Hierarchy For All Packages

Package Hierarchies:

• io.github.bigbio.pgatk.io.apl,
• io.github.bigbio.pgatk.io.braf,
• io.github.bigbio.pgatk.io.clustering,
• io.github.bigbio.pgatk.io.clustering.indexing,
• io.github.bigbio.pgatk.io.common,
• io.github.bigbio.pgatk.io.common.cluster,
• io.github.bigbio.pgatk.io.common.modification,
• io.github.bigbio.pgatk.io.common.psms,
• io.github.bigbio.pgatk.io.common.spectra,
• io.github.bigbio.pgatk.io.mapcache,
• io.github.bigbio.pgatk.io.mgf,
• io.github.bigbio.pgatk.io.msp,
• io.github.bigbio.pgatk.io.mzml,
• io.github.bigbio.pgatk.io.mzxml,
• io.github.bigbio.pgatk.io.mzxml.mzxml.model,
• io.github.bigbio.pgatk.io.mzxml.mzxml.unmarshaller,
• io.github.bigbio.pgatk.io.mzxml.mzxml.xml.util,
• io.github.bigbio.pgatk.io.objectdb,
• io.github.bigbio.pgatk.io.pride,
• io.github.bigbio.pgatk.io.properties,
• io.github.bigbio.pgatk.io.utils,
• io.github.bigbio.pgatk.io.utils.msnumpress

