Hierarchy For All Packages

Package Hierarchies:

• org.nmdp.ngs.align,
• org.nmdp.ngs.fca,
• org.nmdp.ngs.feature,
• org.nmdp.ngs.feature.parser,
• org.nmdp.ngs.gtr,
• org.nmdp.ngs.gtr.jaxb,
• org.nmdp.ngs.hml,
• org.nmdp.ngs.hml.jaxb,
• org.nmdp.ngs.hml.rules,
• org.nmdp.ngs.range,
• org.nmdp.ngs.range.rtree,
• org.nmdp.ngs.range.tree,
• org.nmdp.ngs.reads,
• org.nmdp.ngs.reads.coverage,
• org.nmdp.ngs.reads.mutation,
• org.nmdp.ngs.reads.paired,
• org.nmdp.ngs.reads.quality,
• org.nmdp.ngs.sra,
• org.nmdp.ngs.sra.jaxb,
• org.nmdp.ngs.sra.jaxb.analysis,
• org.nmdp.ngs.sra.jaxb.common,
• org.nmdp.ngs.sra.jaxb.experiment,
• org.nmdp.ngs.sra.jaxb.run,
• org.nmdp.ngs.sra.jaxb.sample,
• org.nmdp.ngs.sra.jaxb.study,
• org.nmdp.ngs.sra.jaxb.submission,
• org.nmdp.ngs.tools,
• org.nmdp.ngs.variant.vcf,
• org.nmdp.ngs.xjc.plugins

Class Hierarchy

• java.lang.Object
  • org.nmdp.ngs.hml.rules.AbstractHmlValidationRule (implements org.nmdp.ngs.hml.HmlValidationRule)
  • org.nmdp.ngs.fca.AbstractLattice<T> (implements org.nmdp.ngs.fca.Lattice<T>)
    • org.nmdp.ngs.fca.ConceptLattice<G,M>
  • org.biojava.bio.symbol.AbstractLocation (implements org.biojava.bio.symbol.Location, java.io.Serializable)
    • org.biojava.bio.symbol.AbstractRangeLocation
      • org.biojava.bio.symbol.RangeLocation (implements java.io.Serializable)
        • org.nmdp.ngs.feature.Locus (implements java.lang.Comparable<T>)
          • org.nmdp.ngs.feature.Allele
  • com.google.inject.AbstractModule (implements com.google.inject.Module)
    • org.nmdp.ngs.hml.rules.MiringModule
  • org.nmdp.ngs.range.tree.AbstractRangeTree<C> (implements org.nmdp.ngs.range.tree.RangeTree<C>)
    • org.nmdp.ngs.range.tree.CenteredRangeTree<C>
    • org.nmdp.ngs.range.tree.RangeList<C>
  • org.nmdp.ngs.gtr.jaxb.AddressType
  • org.nmdp.ngs.gtr.jaxb.AddressType.Country
  • org.nmdp.ngs.gtr.jaxb.AddressType.State
  • org.nmdp.ngs.align.Alignments
  • org.nmdp.ngs.hml.jaxb.Allele
  • org.nmdp.ngs.feature.Allele.Builder
  • org.nmdp.ngs.hml.jaxb.AlleleAssignment
  • org.nmdp.ngs.hml.jaxb.AlleleList
  • org.nmdp.ngs.reads.mutation.AmbiguousSubstitutionMutationStrategy (implements org.nmdp.ngs.reads.MutationStrategy)
  • org.nmdp.ngs.sra.jaxb.analysis.Analysis
  • org.nmdp.ngs.sra.jaxb.analysis.Analysis.AnalysisAttributes
  • org.nmdp.ngs.sra.jaxb.analysis.Analysis.AnalysisLinks
  • org.nmdp.ngs.sra.jaxb.analysis.Analysis.AnalysisRef
  • org.nmdp.ngs.sra.jaxb.analysis.Analysis.AnalysisType
  • org.nmdp.ngs.sra.jaxb.analysis.Analysis.AnalysisType.SamplePhenotype
  • org.nmdp.ngs.sra.jaxb.analysis.Analysis.AnalysisType.SequenceAnnotation
  • org.nmdp.ngs.sra.jaxb.analysis.Analysis.AnalysisType.SequenceAssembly
  • org.nmdp.ngs.sra.jaxb.analysis.Analysis.Files
  • org.nmdp.ngs.sra.jaxb.analysis.Analysis.RunRef
  • org.nmdp.ngs.sra.jaxb.analysis.Analysis.SampleRef
  • org.nmdp.ngs.sra.jaxb.analysis.Analysis.StudyRef
  • org.nmdp.ngs.sra.jaxb.analysis.AnalysisFileType
  • org.nmdp.ngs.sra.jaxb.analysis.AnalysisFileType.Checklist
  • org.nmdp.ngs.sra.jaxb.analysis.AnalysisSet
  • org.nmdp.ngs.sra.jaxb.common.AttributeType
  • org.nmdp.ngs.sra.jaxb.submission.AttributeType
  • org.nmdp.ngs.sra.jaxb.study.AttributeType
  • org.nmdp.ngs.sra.jaxb.run.AttributeType
  • org.nmdp.ngs.sra.jaxb.sample.AttributeType
  • org.nmdp.ngs.sra.jaxb.analysis.AttributeType
  • org.nmdp.ngs.sra.jaxb.experiment.AttributeType
  • org.nmdp.ngs.align.BedReader
  • org.nmdp.ngs.align.BedRecord
  • org.nmdp.ngs.align.BedWriter
  • org.nmdp.ngs.align.BiojavaPairwiseAlignment (implements java.io.Serializable)
  • org.nmdp.ngs.align.Blastn
  • org.nmdp.ngs.gtr.jaxb.CertificationType
    • org.nmdp.ngs.gtr.jaxb.LabCertificationType
  • org.nmdp.ngs.gtr.jaxb.ClinvarPublicSetType
  • org.nmdp.ngs.gtr.jaxb.ClinvarPublicSetType.AcronymSet
  • org.nmdp.ngs.gtr.jaxb.ClinvarPublicSetType.DescrSet
  • org.nmdp.ngs.gtr.jaxb.ClinvarPublicSetType.SynonymSet
  • org.nmdp.ngs.reads.mutation.CompositeMutationStrategy (implements org.nmdp.ngs.reads.MutationStrategy)
  • org.nmdp.ngs.fca.Concept (implements org.nmdp.ngs.fca.Partial<T>)
  • org.nmdp.ngs.fca.Concept.Builder<G,M>
  • org.nmdp.ngs.hml.jaxb.ConsensusSequence
  • org.nmdp.ngs.hml.jaxb.ConsensusSequenceBlock
  • org.nmdp.ngs.gtr.jaxb.ContactType
    • org.nmdp.ngs.gtr.jaxb.OrganizationType.LabContact
    • org.nmdp.ngs.gtr.jaxb.PersonnelType.PublicContact
