- LAST - Static variable in class compbio.engine.client.CommandBuilder.Parameter
-
- lastAccessTime - Variable in class compbio.engine.FilePuller
-
- launderThrowable(Throwable) - Static method in class compbio.engine.local.LocalEngineUtil
-
Coerce an unchecked Throwable to a RuntimeException or Error
- LifeSpanInHours - Variable in class compbio.stat.collector.DirCleaner
-
- Limit<T> - Class in compbio.metadata
-
A value object containing a maximum number of sequences and a maximum average
sequence length for a preset.
- Limit() - Constructor for class compbio.metadata.Limit
-
- Limit(int, int, String) - Constructor for class compbio.metadata.Limit
-
Instantiate the limit
- Limit(int, int, String, boolean) - Constructor for class compbio.metadata.Limit
-
- limit - Variable in class compbio.metadata.LimitsManager
-
- LimitExceededException - Exception in compbio.metadata
-
This exception is thrown if the task larger in size that the limit that
applies to the calculation.
- LimitExceededException(String) - Constructor for exception compbio.metadata.LimitExceededException
-
- LimitExceededExceptionBean - Class in compbio.data.msa.jaxws
-
This class was generated by the JAX-WS RI.
- LimitExceededExceptionBean() - Constructor for class compbio.data.msa.jaxws.LimitExceededExceptionBean
-
- limitList - Static variable in class compbio.ws.client.Constraints
-
- limitMan - Static variable in class compbio.ws.server.ClustalOWS
-
- limitMan - Static variable in class compbio.ws.server.ClustalWS
-
- limitMan - Variable in class compbio.ws.server.GenericMetadataService
-
- limitMan - Static variable in class compbio.ws.server.GLprobsWS
-
- limitMan - Static variable in class compbio.ws.server.MafftWS
-
- limitMan - Static variable in class compbio.ws.server.MSAprobsWS
-
- limitMan - Static variable in class compbio.ws.server.MuscleWS
-
- limitMan - Static variable in class compbio.ws.server.ProbconsWS
-
- limitMan - Static variable in class compbio.ws.server.TcoffeeWS
-
- limits - Variable in class compbio.engine.client.SkeletalExecutable
-
- LimitsManager<T> - Class in compbio.metadata
-
A collection of Limits
- LimitsManager() - Constructor for class compbio.metadata.LimitsManager
-
- line_delimiter - Static variable in class compbio.ws.client.Services.ServiceInfo
-
- listAllServices(String) - Static method in class compbio.ws.client.Jws2Client
-
- listLimits(String[]) - Static method in class compbio.ws.client.CmdHelper
-
Checks whether limitList parameter is in the command line
- listParameters(String[]) - Static method in class compbio.ws.client.CmdHelper
-
Searches the command line keys in the array of parameters
- listPresets(String[]) - Static method in class compbio.ws.client.CmdHelper
-
Check whether presetList is set in the command line
- listServices(String[]) - Static method in class compbio.ws.client.CmdHelper
-
list available services
- listServices - Static variable in class compbio.ws.client.Constraints
-
- listServicesOld - Static variable in class compbio.ws.client.Constraints
-
- livesOverLifeSpan(JobDirectory) - Method in class compbio.stat.collector.DirCleaner
-
- load(InputStream) - Static method in class compbio.engine.client.RunConfiguration
-
- loadAlignment() - Static method in class compbio.ws.client.WSTester
-
Converting input to a form accepted by WS
- LoadBalancer - Class in compbio.engine
-
This class decides where to execute the job.
- LoadBalancer() - Constructor for class compbio.engine.LoadBalancer
-
- loadExecutable(String) - Static method in class compbio.engine.client.EngineUtil
-
- loadExecutable(String) - Static method in class compbio.engine.client.Util
-
- loadParameters(File) - Static method in class compbio.ws.client.IOHelper
-
Load parameters from file
- loadRNAAlignment() - Static method in class compbio.ws.client.WSTester
-
Converting input to a form accepted by WS
- loadRunConfiguration(RunConfiguration) - Method in class compbio.engine.client.ConfExecutable
-
- loadRunConfiguration(InputStream) - Method in class compbio.engine.client.ConfExecutable
-
- loadRunConfiguration(InputStream) - Method in interface compbio.engine.client.ConfiguredExecutable
-
- loadRunConfiguration(RunConfiguration) - Method in interface compbio.engine.client.Executable
-
- loadRunConfiguration(RunConfiguration) - Method in class compbio.engine.client.SkeletalExecutable
-
- loadSeqs(int) - Static method in class compbio.ws.client.WSTester
-
Converting input to a form accepted by WS
- LOCAL_ENGINE_LIMIT_PRESET - Static variable in class compbio.metadata.PresetManager
-
- LOCAL_WORK_DIRECTORY - Static variable in class compbio.engine.Configurator
-
- localcf - Variable in class compbio.stat.servlet.StatisticCollector
-
- localcl - Variable in class compbio.ws.server.MainManager
-
- LocalEngineUtil - Class in compbio.engine.local
-
- LocalEngineUtil() - Constructor for class compbio.engine.local.LocalEngineUtil
-
- LocalExecutorService - Class in compbio.engine.local
-
- LocalExecutorService(int, int, long, TimeUnit, BlockingQueue<Runnable>) - Constructor for class compbio.engine.local.LocalExecutorService
-
- LocalRunner - Class in compbio.engine.local
-
- LocalRunner(ConfiguredExecutable<?>) - Constructor for class compbio.engine.local.LocalRunner
-
- localStat - Variable in class compbio.stat.servlet.util.StatCollection
-
- log - Static variable in class compbio.data.sequence.ClustalAlignmentUtil
-
- log - Static variable in class compbio.engine.Cleaner
-
- log - Static variable in class compbio.engine.client.CommandBuilder
-
- log - Static variable in class compbio.engine.client.ConfExecutable
-
- log - Static variable in class compbio.engine.client.EngineUtil
-
- log - Static variable in class compbio.engine.client.EnvVariableProcessor
-
- log - Static variable in class compbio.engine.client.RunConfiguration
-
- log - Static variable in class compbio.engine.client.SkeletalExecutable
-
- log - Static variable in class compbio.engine.client.Util
-
- log - Static variable in class compbio.engine.cluster.drmaa.AsyncClusterRunner
-
- log - Static variable in class compbio.engine.cluster.drmaa.AsyncJobRunner
-
- log - Static variable in class compbio.engine.cluster.drmaa.ClusterEngineUtil
-
- log - Static variable in class compbio.engine.cluster.drmaa.ClusterRunner
-
- log - Static variable in class compbio.engine.cluster.drmaa.ClusterSession
-
- log - Static variable in class compbio.engine.cluster.drmaa.ClusterUtil
-
- log - Static variable in class compbio.engine.cluster.drmaa.JobRunner
-
- log - Static variable in class compbio.engine.conf.DirectoryManager
-
- log - Static variable in class compbio.engine.conf.PropertyHelperManager
-
- log - Static variable in class compbio.engine.conf.RunnerConfigMarshaller
-
- log - Static variable in class compbio.engine.Configurator
-
- log - Static variable in class compbio.engine.FilePuller
-
- log - Static variable in class compbio.engine.LoadBalancer
-
- log - Static variable in class compbio.engine.local.AsyncLocalRunner
-
- log - Static variable in class compbio.engine.local.ExecutableWrapper
-
- log - Static variable in class compbio.engine.local.LocalEngineUtil
-
- log - Static variable in class compbio.engine.local.LocalExecutorService
-
- log - Static variable in class compbio.engine.local.LocalRunner
-
- log - Static variable in class compbio.engine.local.StreamGobbler
-
- log - Static variable in class compbio.engine.ProgressGetter
-
- log - Static variable in class compbio.engine.PulledFileCache
-
- log - Static variable in class compbio.engine.SubmissionManager
-
- log - Static variable in class compbio.runner.conservation.AACon
-
- log - Static variable in class compbio.runner.disorder.Disembl
-
- log - Static variable in class compbio.runner.disorder.GlobPlot
-
- log - Static variable in class compbio.runner.disorder.IUPred
-
- log - Static variable in class compbio.runner.disorder.Jronn
-
- log - Static variable in class compbio.runner.msa.ClustalO
-
- log - Static variable in class compbio.runner.msa.ClustalW
-
- log - Static variable in class compbio.runner.msa.GLprobs
-
- log - Static variable in class compbio.runner.msa.Mafft
-
- log - Static variable in class compbio.runner.msa.MSAprobs
-
- log - Static variable in class compbio.runner.msa.Muscle
-
- log - Static variable in class compbio.runner.msa.Probcons
-
- log - Static variable in class compbio.runner.msa.Tcoffee
-
- log - Static variable in class compbio.runner.OptionCombinator
-
- log - Static variable in class compbio.runner.RunnerUtil
-
- log - Static variable in class compbio.runner.structure.RNAalifold
-
- log - Static variable in class compbio.runner.Util
-
- log - Static variable in class compbio.stat.collector.DirCleaner
-
- log - Static variable in class compbio.stat.collector.ExecutionStatCollector
-
- log - Static variable in class compbio.stat.collector.InputFilter
-
- log - Static variable in class compbio.stat.collector.JobDirectory
-
- log - Static variable in class compbio.stat.collector.StatDB
-
- log - Static variable in class compbio.stat.servlet.DisplayStat
-
- log - Static variable in class compbio.stat.servlet.HttpCodeResponseServiceStatus
-
- log - Static variable in class compbio.stat.servlet.ServiceStatus
-
- log - Variable in class compbio.stat.servlet.StatisticCollector
-
- log - Static variable in class compbio.stat.servlet.util.StatCollection
-
- log - Static variable in class compbio.ws.client.AAConClient
-
Use java.util.Logger instead of log4j logger to reduce the size of the
client package
- log - Static variable in class compbio.ws.client.Jws2Client
-
Use java.util.Logger instead of log4j logger to reduce the size of the client package
- log - Static variable in class compbio.ws.server.AAConWS
-
- log - Static variable in class compbio.ws.server.ClustalOWS
-
- log - Static variable in class compbio.ws.server.ClustalWS
-
- log - Static variable in class compbio.ws.server.DisemblWS
-
- log - Static variable in class compbio.ws.server.GAUtils
-
- log - Variable in class compbio.ws.server.GenericMetadataService
-
- log - Static variable in class compbio.ws.server.GlobPlotWS
-
- log - Static variable in class compbio.ws.server.GLprobsWS
-
- log - Static variable in class compbio.ws.server.IUPredWS
-
- log - Static variable in class compbio.ws.server.JronnWS
-
- log - Static variable in class compbio.ws.server.MafftWS
-
- log - Variable in class compbio.ws.server.MainManager
-
- log - Static variable in class compbio.ws.server.MSAprobsWS
-
- log - Static variable in class compbio.ws.server.MuscleWS
-
- log - Static variable in class compbio.ws.server.ProbconsWS
-
- log - Static variable in class compbio.ws.server.RegistryWS
-
- log - Static variable in class compbio.ws.server.RNAalifoldWS
-
- log - Variable in class compbio.ws.server.SetExecutableFlag
-
- log - Static variable in class compbio.ws.server.TcoffeeWS
-
- logStatistics(JobInfo) - Static method in class compbio.engine.cluster.drmaa.ClusterSession
-
- LONG_OUTPUT - Static variable in class compbio.runner.disorder.IUPred
-
- LOOPS_EXPECTATION_THRESHOLD - Variable in class compbio.runner.disorder.Disembl
-