所有程序包的分层结构

程序包分层结构:

• edu.sysu.pmglab.gbc,
• edu.sysu.pmglab.gbc.annotation,
• edu.sysu.pmglab.gbc.annotation.impl,
• edu.sysu.pmglab.gbc.annotation.impl.clinvar,
• edu.sysu.pmglab.gbc.annotation.impl.dbnsfp,
• edu.sysu.pmglab.gbc.annotation.impl.dbSNP,
• edu.sysu.pmglab.gbc.annotation.impl.liftOver,
• edu.sysu.pmglab.gbc.annotation.impl.regBase,
• edu.sysu.pmglab.gbc.command,
• edu.sysu.pmglab.gbc.linkagedisequilibrium,
• edu.sysu.pmglab.gbc.qualitycontrol,
• edu.sysu.pmglab.gbc.qualitycontrol.genotype,
• edu.sysu.pmglab.gbc.qualitycontrol.info,
• edu.sysu.pmglab.gbc.qualitycontrol.variant,
• edu.sysu.pmglab.gbc.toolkit,
• edu.sysu.pmglab.gbc.toolkit.bed,
• edu.sysu.pmglab.gbc.variant,
• edu.sysu.pmglab.gbc.variant.genotype

类分层结构

• java.lang.Object
  • edu.sysu.pmglab.gbc.annotation.impl.AnnotateField (implements java.lang.Iterable<T>)
  • edu.sysu.pmglab.gbc.toolkit.BEDExporter
  • edu.sysu.pmglab.gbc.toolkit.bed.BEDGenotypes (implements edu.sysu.pmglab.gbc.variant.genotype.IGenotypes)
  • edu.sysu.pmglab.gbc.toolkit.bed.BEDPartWriter (implements java.lang.AutoCloseable, java.io.Closeable)
  • edu.sysu.pmglab.gbc.toolkit.bed.BEDReader (implements java.lang.AutoCloseable, java.io.Closeable)
  • edu.sysu.pmglab.gbc.toolkit.bed.BEDWriter (implements java.lang.AutoCloseable, java.io.Closeable)
  • edu.sysu.pmglab.gbc.variant.genotype.CacheGenotypes (implements edu.sysu.pmglab.gbc.variant.genotype.IGenotypes)
  • edu.sysu.pmglab.ccf.CCFFormat
    • edu.sysu.pmglab.gbc.GTBFormat
  • edu.sysu.pmglab.gbc.variant.Chromosome (implements java.lang.Comparable<T>)
  • edu.sysu.pmglab.gbc.annotation.impl.dbSNP.CoordinateBasedDBSNP (implements java.lang.AutoCloseable, java.io.Closeable)
  • edu.sysu.pmglab.gbc.annotation.Database (implements java.lang.Iterable<T>)
    • edu.sysu.pmglab.gbc.annotation.CCFCoordinateDatabase
    • edu.sysu.pmglab.gbc.annotation.CCFCoordinateRangeDatabase
    • edu.sysu.pmglab.gbc.annotation.CCFMapperDatabase
    • edu.sysu.pmglab.gbc.annotation.GTBDatabase
      • edu.sysu.pmglab.gbc.annotation.impl.clinvar.ClinVar
      • edu.sysu.pmglab.gbc.annotation.impl.clinvar.ClinVarDatabase
      • edu.sysu.pmglab.gbc.annotation.impl.dbnsfp.dbNSFPRankScore
      • edu.sysu.pmglab.gbc.annotation.impl.dbnsfp.dbNSFPRankScoreDatabase
      • edu.sysu.pmglab.gbc.annotation.impl.dbSNP.DBSNPDatabase
      • edu.sysu.pmglab.gbc.annotation.impl.regBase.RegBaseDatabase
    • edu.sysu.pmglab.gbc.annotation.impl.liftOver.LiftOverDatabase
  • edu.sysu.pmglab.gbc.annotation.Database.Reader
    • edu.sysu.pmglab.gbc.annotation.CCFCoordinateDatabase.Reader
    • edu.sysu.pmglab.gbc.annotation.CCFCoordinateRangeDatabase.Reader
    • edu.sysu.pmglab.gbc.annotation.CCFCoordinateRangeDatabase.ReaderWithOverlapInterval
    • edu.sysu.pmglab.gbc.annotation.CCFMapperDatabase.Reader
    • edu.sysu.pmglab.gbc.annotation.GTBDatabase.Reader
  • edu.sysu.pmglab.gbc.command.GBCEntry
  • edu.sysu.pmglab.gbc.variant.genotype.Genotype
  • edu.sysu.pmglab.gbc.qualitycontrol.genotype.GenotypeADController (implements edu.sysu.pmglab.gbc.qualitycontrol.genotype.IGenotypeController)
  • edu.sysu.pmglab.gbc.qualitycontrol.genotype.GenotypeDPController (implements edu.sysu.pmglab.gbc.qualitycontrol.genotype.IGenotypeController)
  • edu.sysu.pmglab.gbc.qualitycontrol.genotype.GenotypeGQController (implements edu.sysu.pmglab.gbc.qualitycontrol.genotype.IGenotypeController)
  • edu.sysu.pmglab.gbc.qualitycontrol.genotype.GenotypePLController (implements edu.sysu.pmglab.gbc.qualitycontrol.genotype.IGenotypeController)
  • edu.sysu.pmglab.gbc.variant.genotype.Genotypes (implements edu.sysu.pmglab.gbc.variant.genotype.IGenotypes)
  • edu.sysu.pmglab.gbc.variant.genotype.GenotypeSequenceEncoder
  • edu.sysu.pmglab.gbc.GTBFilter
  • edu.sysu.pmglab.gbc.GTBIndexer
  • edu.sysu.pmglab.gbc.GTBManager
  • edu.sysu.pmglab.gbc.GTBPartWriter
  • edu.sysu.pmglab.gbc.GTBReader (implements java.lang.AutoCloseable, java.lang.Iterable<T>)
  • edu.sysu.pmglab.gbc.GTBWriter
  • edu.sysu.pmglab.gbc.GTBWriter.Builder
  • edu.sysu.pmglab.gbc.command.IndexParser
  • edu.sysu.pmglab.gbc.variant.Individual
  • edu.sysu.pmglab.gbc.annotation.impl.liftOver.LiftOver
  • edu.sysu.pmglab.gbc.annotation.impl.liftOver.LiftOver.Chain
  • edu.sysu.pmglab.easytools.Parallelizable
    • edu.sysu.pmglab.gbc.toolkit.GTBAppender
      • edu.sysu.pmglab.gbc.annotation.GTBAppendAnnotator
    • edu.sysu.pmglab.gbc.toolkit.GTBConcat
    • edu.sysu.pmglab.gbc.toolkit.GTBEditor
      • edu.sysu.pmglab.gbc.annotation.GTBAnnotator
      • edu.sysu.pmglab.gbc.toolkit.GTBExporter
      • edu.sysu.pmglab.gbc.toolkit.GTBSorter
      • edu.sysu.pmglab.gbc.toolkit.GTBSplitter
      • edu.sysu.pmglab.gbc.toolkit.TSVExporter
      • edu.sysu.pmglab.gbc.toolkit.VCFExporter
    • edu.sysu.pmglab.gbc.GTBIndexer.Builder
    • edu.sysu.pmglab.gbc.toolkit.GTBMerger
    • edu.sysu.pmglab.gbc.linkagedisequilibrium.LDCalculator
    • edu.sysu.pmglab.gbc.MAF2GTB
    • edu.sysu.pmglab.gbc.VCF2GTB
  • edu.sysu.pmglab.gbc.annotation.impl.regBase.RegBase (implements java.lang.AutoCloseable, java.io.Closeable)
  • edu.sysu.pmglab.gbc.annotation.impl.dbSNP.RSBasedDBSNP (implements java.lang.AutoCloseable, java.io.Closeable)
  • edu.sysu.pmglab.gbc.toolkit.bed.SeekableBEDReader (implements java.lang.AutoCloseable, java.io.Closeable)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • java.lang.RuntimeException
        • edu.sysu.pmglab.gbc.variant.genotype.BEGCoderException
        • edu.sysu.pmglab.gbc.annotation.DatabaseException
        • edu.sysu.pmglab.gbc.GTBComponentException
  • edu.sysu.pmglab.container.TrieTree<T> (implements java.lang.Cloneable, java.lang.Iterable<T>)
    • edu.sysu.pmglab.ccf.CCFMeta
      • edu.sysu.pmglab.gbc.GTBMeta
  • edu.sysu.pmglab.gbc.variant.Variant (implements java.lang.Comparable<T>)
  • edu.sysu.pmglab.gbc.qualitycontrol.variant.VariantACController (implements java.util.function.Function<T,R>)
  • edu.sysu.pmglab.gbc.qualitycontrol.variant.VariantAFController (implements java.util.function.Function<T,R>)
  • edu.sysu.pmglab.gbc.qualitycontrol.VariantAlleleNumController (implements java.util.function.Function<T,R>)
  • edu.sysu.pmglab.gbc.qualitycontrol.variant.VariantANController (implements java.util.function.Function<T,R>)
  • edu.sysu.pmglab.gbc.qualitycontrol.info.VariantFieldController (implements java.util.function.Function<T,R>)
  • edu.sysu.pmglab.gbc.qualitycontrol.info.VariantFSController (implements java.util.function.Function<T,R>)
  • edu.sysu.pmglab.gbc.qualitycontrol.info.VariantMQController (implements java.util.function.Function<T,R>)
  • edu.sysu.pmglab.gbc.qualitycontrol.VariantPhredQualityScoreController (implements java.util.function.Function<T,R>)
  • edu.sysu.pmglab.gbc.variant.Variants (implements java.lang.Comparable<T>, java.lang.Iterable<T>)