  • org.nmdp.ngs.gtr.jaxb.CredentialType
    • org.nmdp.ngs.gtr.jaxb.PersonType.Credential
  • org.nmdp.ngs.gtr.jaxb.DataSourceType
  • org.nmdp.ngs.gtr.jaxb.DegreeType
    • org.nmdp.ngs.gtr.jaxb.PersonType.Degree
  • org.nmdp.ngs.reads.mutation.DeletionMutationStrategy (implements org.nmdp.ngs.reads.MutationStrategy)
  • org.nmdp.ngs.hml.jaxb.DiploidCombination
  • org.nmdp.ngs.tools.DownsampleFastq (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.tools.DownsampleInterleavedFastq (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.tools.EvaluateScaffolds (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.sra.jaxb.experiment.Experiment
  • org.nmdp.ngs.sra.jaxb.experiment.Experiment.ExperimentAttributes
  • org.nmdp.ngs.sra.jaxb.experiment.Experiment.ExperimentLinks
  • org.nmdp.ngs.sra.jaxb.experiment.Experiment.StudyRef
  • org.nmdp.ngs.sra.jaxb.experiment.ExperimentSet
  • org.nmdp.ngs.tools.ExtractConsensus (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.tools.ExtractExpectedGlstrings (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.tools.ExtractExpectedHaploids (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.tools.FastaToFastq (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.tools.FastqDescription (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.tools.FastqToFasta (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.tools.FastqToSsake (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.feature.parser.FeatureParser (implements org.nmdp.ngs.feature.parser.FeatureParserConstants)
  • org.nmdp.ngs.feature.parser.FeatureParserTokenManager (implements org.nmdp.ngs.feature.parser.FeatureParserConstants)
  • org.nmdp.ngs.gtr.jaxb.FileType
  • org.nmdp.ngs.tools.FilterConsensus (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.tools.FilterInterpretableExons (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.tools.FilterSamples (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.tools.FilterVcf (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.align.GapPenalties
  • org.nmdp.ngs.align.GapPenalties.Builder
  • org.nmdp.ngs.tools.GenerateBed (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.reads.GeneratePairedEndReads (implements java.lang.Runnable)
  • org.nmdp.ngs.tools.GeneratePairedEndReads (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.reads.GenerateReads (implements java.lang.Runnable)
  • org.nmdp.ngs.tools.GenerateReads (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.gtr.jaxb.GeneSetType
  • org.nmdp.ngs.align.Genewise
  • org.nmdp.ngs.align.GenewiseExon
  • org.nmdp.ngs.hml.jaxb.GenotypeList
  • org.nmdp.ngs.hml.jaxb.Glstring
  • org.nmdp.ngs.gtr.jaxb.GTRLabResearchTestType
    • org.nmdp.ngs.gtr.jaxb.GTRPublicData.GTRLabData.GTRLabResearchTest
  • org.nmdp.ngs.gtr.jaxb.GTRLabResearchTestType.Method
  • org.nmdp.ngs.gtr.jaxb.GTRLabResearchTestType.Method.TopCategory
  • org.nmdp.ngs.gtr.jaxb.GTRLabResearchTestType.Method.TopCategory.Category
  • org.nmdp.ngs.gtr.jaxb.GTRLabResearchTestType.Method.TopCategory.Category.Methodology
  • org.nmdp.ngs.gtr.jaxb.GTRLabResearchTestType.MethodAdd
  • org.nmdp.ngs.gtr.jaxb.GTRLabResearchTestType.MethodAdd.Exons
  • org.nmdp.ngs.gtr.jaxb.GTRLabResearchTestType.Participation
  • org.nmdp.ngs.gtr.jaxb.GTRLabResearchTestType.Study
  • org.nmdp.ngs.gtr.jaxb.GTRLabResearchTestType.StudyPerson
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType
    • org.nmdp.ngs.gtr.jaxb.GTRPublicData.GTRLabData.GTRLabTest
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.Availability
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.Availability.TestExternal
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.ClinicalUtility.Type
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.Indications
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.Indications.Inheritance
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.Indications.Mechanism
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.ManufacturerTestName
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.Method
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.Method.TopCategory
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.Method.TopCategory.Category
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.Method.TopCategory.Category.Methodology
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.MethodAdd
