A B C D E F G H I J K L M N O P R S T U V W _

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

Category - Class in compbio.data.msa

Class that splits Services to categories.

CATEGORY_ALIGNMENT - Static variable in class compbio.data.msa.Category

All of the Category names

CATEGORY_CONSERVATION - Static variable in class compbio.data.msa.Category

CATEGORY_DISORDER - Static variable in class compbio.data.msa.Category

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

CLUSTAL_INFO - Static variable in enum compbio.ws.client.Services

CLUSTAL_OMEGA_INFO - Static variable in enum compbio.ws.client.Services

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.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.SetExecutableFlag

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.SetExecutableFlag

This listener is designed to run only once when the web application is deployed to set executable flag for binaries.

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