接口分层结构

• java.util.function.BiFunction<T,U,R>
  • edu.sysu.pmglab.gbc.qualitycontrol.genotype.IGenotypeController
• edu.sysu.pmglab.gbc.linkagedisequilibrium.ILDModel
• edu.sysu.pmglab.gbc.linkagedisequilibrium.ILDProperty
• java.lang.Iterable<T>
  • edu.sysu.pmglab.gbc.variant.genotype.IGenotypes
• edu.sysu.pmglab.gbc.variant.genotype.MBEGDecoder
• edu.sysu.pmglab.gbc.variant.genotype.MBEGEncoder

枚举分层结构

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • edu.sysu.pmglab.gbc.toolkit.GTBMerger.MergeOperator
    • edu.sysu.pmglab.gbc.variant.PositionType
    • edu.sysu.pmglab.gbc.variant.Strand
    • edu.sysu.pmglab.gbc.variant.Codon
    • edu.sysu.pmglab.gbc.linkagedisequilibrium.HaplotypeLD (implements edu.sysu.pmglab.gbc.linkagedisequilibrium.ILDModel)
    • edu.sysu.pmglab.gbc.linkagedisequilibrium.GenotypeLD (implements edu.sysu.pmglab.gbc.linkagedisequilibrium.ILDModel)
    • edu.sysu.pmglab.gbc.GTBManager.Type
    • edu.sysu.pmglab.gbc.variant.RefGenomeVersion