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.MethodAdd.Exons
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.OtherName
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.QualityControl
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.Regulations
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.Regulations.FDARegulatoryClearance
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.Regulations.TestCertification
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.Specimen
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.TestAddService
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.TestResults
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.TestResults.ReContact
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.TestResults.Research
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.TestResults.VUS
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.TestResults.VUS.RecruitFamily
  • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.TestService
  • org.nmdp.ngs.gtr.jaxb.GTROrgType
  • org.nmdp.ngs.gtr.jaxb.GTROrgType.DiseaseTesting
  • org.nmdp.ngs.gtr.jaxb.GTROrgType.DiseaseTesting.Method
  • org.nmdp.ngs.gtr.jaxb.GTROrgType.DiseaseTesting.Method.TopCategory
  • org.nmdp.ngs.gtr.jaxb.GTROrgType.DiseaseTesting.Method.TopCategory.Category
  • org.nmdp.ngs.gtr.jaxb.GTROrgType.GeneTesting
  • org.nmdp.ngs.gtr.jaxb.GTRPublicData
  • org.nmdp.ngs.gtr.jaxb.GTRPublicData.GTRLabData
  • org.nmdp.ngs.gtr.GtrReader
  • org.nmdp.ngs.gtr.GtrWriter
  • org.nmdp.ngs.hml.jaxb.Haploid
  • org.nmdp.ngs.align.HighScoringPair
  • org.nmdp.ngs.hml.jaxb.Hml
  • org.nmdp.ngs.hml.jaxb.Hmlid
  • org.nmdp.ngs.hml.HmlReader
  • org.nmdp.ngs.hml.HmlUtils
  • org.nmdp.ngs.hml.rules.HmlValidationRules
  • org.nmdp.ngs.hml.HmlWriter
  • org.nmdp.ngs.align.HspReader
  • org.nmdp.ngs.tools.HspToBed (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.align.HspWriter
  • org.nmdp.ngs.sra.jaxb.common.IdentifierType
  • org.nmdp.ngs.sra.jaxb.submission.IdentifierType
  • org.nmdp.ngs.sra.jaxb.study.IdentifierType
  • org.nmdp.ngs.sra.jaxb.run.IdentifierType
  • org.nmdp.ngs.sra.jaxb.sample.IdentifierType
  • org.nmdp.ngs.sra.jaxb.analysis.IdentifierType
  • org.nmdp.ngs.sra.jaxb.experiment.IdentifierType
  • org.nmdp.ngs.reads.mutation.IdentityMutationStrategy (implements org.nmdp.ngs.reads.MutationStrategy)
  • org.nmdp.ngs.reads.mutation.IndelMutationStrategy (implements org.nmdp.ngs.reads.MutationStrategy)
  • org.nmdp.ngs.reads.mutation.InsertionMutationStrategy (implements org.nmdp.ngs.reads.MutationStrategy)
  • org.nmdp.ngs.tools.InterleaveFastq (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.tools.IntersectBed (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.sra.jaxb.experiment.LibraryDescriptorType
  • org.nmdp.ngs.sra.jaxb.experiment.LibraryDescriptorType.LibraryLayout
  • org.nmdp.ngs.sra.jaxb.experiment.LibraryDescriptorType.LibraryLayout.Paired
  • org.nmdp.ngs.sra.jaxb.experiment.LibraryDescriptorType.LibraryLayout.Single
  • org.nmdp.ngs.sra.jaxb.experiment.LibraryDescriptorType.TargetedLoci
  • org.nmdp.ngs.sra.jaxb.experiment.LibraryDescriptorType.TargetedLoci.Locus
  • org.nmdp.ngs.sra.jaxb.experiment.LibraryType
  • org.nmdp.ngs.tools.LiftoverBed (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.sra.jaxb.common.LinkType
  • org.nmdp.ngs.sra.jaxb.submission.LinkType
  • org.nmdp.ngs.sra.jaxb.study.LinkType
  • org.nmdp.ngs.sra.jaxb.run.LinkType
  • org.nmdp.ngs.sra.jaxb.sample.LinkType
  • org.nmdp.ngs.sra.jaxb.analysis.LinkType
  • org.nmdp.ngs.sra.jaxb.experiment.LinkType
  • org.nmdp.ngs.sra.jaxb.common.LinkType.EntrezLink
  • org.nmdp.ngs.sra.jaxb.submission.LinkType.EntrezLink
  • org.nmdp.ngs.sra.jaxb.study.LinkType.EntrezLink
  • org.nmdp.ngs.sra.jaxb.run.LinkType.EntrezLink
  • org.nmdp.ngs.sra.jaxb.sample.LinkType.EntrezLink
  • org.nmdp.ngs.sra.jaxb.analysis.LinkType.EntrezLink
  • org.nmdp.ngs.sra.jaxb.experiment.LinkType.EntrezLink
  • org.nmdp.ngs.sra.jaxb.common.LinkType.UrlLink
  • org.nmdp.ngs.sra.jaxb.submission.LinkType.UrlLink
  • org.nmdp.ngs.sra.jaxb.study.LinkType.UrlLink
  • org.nmdp.ngs.sra.jaxb.run.LinkType.UrlLink
  • org.nmdp.ngs.sra.jaxb.sample.LinkType.UrlLink
  • org.nmdp.ngs.sra.jaxb.analysis.LinkType.UrlLink
  • org.nmdp.ngs.sra.jaxb.experiment.LinkType.UrlLink
  • org.nmdp.ngs.feature.Locus.Util
  • org.nmdp.ngs.hml.jaxb.LocusBlock
