Hierarchy For All Packages

Package Hierarchies:

• org.biojava.nbio.genome,
• org.biojava.nbio.genome.homology,
• org.biojava.nbio.genome.io.fastq,
• org.biojava.nbio.genome.parsers.cytoband,
• org.biojava.nbio.genome.parsers.geneid,
• org.biojava.nbio.genome.parsers.genename,
• org.biojava.nbio.genome.parsers.gff,
• org.biojava.nbio.genome.parsers.twobit,
• org.biojava.nbio.genome.query,
• org.biojava.nbio.genome.uniprot,
• org.biojava.nbio.genome.util

Class Hierarchy

• java.lang.Object
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        • org.biojava.nbio.genome.parsers.gff.FeatureList
  • org.biojava.nbio.genome.App
  • org.biojava.nbio.genome.homology.BlastHomologyHits
  • org.biojava.nbio.genome.query.BlastXMLQuery
  • org.biojava.nbio.genome.util.ChromosomeMappingTools
  • org.biojava.nbio.genome.parsers.genename.ChromPos
  • org.biojava.nbio.genome.parsers.cytoband.Cytoband (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.nbio.genome.parsers.cytoband.CytobandParser
  • org.biojava.nbio.genome.io.fastq.Fastq
  • org.biojava.nbio.genome.io.fastq.FastqBuilder
  • org.biojava.nbio.genome.io.fastq.FastqTools
  • org.biojava.nbio.genome.parsers.gff.Feature (implements org.biojava.nbio.genome.parsers.gff.FeatureI)
  • org.biojava.nbio.genome.parsers.gff.FeatureHelper
  • org.biojava.nbio.genome.parsers.gff.GCStats
  • org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser
  • org.biojava.nbio.genome.GeneFeatureHelper
  • org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader
  • org.biojava.nbio.genome.parsers.geneid.GeneIDXMLReader
  • org.biojava.nbio.genome.parsers.gff.GeneMarkGTFReader
  • org.biojava.nbio.genome.parsers.genename.GeneName (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.biojava.nbio.genome.parsers.genename.GeneNamesParser
  • org.biojava.nbio.genome.homology.GFF3FromUniprotBlastHits
  • org.biojava.nbio.genome.parsers.gff.GFF3Reader
  • org.biojava.nbio.genome.parsers.gff.GFF3Writer
  • org.biojava.nbio.genome.io.fastq.IlluminaFastqReader
  • org.biojava.nbio.genome.io.fastq.IlluminaFastqWriter
  • java.io.InputStream (implements java.io.Closeable)
    • org.biojava.nbio.genome.parsers.twobit.TwoBitParser
  • org.biojava.nbio.genome.parsers.gff.Location (implements java.lang.Iterable<T>)
  • org.biojava.nbio.genome.parsers.gff.LocIterator (implements java.util.Iterator<E>)
  • org.biojava.nbio.genome.query.OutputHitsGFF
  • org.biojava.nbio.genome.util.ProteinMappingTools
  • org.biojava.nbio.genome.io.fastq.SangerFastqReader
  • org.biojava.nbio.genome.io.fastq.SangerFastqWriter
  • org.biojava.nbio.genome.parsers.twobit.SimpleTwoBitFileProvider
  • org.biojava.nbio.genome.io.fastq.SolexaFastqReader
  • org.biojava.nbio.genome.io.fastq.SolexaFastqWriter
  • org.biojava.nbio.genome.util.SplitFasta
  • org.biojava.nbio.genome.parsers.twobit.TwoBitFacade
  • org.biojava.nbio.genome.uniprot.UniprotToFasta

Interface Hierarchy

• org.biojava.nbio.genome.io.fastq.FastqReader
• org.biojava.nbio.genome.io.fastq.FastqWriter
• org.biojava.nbio.genome.parsers.gff.FeatureI
• org.biojava.nbio.genome.io.fastq.ParseListener
• org.biojava.nbio.genome.io.fastq.StreamListener

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.biojava.nbio.genome.io.fastq.FastqVariant
    • org.biojava.nbio.genome.parsers.cytoband.StainType (implements java.io.Serializable)