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Package org.broad.igv.feature

Abstract
abstract class AbstractCacher
Class to handle caching data f rom any source of features Su bclasses must override qu...
Abstract
abstract class AbstractFeature
Abstract
abstract class AbstractFeatureParser
class AminoAcid
class AminoAcidManager
class AminoAcidSequence
Represents an amino acid seque nce for an exon
class BasePairFileUtils
class BasicFeature
A convenience class providing default implementation for ma ny IGVFeature methods.
class CachingFeatureSource
A FeatureSource wrapper which provides caching. The cache i s only cleared when the s...
class Chromosome
Simple representation of a chr omosome. Basically a name, le ngth, and optionally a li...
class Codon
class CodonAA
class CytoBandFileParser
Class description
class Cytoband
class EmblFeatureTableParser
Parses exon information from t he feature table section of a n embl file. Note -- this...
class EncodePeakFeature
Representation of a feature fr om an Encode "peak" file TODO Extending BasicFeature i...
class Exon
A sub region of a feature. For example, a Gene exon
class FeatureCodecParser
FeatureParser which reads feat ures using a codec. Intended as a bridge between Featu...
class FeatureDB
This is a placeholder class fo r a true "feature database" w rapper. Its purpose is to...
class FeatureFileUtils
Interface
interface FeatureParser
Enum
enum FeatureType
class FeatureUtils
class GFFFeature
class GFFParser
class GisticFileParser
class GisticScore
Interface
interface IExon
This class mainly exists so we can create a Proxy object of Exons User: jacob Date: ...
Interface
interface IGVFeature
class LocAndVal
class Locus
Interface
interface LocusScore
class MaximumContigGenomeException
class Mutation
Represents a mutation // TODO -- refactor this to not imple ment "IGVFeature"
class MutationTrackLoader
Parses a mutation file, such a s ".mut" or ".maf" (mutation annotation file)
Interface
interface NamedFeature
class PSLRecord
class Range
Basic class to specify a genom ic interval. Coordinates are intended to be 0-based ha...
class RegionOfInterest
class SeqLenAndBinnedPairs
class SeqLenAndPairs
class SequenceOntology
A static class for defining id entifiers from the Sequence O ntology project and relat...
class ShapeFileUtils
Interface
interface SignalFeature
class SpliceJunctionFeature
A feature class for splice jun ctions, with depth informatio n for flanking regions if...
Enum
enum Strand
class UCSCSnpFeature
Representation of a feature fr om a UCSC "snp" file
class WrappedIterator
User: jacob Date: 2012/05/15
Interface
interface CloseableTribbleIterator
Interface
interface Feature
class GenomeException
Interface
interface FeatureSource
A queryable source for Feature s. Used by FeatureTrack autho r: jrobinso Date: Jan 31,...
strandNULL_AMINO_ACIDAANameMap 0..* instancesequence 0..* strandexons 0..* sourcecytobands 0..* aminoAcidstrandaminoAcidaminoAcidSequencefeatureMap 0..* 0..* strand