  • org.nmdp.ngs.tools.MaskedToBed (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.reads.coverage.MeanCoverageStrategy
  • org.nmdp.ngs.gtr.jaxb.MeasureSetType
  • org.nmdp.ngs.gtr.jaxb.MeasureSetType.Measure
  • org.nmdp.ngs.gtr.jaxb.MeasureSetType.Measure.Affects
  • org.nmdp.ngs.gtr.jaxb.MeasureSetType.Measure.FoundIn
  • org.nmdp.ngs.gtr.jaxb.MeasureSetType.Measure.FoundIn.Location
  • org.nmdp.ngs.gtr.jaxb.MeasureSetType.Measure.Location
  • org.nmdp.ngs.gtr.jaxb.MeasureTraitType
  • org.nmdp.ngs.gtr.jaxb.MeasureTraitType.Assertion
  • org.nmdp.ngs.gtr.jaxb.MeasureTraitType.ClinVarAcc
  • org.nmdp.ngs.gtr.jaxb.MeasureTraitType.DescrSet
  • org.nmdp.ngs.gtr.jaxb.MeasureTraitType.ObservedIn
  • org.nmdp.ngs.gtr.jaxb.MeasureTraitType.Title
  • org.nmdp.ngs.tools.MergeFastq (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.reads.coverage.MinimumCoverageStrategy
  • org.nmdp.ngs.sra.jaxb.common.NameType
    • org.nmdp.ngs.sra.jaxb.common.QualifiedNameType
  • org.nmdp.ngs.sra.jaxb.submission.NameType
    • org.nmdp.ngs.sra.jaxb.submission.QualifiedNameType
  • org.nmdp.ngs.sra.jaxb.study.NameType
    • org.nmdp.ngs.sra.jaxb.study.QualifiedNameType
  • org.nmdp.ngs.sra.jaxb.run.NameType
    • org.nmdp.ngs.sra.jaxb.run.QualifiedNameType
  • org.nmdp.ngs.sra.jaxb.sample.NameType
    • org.nmdp.ngs.sra.jaxb.sample.QualifiedNameType
  • org.nmdp.ngs.sra.jaxb.analysis.NameType
    • org.nmdp.ngs.sra.jaxb.analysis.QualifiedNameType
  • org.nmdp.ngs.sra.jaxb.experiment.NameType
    • org.nmdp.ngs.sra.jaxb.experiment.QualifiedNameType
  • org.nmdp.ngs.gtr.jaxb.ObjectFactory
  • org.nmdp.ngs.hml.jaxb.ObjectFactory
  • org.nmdp.ngs.sra.jaxb.common.ObjectFactory
  • org.nmdp.ngs.sra.jaxb.submission.ObjectFactory
  • org.nmdp.ngs.sra.jaxb.study.ObjectFactory
  • org.nmdp.ngs.sra.jaxb.run.ObjectFactory
  • org.nmdp.ngs.sra.jaxb.sample.ObjectFactory
  • org.nmdp.ngs.sra.jaxb.analysis.ObjectFactory
  • org.nmdp.ngs.sra.jaxb.experiment.ObjectFactory
  • org.nmdp.ngs.gtr.jaxb.OrganizationType
  • org.nmdp.ngs.gtr.jaxb.OrganizationType.LabAffiliations
  • org.nmdp.ngs.gtr.jaxb.OrganizationType.LabServices
  • org.nmdp.ngs.reads.paired.PairedEndAdapter (implements org.nmdp.ngs.reads.paired.PairedEndListener)
  • org.nmdp.ngs.reads.paired.PairedEndFastqReader
  • org.nmdp.ngs.align.ParallelBiojavaPairwiseAlignment
  • org.nmdp.ngs.gtr.jaxb.PersonnelType
  • org.nmdp.ngs.gtr.jaxb.PersonType
  • org.nmdp.ngs.gtr.jaxb.PersonType.Certification
  • org.nmdp.ngs.gtr.jaxb.PersonType.Name
  • org.nmdp.ngs.gtr.jaxb.PhenotypeSetType
  • org.nmdp.ngs.sra.jaxb.common.PipelineType
  • org.nmdp.ngs.sra.jaxb.submission.PipelineType
  • org.nmdp.ngs.sra.jaxb.study.PipelineType
  • org.nmdp.ngs.sra.jaxb.run.PipelineType
  • org.nmdp.ngs.sra.jaxb.sample.PipelineType
  • org.nmdp.ngs.sra.jaxb.analysis.PipelineType
  • org.nmdp.ngs.sra.jaxb.experiment.PipelineType
  • org.nmdp.ngs.sra.jaxb.common.PipelineType.PipeSection
  • org.nmdp.ngs.sra.jaxb.submission.PipelineType.PipeSection
  • org.nmdp.ngs.sra.jaxb.study.PipelineType.PipeSection
  • org.nmdp.ngs.sra.jaxb.run.PipelineType.PipeSection
  • org.nmdp.ngs.sra.jaxb.sample.PipelineType.PipeSection
  • org.nmdp.ngs.sra.jaxb.analysis.PipelineType.PipeSection
  • org.nmdp.ngs.sra.jaxb.experiment.PipelineType.PipeSection
  • org.nmdp.ngs.sra.jaxb.common.PlatformType
  • org.nmdp.ngs.sra.jaxb.submission.PlatformType
  • org.nmdp.ngs.sra.jaxb.study.PlatformType
  • org.nmdp.ngs.sra.jaxb.run.PlatformType
  • org.nmdp.ngs.sra.jaxb.sample.PlatformType
  • org.nmdp.ngs.sra.jaxb.analysis.PlatformType
  • org.nmdp.ngs.sra.jaxb.experiment.PlatformType
  • org.nmdp.ngs.sra.jaxb.common.PlatformType.AbiSolid
  • org.nmdp.ngs.sra.jaxb.submission.PlatformType.AbiSolid
  • org.nmdp.ngs.sra.jaxb.study.PlatformType.AbiSolid
  • org.nmdp.ngs.sra.jaxb.run.PlatformType.AbiSolid
  • org.nmdp.ngs.sra.jaxb.sample.PlatformType.AbiSolid
  • org.nmdp.ngs.sra.jaxb.analysis.PlatformType.AbiSolid
  • org.nmdp.ngs.sra.jaxb.experiment.PlatformType.AbiSolid
  • org.nmdp.ngs.sra.jaxb.common.PlatformType.Capillary
  • org.nmdp.ngs.sra.jaxb.submission.PlatformType.Capillary
  • org.nmdp.ngs.sra.jaxb.study.PlatformType.Capillary
  • org.nmdp.ngs.sra.jaxb.run.PlatformType.Capillary
  • org.nmdp.ngs.sra.jaxb.sample.PlatformType.Capillary
  • org.nmdp.ngs.sra.jaxb.analysis.PlatformType.Capillary
  • org.nmdp.ngs.sra.jaxb.experiment.PlatformType.Capillary
  • org.nmdp.ngs.sra.jaxb.common.PlatformType.CompleteGenomics
  • org.nmdp.ngs.sra.jaxb.submission.PlatformType.CompleteGenomics
  • org.nmdp.ngs.sra.jaxb.study.PlatformType.CompleteGenomics
  • org.nmdp.ngs.sra.jaxb.run.PlatformType.CompleteGenomics
  • org.nmdp.ngs.sra.jaxb.sample.PlatformType.CompleteGenomics
  • org.nmdp.ngs.sra.jaxb.analysis.PlatformType.CompleteGenomics
  • org.nmdp.ngs.sra.jaxb.experiment.PlatformType.CompleteGenomics
  • org.nmdp.ngs.sra.jaxb.common.PlatformType.Helicos
  • org.nmdp.ngs.sra.jaxb.submission.PlatformType.Helicos
  • org.nmdp.ngs.sra.jaxb.study.PlatformType.Helicos
  • org.nmdp.ngs.sra.jaxb.run.PlatformType.Helicos
  • org.nmdp.ngs.sra.jaxb.sample.PlatformType.Helicos
  • org.nmdp.ngs.sra.jaxb.analysis.PlatformType.Helicos
  • org.nmdp.ngs.sra.jaxb.experiment.PlatformType.Helicos
  • org.nmdp.ngs.sra.jaxb.common.PlatformType.Illumina
  • org.nmdp.ngs.sra.jaxb.submission.PlatformType.Illumina
  • org.nmdp.ngs.sra.jaxb.study.PlatformType.Illumina
  • org.nmdp.ngs.sra.jaxb.run.PlatformType.Illumina
  • org.nmdp.ngs.sra.jaxb.sample.PlatformType.Illumina
  • org.nmdp.ngs.sra.jaxb.analysis.PlatformType.Illumina
  • org.nmdp.ngs.sra.jaxb.experiment.PlatformType.Illumina
  • org.nmdp.ngs.sra.jaxb.common.PlatformType.IonTorrent
  • org.nmdp.ngs.sra.jaxb.submission.PlatformType.IonTorrent
  • org.nmdp.ngs.sra.jaxb.study.PlatformType.IonTorrent
  • org.nmdp.ngs.sra.jaxb.run.PlatformType.IonTorrent
  • org.nmdp.ngs.sra.jaxb.sample.PlatformType.IonTorrent
  • org.nmdp.ngs.sra.jaxb.analysis.PlatformType.IonTorrent
  • org.nmdp.ngs.sra.jaxb.experiment.PlatformType.IonTorrent
  • org.nmdp.ngs.sra.jaxb.common.PlatformType.Ls454
  • org.nmdp.ngs.sra.jaxb.submission.PlatformType.Ls454
  • org.nmdp.ngs.sra.jaxb.study.PlatformType.Ls454
  • org.nmdp.ngs.sra.jaxb.run.PlatformType.Ls454
  • org.nmdp.ngs.sra.jaxb.sample.PlatformType.Ls454
  • org.nmdp.ngs.sra.jaxb.analysis.PlatformType.Ls454
  • org.nmdp.ngs.sra.jaxb.experiment.PlatformType.Ls454
  • org.nmdp.ngs.sra.jaxb.common.PlatformType.PacbioSmrt
  • org.nmdp.ngs.sra.jaxb.submission.PlatformType.PacbioSmrt
  • org.nmdp.ngs.sra.jaxb.study.PlatformType.PacbioSmrt
  • org.nmdp.ngs.sra.jaxb.run.PlatformType.PacbioSmrt
  • org.nmdp.ngs.sra.jaxb.sample.PlatformType.PacbioSmrt
  • org.nmdp.ngs.sra.jaxb.analysis.PlatformType.PacbioSmrt
  • org.nmdp.ngs.sra.jaxb.experiment.PlatformType.PacbioSmrt
  • com.sun.tools.xjc.Plugin
    • org.nmdp.ngs.xjc.plugins.SentenceCasePlugin
  • org.nmdp.ngs.sra.jaxb.experiment.PoolMemberType
  • org.nmdp.ngs.sra.jaxb.experiment.PoolMemberType.ReadLabel
  • org.nmdp.ngs.sra.jaxb.common.ProcessingType
  • org.nmdp.ngs.sra.jaxb.submission.ProcessingType
  • org.nmdp.ngs.sra.jaxb.study.ProcessingType
  • org.nmdp.ngs.sra.jaxb.run.ProcessingType
  • org.nmdp.ngs.sra.jaxb.sample.ProcessingType
  • org.nmdp.ngs.sra.jaxb.analysis.ProcessingType
  • org.nmdp.ngs.sra.jaxb.experiment.ProcessingType
  • org.nmdp.ngs.hml.jaxb.Property
  • org.nmdp.ngs.range.rtree.RangeGeometries
  • org.nmdp.ngs.range.Ranges
  • org.nmdp.ngs.hml.jaxb.RawReads
  • org.nmdp.ngs.reads.quality.RealDistributionQualityStrategy (implements org.nmdp.ngs.reads.QualityStrategy)
  • org.nmdp.ngs.sra.jaxb.common.ReferenceAssemblyType
  • org.nmdp.ngs.sra.jaxb.submission.ReferenceAssemblyType
  • org.nmdp.ngs.sra.jaxb.study.ReferenceAssemblyType
  • org.nmdp.ngs.sra.jaxb.run.ReferenceAssemblyType
  • org.nmdp.ngs.sra.jaxb.sample.ReferenceAssemblyType
  • org.nmdp.ngs.sra.jaxb.analysis.ReferenceAssemblyType
  • org.nmdp.ngs.sra.jaxb.experiment.ReferenceAssemblyType
  • org.nmdp.ngs.sra.jaxb.common.ReferenceAssemblyType.Custom
  • org.nmdp.ngs.sra.jaxb.submission.ReferenceAssemblyType.Custom
  • org.nmdp.ngs.sra.jaxb.study.ReferenceAssemblyType.Custom
  • org.nmdp.ngs.sra.jaxb.run.ReferenceAssemblyType.Custom
  • org.nmdp.ngs.sra.jaxb.sample.ReferenceAssemblyType.Custom
  • org.nmdp.ngs.sra.jaxb.analysis.ReferenceAssemblyType.Custom
  • org.nmdp.ngs.sra.jaxb.experiment.ReferenceAssemblyType.Custom
  • org.nmdp.ngs.sra.jaxb.common.ReferenceAssemblyType.Custom.UrlLink
  • org.nmdp.ngs.sra.jaxb.submission.ReferenceAssemblyType.Custom.UrlLink
  • org.nmdp.ngs.sra.jaxb.study.ReferenceAssemblyType.Custom.UrlLink
  • org.nmdp.ngs.sra.jaxb.run.ReferenceAssemblyType.Custom.UrlLink
  • org.nmdp.ngs.sra.jaxb.sample.ReferenceAssemblyType.Custom.UrlLink
