+Class Hierarchy +

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Foverview-tree.html;fp=website%2Ffull_javadoc%2Foverview-tree.html;h=7b5b61293f14cfec7724777cb85c9e859f570532;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;p=jabaws.git diff --git a/website/full_javadoc/overview-tree.html b/website/full_javadoc/overview-tree.html new file mode 100644 index 0000000..7b5b612 --- /dev/null +++ b/website/full_javadoc/overview-tree.html @@ -0,0 +1,251 @@ + + + + + + +Class Hierarchy + + + + + + + + + + + + +

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Overview

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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
  +
+

+

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Overview

Package

Class

Use

Tree

Deprecated

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Help

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