABAWS registry -
ConservationMethod - Enum in compbio.data.sequence: Enumeration listing of all the supported methods.
contextDestroyed(ServletContextEvent) - -Method in class compbio.stat.servlet.StatisticCollector -: -
contextDestroyed(ServletContextEvent) - -Method in class compbio.ws.server.ShutdownEngines -: -
contextInitialized(ServletContextEvent) - -Method in class compbio.stat.servlet.StatisticCollector -: -
contextInitialized(ServletContextEvent) - -Method in class compbio.ws.server.ShutdownEngines -: -
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<T>>) - -Method in class compbio.ws.server._MsaService -: -
customAlign(List<FastaSequence>, List<Option<ClustalO>>) - -Method in class compbio.ws.server.ClustalOWS -: -
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 -: -
CustomAnalize - Class in compbio.data.msa.jaxws
CustomAnalize() - -Constructor for class compbio.data.msa.jaxws.CustomAnalize -: -
customAnalize(List<FastaSequence>, List<Option<T>>) - -Method in interface compbio.data.msa.SequenceAnnotation -: Analyse the sequences according to custom settings defined in options - list. -
customAnalize(List<FastaSequence>, List<Option<Disembl>>) - -Method in class compbio.ws.server.DisemblWS -: -
customAnalize(List<FastaSequence>, List<Option<GlobPlot>>) - -Method in class compbio.ws.server.GlobPlotWS -: -
customAnalize(List<FastaSequence>, List<Option<T>>) - -Method in class compbio.ws.server.SequenceAnnotationService -: -
CustomAnalizeResponse - Class in compbio.data.msa.jaxws
CustomAnalizeResponse() - -Constructor for class compbio.data.msa.jaxws.CustomAnalizeResponse -: -