Class Hierarchy

• java.lang.Object
  • io.github.bigbio.pgatk.io.pride.AccessionLocalization
  • io.github.bigbio.pgatk.io.pride.AnnotatedSpectrum (implements io.github.bigbio.pgatk.io.common.spectra.Spectrum)
  • io.github.bigbio.pgatk.io.apl.AplIndexedReader (implements io.github.bigbio.pgatk.io.common.MzIterableReader, io.github.bigbio.pgatk.io.common.MzReader)
  • io.github.bigbio.pgatk.io.apl.AplSpectrum (implements io.github.bigbio.pgatk.io.common.spectra.Spectrum)
  • io.github.bigbio.pgatk.io.pride.ArchiveSpectrum (implements io.github.bigbio.pgatk.io.common.spectra.Spectrum)
  • io.github.bigbio.pgatk.io.pride.AvroModification
  • io.github.bigbio.pgatk.io.pride.AvroTerm
  • io.github.bigbio.pgatk.io.pride.AvroTuple
  • io.github.bigbio.pgatk.io.pride.BinaryPeaks
  • io.github.bigbio.pgatk.io.properties.BinaryPropertyStorage (implements java.io.Serializable)
  • io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster (implements io.github.bigbio.pgatk.io.common.cluster.ICluster)
  • io.github.bigbio.pgatk.io.clustering.indexing.ClusteringFileIndex
  • io.github.bigbio.pgatk.io.clustering.indexing.ClusteringFileIndexer (implements io.github.bigbio.pgatk.io.clustering.indexing.IIndexer)
  • io.github.bigbio.pgatk.io.common.cluster.ClusteringFileModification (implements io.github.bigbio.pgatk.io.common.modification.IModification)
  • io.github.bigbio.pgatk.io.common.cluster.ClusteringFilePSM (implements io.github.bigbio.pgatk.io.common.psms.IPeptideSpectrumMatch)
  • io.github.bigbio.pgatk.io.clustering.ClusteringFileReader (implements io.github.bigbio.pgatk.io.clustering.IClusterSourceReader)
  • io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference (implements io.github.bigbio.pgatk.io.common.cluster.ISpectrumReference)
  • io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference.Peak
  • io.github.bigbio.pgatk.io.clustering.indexing.ClusteringIndexElement (implements java.io.Serializable)
  • io.github.bigbio.pgatk.io.common.CvParam (implements io.github.bigbio.pgatk.io.common.Param, java.io.Serializable)
  • io.github.bigbio.pgatk.io.pride.CvParam
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.objectdb.DbMutex
  • io.github.bigbio.pgatk.io.common.DefaultSpectrum (implements java.io.Serializable, io.github.bigbio.pgatk.io.common.spectra.Spectrum)
  • io.github.bigbio.pgatk.io.pride.ExonInfo
  • io.github.bigbio.pgatk.io.pride.GeneCoordinates
  • io.github.bigbio.pgatk.io.pride.IdentifiedModification
  • io.github.bigbio.pgatk.io.common.IndexElementImpl (implements io.github.bigbio.pgatk.io.common.IndexElement)
  • io.github.bigbio.pgatk.io.properties.InMemoryPropertyStorage (implements io.github.bigbio.pgatk.io.properties.IPropertyStorage)
    • io.github.bigbio.pgatk.io.properties.ChronicleMapPropertyStorage<T>
    • io.github.bigbio.pgatk.io.properties.EcachePropertyStorage<V>
    • io.github.bigbio.pgatk.io.properties.LevelDBPropertyStorage<T>
    • io.github.bigbio.pgatk.io.properties.MapDBPropertyStorage<T>
    • io.github.bigbio.pgatk.io.properties.SparkeyPropertyStorage<T>
  • io.github.bigbio.pgatk.io.properties.KnownProperties
  • io.github.bigbio.pgatk.io.msp.LibrarySpectrumBuilder
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.mgf.MgfIndexedReader (implements io.github.bigbio.pgatk.io.common.MzIterableReader, io.github.bigbio.pgatk.io.common.MzReader)
  • io.github.bigbio.pgatk.io.mgf.MgfUtils
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.ModelConstants
  • io.github.bigbio.pgatk.io.mgf.Ms2Query (implements io.github.bigbio.pgatk.io.common.spectra.Spectrum)
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.utils.msnumpress.MSNumpress
  • io.github.bigbio.pgatk.io.msp.MspAttributeReader
  • io.github.bigbio.pgatk.io.msp.MspSpectrum (implements io.github.bigbio.pgatk.io.common.spectra.Spectrum)
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.common.MzIterableChannelReader
    • io.github.bigbio.pgatk.io.mgf.MgfIterableReader (implements io.github.bigbio.pgatk.io.common.MzIterableReader)
    • io.github.bigbio.pgatk.io.msp.MspIterableReader (implements io.github.bigbio.pgatk.io.common.MzIterableReader)
    • io.github.bigbio.pgatk.io.mzxml.MzXMLIterableReader (implements io.github.bigbio.pgatk.io.common.MzIterableReader)
  • io.github.bigbio.pgatk.io.mzml.MzMlIndexedReader (implements io.github.bigbio.pgatk.io.common.MzIterableReader, io.github.bigbio.pgatk.io.common.MzReader)
  • io.github.bigbio.pgatk.io.mzml.MzMLSpectrum (implements io.github.bigbio.pgatk.io.common.spectra.Spectrum)
  • io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader (implements io.github.bigbio.pgatk.io.common.MzReader)
  • io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader.MzXMLScanIterator (implements java.lang.Iterable<T>, java.util.Iterator<E>)
  • io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader.SpectrumIterator (implements java.util.Iterator<E>)
  • io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum (implements io.github.bigbio.pgatk.io.common.spectra.Spectrum)
  • io.github.bigbio.pgatk.io.mzxml.mzxml.unmarshaller.MzXMLUnmarshallerFactory
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.NameValue (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory
  • io.github.bigbio.pgatk.io.objectdb.ObjectsCache
  • io.github.bigbio.pgatk.io.objectdb.ObjectsDB
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.OntologyEntry (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
    • io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsManufacturer (implements java.io.Serializable)
    • io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsMassAnalyzer (implements java.io.Serializable)
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.Orientation (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.ParentFile (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.Pattern (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.clustering.PeakMzComparator (implements java.util.Comparator<T>)
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.pride.PrideAvroReader
  • io.github.bigbio.pgatk.io.pride.PrideAvroWriter
  • io.github.bigbio.pgatk.io.pride.PrideJsonIndexedReader (implements io.github.bigbio.pgatk.io.common.MzReader)
  • io.github.bigbio.pgatk.io.pride.PrideJsonIterableReader (implements io.github.bigbio.pgatk.io.common.MzIterableReader)
  • io.github.bigbio.pgatk.io.pride.PrideJsonWriter
  • io.github.bigbio.pgatk.io.properties.PropertyStorageFactory
  • java.io.RandomAccessFile (implements java.io.Closeable, java.io.DataInput, java.io.DataOutput)
    • io.github.bigbio.pgatk.io.braf.BufferedRandomAccessFile
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.Robot (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.ScanOrigin (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.Separation (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.SeparationTechnique (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.common.psms.SequenceCount
  • io.github.bigbio.pgatk.io.objectdb.SimpleSemaphore
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.Software (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spot (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spotting (implements io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject, java.io.Serializable)
  • io.github.bigbio.pgatk.io.properties.StoredProperties
  • io.github.bigbio.pgatk.io.utils.StringUtils
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • io.github.bigbio.pgatk.io.mzxml.MzXMLParsingException
      • io.github.bigbio.pgatk.io.common.PgatkIOException
  • io.github.bigbio.pgatk.io.utils.Triple<K,V,T> (implements java.io.Serializable)
  • io.github.bigbio.pgatk.io.utils.Tuple<K,V> (implements io.github.bigbio.pgatk.io.utils.ITuple<K,V>)
  • javax.xml.bind.annotation.adapters.XmlAdapter<ValueType,BoundType>
    • io.github.bigbio.pgatk.io.mzxml.mzxml.xml.util.AnySimpleTypeAdapter
    • io.github.bigbio.pgatk.io.mzxml.mzxml.xml.util.NonNegativeIntegerAdapter
  • org.zoodb.api.impl.ZooPC (implements java.io.Serializable)
    • io.github.bigbio.pgatk.io.objectdb.DbObject
      • io.github.bigbio.pgatk.io.objectdb.LongObject
        • io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage
        • io.github.bigbio.pgatk.io.common.SpectrumProperty