  • org.nmdp.ngs.sra.jaxb.analysis.ReferenceAssemblyType.Custom.UrlLink
  • org.nmdp.ngs.sra.jaxb.experiment.ReferenceAssemblyType.Custom.UrlLink
  • org.nmdp.ngs.sra.jaxb.common.ReferenceAssemblyType.Standard
  • org.nmdp.ngs.sra.jaxb.submission.ReferenceAssemblyType.Standard
  • org.nmdp.ngs.sra.jaxb.study.ReferenceAssemblyType.Standard
  • org.nmdp.ngs.sra.jaxb.run.ReferenceAssemblyType.Standard
  • org.nmdp.ngs.sra.jaxb.sample.ReferenceAssemblyType.Standard
  • org.nmdp.ngs.sra.jaxb.analysis.ReferenceAssemblyType.Standard
  • org.nmdp.ngs.sra.jaxb.experiment.ReferenceAssemblyType.Standard
  • org.nmdp.ngs.hml.jaxb.ReferenceDatabase
  • org.nmdp.ngs.hml.jaxb.ReferenceDatabase.ReferenceSequence
  • org.nmdp.ngs.sra.jaxb.common.ReferenceSequenceType
  • org.nmdp.ngs.sra.jaxb.submission.ReferenceSequenceType
  • org.nmdp.ngs.sra.jaxb.study.ReferenceSequenceType
  • org.nmdp.ngs.sra.jaxb.run.ReferenceSequenceType
  • org.nmdp.ngs.sra.jaxb.sample.ReferenceSequenceType
  • org.nmdp.ngs.sra.jaxb.analysis.ReferenceSequenceType
    • org.nmdp.ngs.sra.jaxb.analysis.Analysis.AnalysisType.SequenceVariation
  • org.nmdp.ngs.sra.jaxb.experiment.ReferenceSequenceType
  • org.nmdp.ngs.sra.jaxb.common.ReferenceSequenceType.Sequence
  • org.nmdp.ngs.sra.jaxb.submission.ReferenceSequenceType.Sequence
  • org.nmdp.ngs.sra.jaxb.study.ReferenceSequenceType.Sequence
  • org.nmdp.ngs.sra.jaxb.run.ReferenceSequenceType.Sequence
  • org.nmdp.ngs.sra.jaxb.sample.ReferenceSequenceType.Sequence
  • org.nmdp.ngs.sra.jaxb.analysis.ReferenceSequenceType.Sequence
  • org.nmdp.ngs.sra.jaxb.experiment.ReferenceSequenceType.Sequence
  • org.nmdp.ngs.hml.jaxb.ReportingCenter
  • org.nmdp.ngs.sra.jaxb.run.Run
  • org.nmdp.ngs.sra.jaxb.run.Run.DataBlock
  • org.nmdp.ngs.sra.jaxb.run.Run.DataBlock.Files
  • org.nmdp.ngs.sra.jaxb.run.Run.DataBlock.Files.File
  • org.nmdp.ngs.sra.jaxb.run.Run.ExperimentRef
  • org.nmdp.ngs.sra.jaxb.run.Run.RunAttributes
  • org.nmdp.ngs.sra.jaxb.run.Run.RunLinks
  • org.nmdp.ngs.sra.jaxb.run.Run.RunType
  • org.nmdp.ngs.sra.jaxb.run.RunSet
  • org.nmdp.ngs.feature.Sample
  • org.nmdp.ngs.hml.jaxb.Sample
  • org.nmdp.ngs.sra.jaxb.sample.Sample
  • org.nmdp.ngs.sra.jaxb.sample.Sample.SampleAttributes
  • org.nmdp.ngs.sra.jaxb.sample.Sample.SampleLinks
  • org.nmdp.ngs.sra.jaxb.sample.Sample.SampleName
  • org.nmdp.ngs.sra.jaxb.experiment.SampleDescriptorType
  • org.nmdp.ngs.sra.jaxb.experiment.SampleDescriptorType.Pool
  • org.nmdp.ngs.sra.jaxb.sample.SampleSet
  • org.nmdp.ngs.hml.jaxb.SbtNgs
  • org.nmdp.ngs.hml.jaxb.SbtSanger
  • org.nmdp.ngs.reads.quality.ScoreFunctionQualityStrategy (implements org.nmdp.ngs.reads.QualityStrategy)
  • org.nmdp.ngs.reads.quality.ScoreFunctions
  • org.nmdp.ngs.hml.jaxb.Sequence
    • org.nmdp.ngs.hml.jaxb.Amplification
    • org.nmdp.ngs.hml.jaxb.Gssp
    • org.nmdp.ngs.hml.jaxb.SubAmplification
  • org.nmdp.ngs.hml.jaxb.SequenceQuality
  • org.nmdp.ngs.sra.jaxb.common.SequencingDirectivesType
  • org.nmdp.ngs.sra.jaxb.submission.SequencingDirectivesType
  • org.nmdp.ngs.sra.jaxb.study.SequencingDirectivesType
  • org.nmdp.ngs.sra.jaxb.run.SequencingDirectivesType
  • org.nmdp.ngs.sra.jaxb.sample.SequencingDirectivesType
  • org.nmdp.ngs.sra.jaxb.analysis.SequencingDirectivesType
  • org.nmdp.ngs.sra.jaxb.experiment.SequencingDirectivesType
  • org.nmdp.ngs.gtr.jaxb.SetElementComplexType
  • org.nmdp.ngs.gtr.jaxb.SetElementType
  • org.nmdp.ngs.feature.parser.SimpleCharStream
  • org.nmdp.ngs.tools.SplitFasta (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.sra.jaxb.common.SpotDescriptorType
  • org.nmdp.ngs.sra.jaxb.submission.SpotDescriptorType
  • org.nmdp.ngs.sra.jaxb.study.SpotDescriptorType
  • org.nmdp.ngs.sra.jaxb.run.SpotDescriptorType
  • org.nmdp.ngs.sra.jaxb.sample.SpotDescriptorType
  • org.nmdp.ngs.sra.jaxb.analysis.SpotDescriptorType
  • org.nmdp.ngs.sra.jaxb.experiment.SpotDescriptorType
  • org.nmdp.ngs.sra.jaxb.common.SpotDescriptorType.SpotDecodeSpec
  • org.nmdp.ngs.sra.jaxb.submission.SpotDescriptorType.SpotDecodeSpec
  • org.nmdp.ngs.sra.jaxb.study.SpotDescriptorType.SpotDecodeSpec
  • org.nmdp.ngs.sra.jaxb.run.SpotDescriptorType.SpotDecodeSpec
  • org.nmdp.ngs.sra.jaxb.sample.SpotDescriptorType.SpotDecodeSpec
  • org.nmdp.ngs.sra.jaxb.analysis.SpotDescriptorType.SpotDecodeSpec
  • org.nmdp.ngs.sra.jaxb.experiment.SpotDescriptorType.SpotDecodeSpec
