Hierarchy For All Packages

Package Hierarchies:

compbio.data._structure, compbio.data.msa, compbio.data.msa.jaxws, compbio.data.sequence, compbio.engine, compbio.engine.client, compbio.engine.cluster.drmaa, compbio.engine.cluster.dundee, compbio.engine.conf, compbio.engine.local, compbio.metadata, compbio.pipeline._jpred, compbio.runner, compbio.runner._impl, compbio.runner._jpred, compbio.runner.conservation, compbio.runner.disorder, compbio.runner.msa, compbio.stat.collector, compbio.stat.servlet, compbio.stat.servlet.util, compbio.ws.client, compbio.ws.server

Class Hierarchy

• java.lang.Object
  • compbio.runner._jpred._Jpred
  • compbio.engine.conf._Key
  • compbio.runner._NativeSpecHelper
  • compbio.runner._SkeletalCommandBuilder (implements compbio.engine.client.Executable<T>)
    • compbio.runner._impl.BlastAll
    • compbio.runner._impl.Mcl
    • compbio.runner._impl.OB
    • compbio.runner._impl.PSIBlast
    • compbio.runner._impl.Ronn
    • compbio.runner._impl.RPSBlast
  • compbio.ws.server._WSLogger
  • compbio.ws.client.AAConClient
  • java.util.concurrent.AbstractExecutorService (implements java.util.concurrent.ExecutorService)
    • java.util.concurrent.ThreadPoolExecutor
      • compbio.engine.local.LocalExecutorService
  • compbio.data.msa.jaxws.Align
  • compbio.data.sequence.Alignment
  • compbio.data.sequence.AlignmentMetadata
  • compbio.data.msa.jaxws.AlignResponse
  • compbio.data.msa.jaxws.Analize
  • compbio.data.msa.jaxws.AnalizeResponse
  • compbio.engine.cluster.drmaa.AsyncJobRunner (implements compbio.engine.AsyncExecutor)
  • compbio.engine.local.AsyncLocalRunner (implements compbio.engine.AsyncExecutor)
  • compbio.pipeline._jpred.BlastBlastComparator
  • compbio.pipeline._jpred.BlastHmmerComparator
  • compbio.runner._impl.BlastParameters
  • compbio.pipeline._jpred.BlastParser
  • compbio.data.msa.jaxws.CancelJob
  • compbio.data.msa.jaxws.CancelJobResponse
  • compbio.data.msa.Category
  • compbio.metadata.ChunkHolder
  • compbio.engine.Cleaner
  • compbio.data.sequence.ClustalAlignmentUtil
  • compbio.ws.server.ClustalOWS (implements compbio.data.msa.MsaWS<T>)
  • compbio.ws.server.ClustalWS (implements compbio.data.msa.MsaWS<T>)
  • compbio.engine.ClusterJobId
  • compbio.engine.cluster.drmaa.ClusterSession
  • compbio.engine.cluster.drmaa.ClusterUtil
  • compbio.engine.client.CommandBuilder<T>
  • compbio.engine.client.ConfExecutable<T> (implements compbio.engine.client.ConfiguredExecutable<T>)
  • compbio.engine.Configurator
  • compbio.data.msa.jaxws.CustomAlign
  • compbio.data.msa.jaxws.CustomAlignResponse
  • compbio.data.msa.jaxws.CustomAnalize
  • compbio.data.msa.jaxws.CustomAnalizeResponse
  • compbio.engine.conf.DirectoryManager
  • compbio.runner._impl.Environment
  • compbio.engine.client.EnvVariableProcessor
  • compbio.engine.local.ExecutableWrapper (implements java.util.concurrent.Callable<V>)
  • compbio.stat.collector.ExecutionStatCollector (implements java.lang.Runnable)
  • compbio.data.sequence.FastaReader (implements java.util.Iterator<E>)
  • compbio.data.sequence.FastaSequence
  • compbio.engine.FilePuller (implements java.util.concurrent.Delayed)
  • compbio.ws.server.GAUtils
  • compbio.ws.server.GenericMetadataService<T>
    • compbio.ws.server._MsaService<T>
    • compbio.ws.server.SequenceAnnotationService<T>
      • compbio.ws.server.AAConWS (implements compbio.data.msa.SequenceAnnotation<T>)
      • compbio.ws.server.DisemblWS (implements compbio.data.msa.SequenceAnnotation<T>)
      • compbio.ws.server.GlobPlotWS (implements compbio.data.msa.SequenceAnnotation<T>)
      • compbio.ws.server.IUPredWS (implements compbio.data.msa.SequenceAnnotation<T>)
      • compbio.ws.server.JronnWS (implements compbio.data.msa.SequenceAnnotation<T>)
  • javax.servlet.GenericServlet (implements java.io.Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig)
    • javax.servlet.http.HttpServlet (implements java.io.Serializable)
      • compbio.stat.servlet.AnnualStat
      • compbio.stat.servlet.DisplayStat
      • compbio.stat.servlet.DownloadRedirector
      • compbio.stat.servlet.HttpCodeResponseServiceStatus
      • compbio.stat.servlet.Joblist
      • compbio.stat.servlet.ServiceStatus
  • compbio.data.msa.jaxws.GetAnnotation
  • compbio.data.msa.jaxws.GetAnnotationResponse
  • compbio.data.msa.jaxws.GetJobStatus
  • compbio.data.msa.jaxws.GetJobStatusResponse
  • compbio.data.msa.jaxws.GetLastTested
  • compbio.data.msa.jaxws.GetLastTestedOn
  • compbio.data.msa.jaxws.GetLastTestedOnResponse
  • compbio.data.msa.jaxws.GetLastTestedResponse
  • compbio.data.msa.jaxws.GetLimit
  • compbio.data.msa.jaxws.GetLimitResponse
  • compbio.data.msa.jaxws.GetLimits
  • compbio.data.msa.jaxws.GetLimitsResponse
  • compbio.data.msa.jaxws.GetPresets
  • compbio.data.msa.jaxws.GetPresetsResponse
  • compbio.data.msa.jaxws.GetResult
  • compbio.data.msa.jaxws.GetResultResponse
  • compbio.data.msa.jaxws.GetRunnerOptions
  • compbio.data.msa.jaxws.GetRunnerOptionsResponse
  • compbio.data.msa.jaxws.GetServiceCategories
  • compbio.data.msa.jaxws.GetServiceCategoriesResponse
  • compbio.data.msa.jaxws.GetServiceDescription
  • compbio.data.msa.jaxws.GetServiceDescriptionResponse
  • compbio.data.msa.jaxws.GetSupportedServices
  • compbio.data.msa.jaxws.GetSupportedServicesResponse
  • compbio.pipeline._jpred.Hit
  • compbio.pipeline._jpred.Hit.EvalueComporator (implements java.util.Comparator<T>)
  • compbio.pipeline._jpred.Hit.NumberComporator (implements java.util.Comparator<T>)
  • compbio.stat.collector.InputFilter
  • compbio.ws.client.IOHelper
  • compbio.data.msa.jaxws.IsOperating
  • compbio.data.msa.jaxws.IsOperatingResponse
  • compbio.pipeline._jpred.JackHmmerHitParser
  • compbio.engine.Job
  • compbio.engine.cluster.drmaa.JobRunner (implements compbio.engine.SyncExecutor)
  • compbio.stat.collector.JobStat
  • compbio.data.msa.jaxws.JobSubmissionExceptionBean
  • compbio.pipeline._jpred.Jpred4
  • compbio.data._structure.JpredResult
  • compbio.ws.client.Jws2Client
  • compbio.metadata.Limit<T>
  • compbio.data.msa.jaxws.LimitExceededExceptionBean
  • compbio.metadata.LimitsManager<T>
  • compbio.engine.LoadBalancer
  • compbio.engine.local.LocalEngineUtil
  • compbio.engine.local.LocalRunner (implements compbio.engine.SyncExecutor)
  • compbio.ws.server.MafftWS (implements compbio.data.msa.MsaWS<T>)
  • compbio.ws.client.MetadataHelper
  • compbio.ws.server.MuscleWS (implements compbio.data.msa.MsaWS<T>)
  • compbio.runner._impl.NetNglyc (implements compbio.engine.client.Executable<T>)
  • compbio.metadata.Option<T> (implements compbio.metadata.Argument<T>)
    • compbio.metadata.Parameter<T>
  • compbio.runner.OptionCombinator
  • compbio.pipeline._jpred.Pairwise
  • compbio.engine.client.PathValidator
  • compbio.metadata.Preset<T>
  • compbio.data.msa.jaxws.PresetAlign
  • compbio.data.msa.jaxws.PresetAlignResponse
  • compbio.data.msa.jaxws.PresetAnalize
  • compbio.data.msa.jaxws.PresetAnalizeResponse
  • compbio.metadata.PresetManager<T>
  • compbio.ws.server.ProbconsWS (implements compbio.data.msa.MsaWS<T>)
  • compbio.engine.ProgressGetter
  • compbio.engine.conf.PropertyHelperManager
  • compbio.pipeline._jpred.PScore
  • compbio.engine.PulledFileCache
  • compbio.data.msa.jaxws.PullExecStatistics
  • compbio.data.msa.jaxws.PullExecStatisticsResponse
  • compbio.data.sequence.Range (implements java.lang.Comparable<T>)
  • compbio.ws.server.RegistryWS (implements compbio.data.msa.JABAService, compbio.data.msa.RegistryWS)
  • compbio.data.msa.jaxws.ResultNotAvailableExceptionBean
  • compbio.engine.client.RunConfiguration
  • compbio.metadata.RunnerConfig<T>
  • compbio.engine.conf.RunnerConfigMarshaller<T>
  • compbio.runner._impl.Runners
  • compbio.data.sequence.Score (implements java.lang.Comparable<T>)
  • compbio.data.sequence.ScoreManager
  • compbio.data.sequence.ScoreManager.ScoreHolder
  • compbio.data.sequence.SequenceUtil
  • compbio.ws.client.ServicesUtil
  • compbio.stat.servlet.ServiceTestResult
  • compbio.ws.server.SetExecutableFlag (implements javax.servlet.ServletContextListener)
  • compbio.ws.server.ShutdownEngines (implements javax.servlet.ServletContextListener)
  • compbio.ws.server.SimpleWSPublisher
  • compbio.engine.client.SkeletalExecutable<T> (implements compbio.engine.client.Executable<T>)
    • compbio.runner.conservation.AACon
    • compbio.runner.msa.ClustalO
    • compbio.runner.msa.ClustalW
    • compbio.runner.disorder.Disembl (implements compbio.engine.client.PipedExecutable<T>)
    • compbio.runner.disorder.GlobPlot (implements compbio.engine.client.PipedExecutable<T>)
    • compbio.runner.disorder.IUPred
    • compbio.runner.disorder.Jronn
    • compbio.runner.msa.Mafft (implements compbio.engine.client.PipedExecutable<T>)
    • compbio.runner.msa.Muscle
    • compbio.runner.msa.Probcons (implements compbio.engine.client.PipedExecutable<T>)
    • compbio.runner.msa.Tcoffee (implements compbio.engine.client.PipedExecutable<T>)
  • compbio.stat.servlet.util.StatCollection
  • compbio.stat.collector.StatDB
  • compbio.stat.servlet.StatisticCollector (implements javax.servlet.ServletContextListener)
  • compbio.engine.cluster.drmaa.StatisticManager
  • compbio.stat.collector.StatProcessor
  • compbio.engine.local.StreamGobbler (implements java.lang.Runnable)
  • compbio.engine.SubmissionManager
  • compbio.ws.server.TcoffeeWS (implements compbio.data.msa.MsaWS<T>)
  • compbio.data.msa.jaxws.TestAllServices
  • compbio.data.msa.jaxws.TestAllServicesResponse
  • compbio.data.msa.jaxws.TestService
  • compbio.data.msa.jaxws.TestServiceResponse
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • compbio.metadata.JobExecutionException
      • compbio.metadata.JobSubmissionException
        • compbio.metadata.LimitExceededException
        • compbio.metadata.UnsupportedRuntimeException
      • compbio.metadata.ResultNotAvailableException
      • compbio.data.sequence.UnknownFileFormatException
      • compbio.metadata.WrongParameterException
  • compbio.stat.servlet.util.Totals
  • compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean
  • compbio.runner.Util
  • compbio.engine.client.Util
  • compbio.metadata.ValueConstrain
  • compbio.data.msa.jaxws.WrongParameterExceptionBean
  • compbio.ws.client.WSTester
  • compbio.ws.server.WSUtil

Interface Hierarchy

• compbio.metadata.Argument<T>
• compbio.engine.AsyncExecutor
• compbio.engine.client.Executable<T>
  • compbio.engine.client.ConfiguredExecutable<T> (also extends compbio.engine.client.PipedExecutable<T>)
  • compbio.engine.client.PipedExecutable<T>
    • compbio.engine.client.ConfiguredExecutable<T> (also extends compbio.engine.client.Executable<T>)
• compbio.data.msa.JABAService
  • compbio.data.msa.MsaWS<T> (also extends compbio.data.msa.JManagement, compbio.data.msa.Metadata<T>)
  • compbio.data.msa.RegistryWS
  • compbio.data.msa.SequenceAnnotation<T> (also extends compbio.data.msa.JManagement, compbio.data.msa.Metadata<T>)
• compbio.data.msa.JManagement
  • compbio.data.msa.MsaWS<T> (also extends compbio.data.msa.JABAService, compbio.data.msa.Metadata<T>)
  • compbio.data.msa.SequenceAnnotation<T> (also extends compbio.data.msa.JABAService, compbio.data.msa.Metadata<T>)
• compbio.data.msa.Metadata<T>
  • compbio.data.msa.MsaWS<T> (also extends compbio.data.msa.JABAService, compbio.data.msa.JManagement)
  • compbio.data.msa.SequenceAnnotation<T> (also extends compbio.data.msa.JABAService, compbio.data.msa.JManagement)
• compbio.engine.SyncExecutor

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • compbio.data.sequence.SMERFSConstraints
    • compbio.data.sequence.DisorderMethod
    • compbio.engine.client.Executable.ExecProvider
    • compbio.metadata.ValueConstrain.Type
    • compbio.metadata.JobStatus
    • compbio.engine.cluster.dundee._Queue
    • compbio.ws.client.Services
    • compbio.data.sequence.Program
    • compbio.data.sequence.ConservationMethod
    • compbio.stat.servlet.util.StatCollection.Stattype
    • compbio.data._structure.JpredAnnotation
    • compbio.data._structure.JnetAnnotation