Interface Hierarchy

• java.lang.Comparable<T>
  • io.github.bigbio.pgatk.io.common.modification.IModification
• io.github.bigbio.pgatk.io.clustering.IClusterSourceListener
• io.github.bigbio.pgatk.io.clustering.indexing.IIndexer
• io.github.bigbio.pgatk.io.common.psms.IPeptideSpectrumMatch
• java.util.Iterator<E>
  • io.github.bigbio.pgatk.io.clustering.IClusterSourceReader
  • io.github.bigbio.pgatk.io.common.MzIterableReader (also extends java.io.Serializable)
    • io.github.bigbio.pgatk.io.clustering.IClusterSourceReader
• io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXMLObject
• io.github.bigbio.pgatk.io.mzxml.mzxml.unmarshaller.MzXMLUnmarshaller
• java.io.Serializable
  • io.github.bigbio.pgatk.io.common.cluster.ICluster
  • io.github.bigbio.pgatk.io.clustering.IClusterSourceReader
  • io.github.bigbio.pgatk.io.mapcache.IMapStorage<V>
    • io.github.bigbio.pgatk.io.properties.IPropertyStorage
  • io.github.bigbio.pgatk.io.common.IndexElement
  • io.github.bigbio.pgatk.io.properties.IPropertyStorage
  • io.github.bigbio.pgatk.io.common.cluster.ISpectrumReference
  • io.github.bigbio.pgatk.io.utils.ITuple<K,V>
  • io.github.bigbio.pgatk.io.common.MzIterableReader (also extends java.util.Iterator<E>)
    • io.github.bigbio.pgatk.io.clustering.IClusterSourceReader
  • io.github.bigbio.pgatk.io.common.MzReader
  • io.github.bigbio.pgatk.io.common.Param
  • io.github.bigbio.pgatk.io.common.spectra.Spectrum
    • io.github.bigbio.pgatk.io.common.cluster.ICluster
    • io.github.bigbio.pgatk.io.common.cluster.ISpectrumReference
• io.github.bigbio.pgatk.io.objectdb.UrParameter
• io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • io.github.bigbio.pgatk.io.mzml.MzMlIndexedReader.MZML_PARAMS
    • io.github.bigbio.pgatk.io.utils.AminoAcid
    • io.github.bigbio.pgatk.io.mgf.MgfUtils.FragmentToleranceUnits
    • io.github.bigbio.pgatk.io.mgf.MgfUtils.MassType
    • io.github.bigbio.pgatk.io.mgf.MgfUtils.SearchType
    • io.github.bigbio.pgatk.io.mgf.MgfUtils.ReportType
    • io.github.bigbio.pgatk.io.mgf.MgfUtils.PeptideToleranceUnit
    • io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXmlElement