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Package org.broad.igv.feature

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