  • org.nmdp.ngs.sra.jaxb.common.SpotDescriptorType.SpotDecodeSpec.ReadSpec
  • org.nmdp.ngs.sra.jaxb.submission.SpotDescriptorType.SpotDecodeSpec.ReadSpec
  • org.nmdp.ngs.sra.jaxb.study.SpotDescriptorType.SpotDecodeSpec.ReadSpec
  • org.nmdp.ngs.sra.jaxb.run.SpotDescriptorType.SpotDecodeSpec.ReadSpec
  • org.nmdp.ngs.sra.jaxb.sample.SpotDescriptorType.SpotDecodeSpec.ReadSpec
  • org.nmdp.ngs.sra.jaxb.analysis.SpotDescriptorType.SpotDecodeSpec.ReadSpec
  • org.nmdp.ngs.sra.jaxb.experiment.SpotDescriptorType.SpotDecodeSpec.ReadSpec
  • org.nmdp.ngs.sra.jaxb.common.SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable
  • org.nmdp.ngs.sra.jaxb.submission.SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable
  • org.nmdp.ngs.sra.jaxb.study.SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable
  • org.nmdp.ngs.sra.jaxb.run.SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable
  • org.nmdp.ngs.sra.jaxb.sample.SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable
  • org.nmdp.ngs.sra.jaxb.analysis.SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable
  • org.nmdp.ngs.sra.jaxb.experiment.SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable
  • org.nmdp.ngs.sra.jaxb.common.SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable.Basecall
  • org.nmdp.ngs.sra.jaxb.submission.SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable.Basecall
  • org.nmdp.ngs.sra.jaxb.study.SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable.Basecall
  • org.nmdp.ngs.sra.jaxb.run.SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable.Basecall
  • org.nmdp.ngs.sra.jaxb.sample.SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable.Basecall
  • org.nmdp.ngs.sra.jaxb.analysis.SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable.Basecall
  • org.nmdp.ngs.sra.jaxb.experiment.SpotDescriptorType.SpotDecodeSpec.ReadSpec.ExpectedBasecallTable.Basecall
  • org.nmdp.ngs.sra.jaxb.common.SpotDescriptorType.SpotDecodeSpec.ReadSpec.RelativeOrder
  • org.nmdp.ngs.sra.jaxb.submission.SpotDescriptorType.SpotDecodeSpec.ReadSpec.RelativeOrder
  • org.nmdp.ngs.sra.jaxb.study.SpotDescriptorType.SpotDecodeSpec.ReadSpec.RelativeOrder
  • org.nmdp.ngs.sra.jaxb.run.SpotDescriptorType.SpotDecodeSpec.ReadSpec.RelativeOrder
  • org.nmdp.ngs.sra.jaxb.sample.SpotDescriptorType.SpotDecodeSpec.ReadSpec.RelativeOrder
  • org.nmdp.ngs.sra.jaxb.analysis.SpotDescriptorType.SpotDecodeSpec.ReadSpec.RelativeOrder
  • org.nmdp.ngs.sra.jaxb.experiment.SpotDescriptorType.SpotDecodeSpec.ReadSpec.RelativeOrder
  • org.nmdp.ngs.sra.SraReader
  • org.nmdp.ngs.sra.SraWriter
  • org.nmdp.ngs.hml.jaxb.Sso
  • org.nmdp.ngs.hml.jaxb.Ssp
  • org.nmdp.ngs.variant.vcf.StreamingVcfParser
  • org.nmdp.ngs.sra.jaxb.study.Study
  • org.nmdp.ngs.sra.jaxb.study.Study.Descriptor
  • org.nmdp.ngs.sra.jaxb.study.Study.Descriptor.RelatedStudies
  • org.nmdp.ngs.sra.jaxb.study.Study.Descriptor.RelatedStudies.RelatedStudy
  • org.nmdp.ngs.sra.jaxb.study.Study.Descriptor.StudyType
  • org.nmdp.ngs.sra.jaxb.study.Study.StudyAttributes
  • org.nmdp.ngs.sra.jaxb.study.Study.StudyLinks
  • org.nmdp.ngs.sra.jaxb.study.StudySet
  • org.nmdp.ngs.sra.jaxb.submission.Submission
  • org.nmdp.ngs.sra.jaxb.submission.Submission.Actions
  • org.nmdp.ngs.sra.jaxb.submission.Submission.Actions.Action
  • org.nmdp.ngs.sra.jaxb.submission.Submission.Actions.Action.Add
  • org.nmdp.ngs.sra.jaxb.submission.Submission.Actions.Action.Cancel
  • org.nmdp.ngs.sra.jaxb.submission.Submission.Actions.Action.Hold
  • org.nmdp.ngs.sra.jaxb.submission.Submission.Actions.Action.Modify
  • org.nmdp.ngs.sra.jaxb.submission.Submission.Actions.Action.Protect
  • org.nmdp.ngs.sra.jaxb.submission.Submission.Actions.Action.Release
  • org.nmdp.ngs.sra.jaxb.submission.Submission.Actions.Action.Suppress
  • org.nmdp.ngs.sra.jaxb.submission.Submission.Actions.Action.Validate
  • org.nmdp.ngs.sra.jaxb.submission.Submission.Contacts
  • org.nmdp.ngs.sra.jaxb.submission.Submission.Contacts.Contact
  • org.nmdp.ngs.sra.jaxb.submission.Submission.SubmissionAttributes
  • org.nmdp.ngs.sra.jaxb.submission.Submission.SubmissionLinks
  • org.nmdp.ngs.sra.jaxb.submission.SubmissionSet
  • org.nmdp.ngs.gtr.jaxb.SubmissionSummaryType
  • org.nmdp.ngs.reads.mutation.SubstitutionMutationStrategy (implements org.nmdp.ngs.reads.MutationStrategy)
  • org.nmdp.ngs.gtr.jaxb.TextCitations
