- CACHE - Static variable in class compbio.engine.PulledFileCache
-
- 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.AsyncClusterRunner
-
- cancelJob(String) - Method in class compbio.engine.cluster.drmaa.AsyncJobRunner
-
- cancelJob(String, ClusterSession) - Static method in class compbio.engine.cluster.drmaa.ClusterEngineUtil
-
- cancelJob(String) - Method in class compbio.engine.cluster.drmaa.ClusterRunner
-
- cancelJob() - Method in class compbio.engine.cluster.drmaa.ClusterRunner
-
- cancelJob(String, ClusterSession) - Static method in class compbio.engine.cluster.drmaa.ClusterUtil
-
- cancelJob(String) - Method in class compbio.engine.cluster.drmaa.JobRunner
-
- 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.GLprobsWS
-
- cancelJob(String) - Method in class compbio.ws.server.MafftWS
-
- cancelJob(String) - Method in class compbio.ws.server.MSAprobsWS
-
- 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
-
- cancelled - Variable in class compbio.stat.servlet.util.Totals
-
- Category - Class in compbio.data.msa
-
- Category(String, Set<Services>) - Constructor for class compbio.data.msa.Category
-
- Category() - Constructor for class compbio.data.msa.Category
-
- 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
-
- CATEGORY_PREDICTION - Static variable in class compbio.data.msa.Category
-
- cbuilder - Variable in class compbio.engine.client.SkeletalExecutable
-
This has to allow duplicate parameters as different options may have the
same value e.g.
- centStructP - Static variable in class compbio.data.sequence.RNAStructReader
-
- cexecutable - Variable in class compbio.engine.Job
-
- checkService(JABAService, Services) - Method in class compbio.ws.client.WSTester
-
Call most of web services functions and check the output
- checkService(Services) - Method in class compbio.ws.client.WSTester
-
Test JABA web service
- checkValue(String) - Method in class compbio.metadata.ValueConstrain
-
Validate that the value is within the constrain boundaries
- chunk - Variable in class compbio.metadata.ChunkHolder
-
- 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() - Constructor for class compbio.metadata.ChunkHolder
-
- ChunkHolder(String, long) - Constructor for class compbio.metadata.ChunkHolder
-
- chunkSize - Variable in class compbio.engine.FilePuller
-
- Cleaner - Class in compbio.engine
-
- Cleaner() - Constructor for class compbio.engine.Cleaner
-
- 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.AsyncClusterRunner
-
- cleanup(String) - Method in class compbio.engine.cluster.drmaa.AsyncJobRunner
-
- cleanup() - Method in class compbio.engine.cluster.drmaa.ClusterRunner
-
- 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
- clear() - Static method in class compbio.engine.PulledFileCache
-
- clearStatTable() - Static method in class compbio.stat.collector.StatDB
-
- 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
- closeSilently(Closeable) - Static method in class compbio.engine.local.StreamGobbler
-
- 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
- clustalOptions - Static variable in class compbio.ws.server.ClustalOWS
-
- clustalOptions - Static variable in class compbio.ws.server.ClustalWS
-
- ClustalOWS - Class in compbio.ws.server
-
- ClustalOWS() - Constructor for class compbio.ws.server.ClustalOWS
-
- clustalPresets - Static variable in class compbio.ws.server.ClustalOWS
-
- clustalPresets - Static variable in class compbio.ws.server.ClustalWS
-
- clustalRNAAlignment - Static variable in class compbio.ws.client.WSTester
-
- 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.ClusterEngineUtil
-
- 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
-
- clustercf - Variable in class compbio.stat.servlet.StatisticCollector
-
- clustercl - Variable in class compbio.ws.server.MainManager
-
- ClusterEngineUtil - Class in compbio.engine.cluster.drmaa
-
- ClusterEngineUtil() - Constructor for class compbio.engine.cluster.drmaa.ClusterEngineUtil
-
- ClusterJobId - Class in compbio.engine
-
- ClusterJobId(String) - Constructor for class compbio.engine.ClusterJobId
-
- clusterJobId - Variable in class compbio.stat.collector.JobStat
-
- ClusterRunner - Class in compbio.engine.cluster.drmaa
-
Single cluster job runner class
- ClusterRunner(ConfiguredExecutable<?>) - Constructor for class compbio.engine.cluster.drmaa.ClusterRunner
-
- ClusterSession - Class in compbio.engine.cluster.drmaa
-
- ClusterSession() - Constructor for class compbio.engine.cluster.drmaa.ClusterSession
-
- clusterStat - Variable in class compbio.stat.servlet.util.StatCollection
-
- ClusterUtil - Class in compbio.engine.cluster.drmaa
-
- ClusterUtil() - Constructor for class compbio.engine.cluster.drmaa.ClusterUtil
-
- clustSession - Static variable in class compbio.engine.cluster.drmaa.ClusterRunner
-
- clustSession - Static variable in class compbio.engine.cluster.drmaa.JobRunner
-
- CmdHelper - Class in compbio.ws.client
-
- CmdHelper() - Constructor for class compbio.ws.client.CmdHelper
-
- COILS_EXPECTATION_THRESHOLD - Variable in class compbio.runner.disorder.Disembl
-
For the region to be considered disordered the values must exceed these
- collectClusterStats() - Static method in class compbio.stat.servlet.StatisticCollector
-
- collectLocalStats() - Static method in class compbio.stat.servlet.StatisticCollector
-
- collectStatistics() - Method in class compbio.stat.collector.ExecutionStatCollector
-
- combineScores(Map<String, Set<Score>>, Map<String, Score>) - Method in class compbio.runner.disorder.IUPred
-
- CommandBuilder<T> - Class in compbio.engine.client
-
- CommandBuilder() - Constructor for class compbio.engine.client.CommandBuilder
-
- CommandBuilder(String) - Constructor for class compbio.engine.client.CommandBuilder
-
- CommandBuilder.Parameter - Class in compbio.engine.client
-
- compareClustalLines(File, String[]) - Static method in class compbio.stat.collector.InputFilter
-
- compareLines(File, String[]) - Static method in class compbio.stat.collector.InputFilter
-
- 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.msa.jaxws - package compbio.data.msa.jaxws
-
- confDir - Static variable in class compbio.engine.conf.PropertyHelperManager
-
- confExec - Variable in class compbio.engine.local.ExecutableWrapper
-
- ConfExecutable<T> - Class in compbio.engine.client
-
- ConfExecutable(Executable<T>, String) - Constructor for class compbio.engine.client.ConfExecutable
-
- ConfExecutable(RunConfiguration) - Constructor for class compbio.engine.client.ConfExecutable
-
- confExecutable - Variable in class compbio.engine.cluster.drmaa.ClusterRunner
-
- confExecutable - Variable in class compbio.engine.cluster.drmaa.JobRunner
-
- config - Static variable in class compbio.ws.server.GAUtils
-
- 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
-
- conn - Static variable in class compbio.stat.collector.StatDB
-
- 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
- connect(String, Services) - Method in class compbio.ws.client.WSTester
-
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.
- ConservationMethod() - Constructor for enum compbio.data.sequence.ConservationMethod
-
- Constraints - Class in compbio.ws.client
-
- Constraints() - Constructor for class compbio.ws.client.Constraints
-
- containsMultipleVariables(String) - Static method in class compbio.engine.client.EnvVariableProcessor
-
- containsValue(List<String>, String) - Method in class compbio.metadata.PresetManager
-
- containValue(String) - Method in class compbio.metadata.Preset
-
- contextDestroyed(ServletContextEvent) - Method in class compbio.stat.servlet.StatisticCollector
-
- contextDestroyed(ServletContextEvent) - Method in class compbio.ws.server.MainManager
-
- contextDestroyed(ServletContextEvent) - Method in class compbio.ws.server.SetExecutableFlag
-
- contextInitialized(ServletContextEvent) - Method in class compbio.stat.servlet.StatisticCollector
-
- contextInitialized(ServletContextEvent) - Method in class compbio.ws.server.MainManager
-
- 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.
- convertInputNameToTreeName() - Method in class compbio.runner.msa.ClustalW
-
Clustal output tree with same name as input file but .dnd extension e.g.
- convertToAbsolute(String) - Static method in class compbio.engine.client.EngineUtil
-
- convertToAbsolute(String) - Static method in class compbio.engine.client.Util
-
- convertToNumber(String[]) - Static method in class compbio.data.sequence.SequenceUtil
-
- copyAndValidateRConfig(RunnerConfig<?>) - Method in class compbio.metadata.RunnerConfig
-
- countMatchesInSequence(String, String) - Static method in class compbio.data.sequence.FastaSequence
-
- cpu - Variable in class compbio.engine.cluster.drmaa.StatisticManager
-
- createOutput(String, String) - Method in class compbio.engine.conf.RunnerConfigMarshaller.MySchemaOutputResolver
-
- createStatTable() - Method in class compbio.stat.collector.StatDB
-
rs.getBoolean(i) will return true for any non-zero value and false for 0
on SMALLINT data column.
- ctx - Variable in class compbio.engine.conf.RunnerConfigMarshaller
-
- 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<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<GLprobs>>) - Method in class compbio.ws.server.GLprobsWS
-
- customAlign(List<FastaSequence>, List<Option<Mafft>>) - Method in class compbio.ws.server.MafftWS
-
- customAlign(List<FastaSequence>, List<Option<MSAprobs>>) - Method in class compbio.ws.server.MSAprobsWS
-
- 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<AACon>>) - Method in class compbio.ws.server.AAConWS
-
- 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<RNAalifold>>) - Method in class compbio.ws.server.RNAalifoldWS
-
- 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
-
- CustomFold - Class in compbio.data.msa.jaxws
-
- CustomFold() - Constructor for class compbio.data.msa.jaxws.CustomFold
-
- CustomFoldResponse - Class in compbio.data.msa.jaxws
-
- CustomFoldResponse() - Constructor for class compbio.data.msa.jaxws.CustomFoldResponse
-