    • org.nmdp.ngs.gtr.jaxb.MeasureTraitType.ClinicalSignificance
  • org.nmdp.ngs.gtr.jaxb.TextCitationsList
    • org.nmdp.ngs.gtr.jaxb.GTRLabTestType.ClinicalUtility
  • org.nmdp.ngs.gtr.jaxb.TextCitationsURL
  • org.nmdp.ngs.gtr.jaxb.TextURL
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Error
      • org.nmdp.ngs.feature.parser.TokenMgrError
    • java.lang.Exception
      • org.biojava.bio.BioException
        • org.nmdp.ngs.feature.LocusException
          • org.nmdp.ngs.feature.AlleleException
        • org.nmdp.ngs.feature.VcfFileException
      • org.nmdp.ngs.hml.HmlValidationException
      • org.nmdp.ngs.feature.parser.ParseException
      • java.lang.RuntimeException
        • org.nmdp.ngs.reads.paired.PairedEndFastqReaderException
  • org.nmdp.ngs.feature.parser.Token (implements java.io.Serializable)
  • org.nmdp.ngs.gtr.jaxb.TraitSetType
  • org.nmdp.ngs.gtr.jaxb.TraitSetType.Trait
  • org.nmdp.ngs.hml.jaxb.Typing
  • org.nmdp.ngs.hml.jaxb.TypingMethod
  • org.nmdp.ngs.hml.jaxb.TypingTestName
  • org.nmdp.ngs.hml.jaxb.TypingTestNames
  • org.nmdp.ngs.gtr.jaxb.URL
  • org.nmdp.ngs.sra.jaxb.common.UrlType
  • org.nmdp.ngs.sra.jaxb.submission.UrlType
  • org.nmdp.ngs.sra.jaxb.study.UrlType
  • org.nmdp.ngs.sra.jaxb.run.UrlType
  • org.nmdp.ngs.sra.jaxb.sample.UrlType
  • org.nmdp.ngs.sra.jaxb.analysis.UrlType
  • org.nmdp.ngs.sra.jaxb.experiment.UrlType
  • org.nmdp.ngs.tools.ValidateHml (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.tools.ValidateInterleavedFastq (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.tools.ValidateInterpretation (implements java.util.concurrent.Callable<V>)
  • org.nmdp.ngs.hml.jaxb.Variant
  • org.nmdp.ngs.hml.jaxb.VariantEffect
  • org.nmdp.ngs.feature.VcfFile
  • org.nmdp.ngs.feature.VcfFile.Header
  • org.nmdp.ngs.feature.VcfFile.Iterator (implements java.util.Iterator<E>)
  • org.nmdp.ngs.feature.VcfFile.Metadata
    • org.nmdp.ngs.feature.VcfFile.Filter
    • org.nmdp.ngs.feature.VcfFile.Info
      • org.nmdp.ngs.feature.VcfFile.Format
  • org.nmdp.ngs.variant.vcf.VcfGenome
  • org.nmdp.ngs.variant.vcf.VcfGenotype
  • org.nmdp.ngs.variant.vcf.VcfGenotype.Builder
  • org.nmdp.ngs.variant.vcf.VcfHeader
  • org.nmdp.ngs.variant.vcf.VcfHeader.Builder
  • org.nmdp.ngs.variant.vcf.VcfHeaderParser
  • org.nmdp.ngs.variant.vcf.VcfParseAdapter (implements org.nmdp.ngs.variant.vcf.VcfParseListener)
  • org.nmdp.ngs.variant.vcf.VcfParser
  • org.nmdp.ngs.variant.vcf.VcfReader
  • org.nmdp.ngs.variant.vcf.VcfRecord
  • org.nmdp.ngs.feature.VcfRecord
  • org.nmdp.ngs.variant.vcf.VcfRecord.Builder
  • org.nmdp.ngs.variant.vcf.VcfRecordParser
  • org.nmdp.ngs.variant.vcf.VcfSample
  • org.nmdp.ngs.variant.vcf.VcfSample.Builder
  • org.nmdp.ngs.variant.vcf.VcfSampleParser
  • org.nmdp.ngs.variant.vcf.VcfStreamAdapter (implements org.nmdp.ngs.variant.vcf.VcfStreamListener)
  • org.nmdp.ngs.variant.vcf.VcfWriter
  • org.nmdp.ngs.gtr.jaxb.XrefType
  • org.nmdp.ngs.sra.jaxb.common.XRefType
  • org.nmdp.ngs.sra.jaxb.submission.XRefType
  • org.nmdp.ngs.sra.jaxb.study.XRefType
  • org.nmdp.ngs.sra.jaxb.run.XRefType
  • org.nmdp.ngs.sra.jaxb.sample.XRefType
  • org.nmdp.ngs.sra.jaxb.analysis.XRefType
  • org.nmdp.ngs.sra.jaxb.experiment.XRefType

Interface Hierarchy

• org.nmdp.ngs.align.BedListener
• org.nmdp.ngs.reads.CoverageStrategy
• org.nmdp.ngs.feature.parser.FeatureParserConstants
• org.nmdp.ngs.hml.HmlValidationRule
  • org.nmdp.ngs.hml.HmlValidator
• org.nmdp.ngs.align.HspListener
• org.nmdp.ngs.fca.Lattice<T>
• org.nmdp.ngs.reads.MutationStrategy
• org.nmdp.ngs.reads.paired.PairedEndListener
• org.nmdp.ngs.align.PairwiseAlignment
• org.nmdp.ngs.fca.Partial<T>
• org.nmdp.ngs.reads.QualityStrategy
• org.nmdp.ngs.range.tree.RangeTree<C>
• org.nmdp.ngs.reads.quality.ScoreFunction
• org.nmdp.ngs.variant.vcf.VcfParseListener
• org.nmdp.ngs.variant.vcf.VcfStreamListener

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.nmdp.ngs.fca.Partial.Order
    • org.nmdp.ngs.fca.Partial.Order.Direction
    • org.nmdp.ngs.feature.VcfFile.Strictness
    • org.nmdp.ngs.feature.VcfFile.Metadata.Type
    • org.nmdp.ngs.feature.Allele.Lesion
    • org.nmdp.ngs.hml.jaxb.Present
    • org.nmdp.ngs.sra.LibrarySelection
    • org.nmdp.ngs.sra.StudyType
    • org.nmdp.ngs.sra.LibraryStrategy
    • org.nmdp.ngs.sra.LibrarySource
    • org.nmdp.ngs.sra.FileType
    • org.nmdp.ngs.sra.InstrumentModel