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class IGVS3Object
class BBFileHeader
class BBFileReader
class BBTotalSummaryBlock
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class BBZoomLevelFormat
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class BBZoomLevelHeader
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class BBZoomLevels
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class BPTree
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class BPTreeChildNode
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class BPTreeChildNodeItem
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class BPTreeHeader
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class BPTreeLeafNode
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class BPTreeLeafNodeItem
Interface
interface BPTreeNode
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class BedFeature
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class RPChromosomeRegion
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class RPTree
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class RPTreeChildNodeItem
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class RPTreeHeader
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class RPTreeLeafNodeItem
Container class for R+ tree le af node data locator. Note: D etermination of data item...
class RPTreeNode
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Abstract
abstract class RPTreeNodeItem
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class RPTreeNodeProxy
class WigItem
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class ZoomDataRecord
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Interface
interface BedPE
class BedPEFeature
Created by jrobinso on 6/29/18 .
class BedPEInterFeature
Interface
interface BedPERenderer
Interface
interface BedPEShape
For hit testing
class InteractionTrack
Created by jrobinso on 6/29/18 .
class NestedArcRenderer
class PEBlockRenderer
class ProportionalArcRenderer
class BigWigDataSource
A hybrid source, implements bo th DataSource and FeatureSour ce. Way of the future?
class Anchor
class BlastMapping
// TODO -- consider implementi ng feature interface
class XYDataPoint
class XYSeries
Abstract
abstract class AbstractDataSource
class BasicScore
class CharArrayList
class ChromosomeSummary
class CombinedDataSource
Data source which combines two other DataSources TODO Multi ple DataSources. There is...
class CompositeScore
Interface
interface CoverageDataSource
Interface
interface DataSource
class DataTile
Class is public to permit unit testing
Interface
interface Dataset
A dataset is an in-memory repr esentation of a numerical dat aset. It is used for non-...
class DatasetDataSource
class GenomeSummaryData
Summarize (using a windowing f unction) numeric data points which are associated with...
class IGVDataset
class IGVDatasetParser
Class description
class NamedScore
class SummaryTile
Represents a chunk of data ove r a fixed window span (defaul t == 1)
class WiggleDataset
class CufflinksDataSource
class CufflinksTrack
Abstract
abstract class CufflinksValue
class ExpDiffValue
class FPKMSampleValue
Represents a value from a cuff links file for a single sampl e
class FPKMValue
Represents a cufflinks value f rom any of a fpkm tracking fi le as described here http...
class ExpressionDataset
class FreqData
class Segment
class SegmentedAsciiDataSet
class SegmentedBinaryDataSet
class SegmentedBinaryLocalReader
Interface
interface SegmentedBinaryReader
class SegmentedChromosomeData
This class encapuslates data f or a single chromosome from a segmented dataset. Its b...
Interface
interface SegmentedDataSet
class SegmentedDataSource
class IGVEventBus
Ludicrously simple event bus - - its all we need.
Interface
interface IGVEventObserver
Created by jrobinson on 6/3/16 .
Abstract
abstract class AbstractFeature
class AminoAcid
class AminoAcidSequence
Represents an amino acid seque nce for an exon
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 CodonAA
class Cytoband
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 GFFFeature
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 Mutation
Represents a mutation // TODO -- refactor this to not imple ment "IGVFeature"
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 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 BasePairData
class BasePairFeature
Created by jrobinson on 3/1/16 .
class BasePairRenderer
class BasePairTrack
Show base-pairing arcs
class SMAPFeature
class SMAPPairedFeature
Created by jrobinson on 2/25/1 6.
class SMAPRenderer
Created by jrobinson on 9/17/1 5.
class CytobandTrack
class DRangerFeature
class DRangerRenderer
class DSIRenderer
Created by jrobinson on 7/19/1 6.
class DSITrack
Created by jrobinson on 7/19/1 6.
class Genome
Simple model of a genome. Keep s an ordered list of Chromoso mes, an alias table, and ...
class GenomeListItem
A container for specific genom e information which can be us ed to manage loaded genom...
class GenomeManager
class IGVSequence
Represents a sequence database composed of plain text files with no white space, one...
class InMemorySequence
A sequence implementation in w hich all data is held in memo ry.
Interface
interface Sequence
class SequenceWrapper
A wrapper class that provides caching for on-disk, queried, and web-service Sequence...
class TwoBitSequence
Created by jrobinso on 6/13/17 .
class FastaBlockCompressedSequence
Created by jrobinso on 6/23/17 .
class FastaDirectorySequence
Implementation of Sequence bac ked by an indexed fasta file
class FastaIndex
Representation of a fasta (.fa i) index. This is a modified version of a similar clas...
class FastaIndexedSequence
Implementation of Sequence bac ked by an indexed fasta file
class GFFFeatureSource
User: jacob Date: 2012-Jun-22
class Cluster
Created by jrobinso on 6/30/18 .
class ClusterTrack
Created by jrobinso on 6/30/18 .
class CachingFeatureReader
class IGVBEDCodec
Created by IntelliJ IDEA. User : jrobinso Date: Dec 20, 2009 Time: 10:15:49 PM
Interface
interface IGVFeatureReader
Interface to replace the Tribb le equivalent. Returns plain "Iterator" rather than "C...
class PAFFeature
Created by jrobinso on 10/31/1 7.
class PSLCodec
class TribbleReaderWrapper
class VCFFeature
class GobyAlignment
A Facade to a Goby alignment e ntry. The facade exposes Goby alignment entries in the...
class GobyAlignmentIterator
An iterator over Goby alignmen t entries. IGV iterator retur n entries that fall withi...
class GobyAlignmentQueryReader
Query reader to parse Goby ali gnment files. The compact ali gnment files must be sort...
class GobyCountArchiveDataSource
A data source for Goby compres sed base-level histograms (.c ounts files).
class Ga4ghAlignment
Created by jrobinso on 6/17/14 . id
class Ga4ghAlignmentReader
Class for testing GlobalAllian ce API. Loads json from a tex t file, for development o...
class Ga4ghDataset
Created by jrobinso on 9/3/14.
class Ga4ghProvider
Created by jrobinso on 8/25/14 .
class Ga4ghReadset
Minimal representation of a re adset for prototype purposes.
class OAuthProvider
class EQTLFeature
Represents an eQTL value SNP S NP_Chr SNP_Pos Gen_ID Gene_Na me Gene_Pos T_Stat P_Val ...
class GWASFeature
class GWASTrack
class GeneList
class MAFIndex
class MAFListReader
Implementation of MAFReader fo r MAF files that are split by chromosome (1 file per c...
class MAFParser
Interface
interface MAFReader
class MAFRenderer
class MultipleAlignmentBlock
class MultipleAlignmentTrack
class BBMethylDataSource
Data source backe by Michael Z iller's custom BB format
class CachingMethylSource
Interface
interface MethylDataSource
class MethylScore
class MethylTrack
Experimental class for specifi c dataset. if(locator.getPath ().contains("RRBS_cpgMeth...
class IGVPreferences
Manages user preferences.
class PreferencesManager
Created by jrobinso on 1/21/17 .
Abstract
abstract class AbstractColorScale
class ArcRenderer
Created by jrobinson on 9/17/1 5.
class BarChartRenderer
Interface
interface ColorScale
class ContinuousColorScale
class CosmicFeatureRenderer
class CytobandRenderer
class DataRange
Encapsulates parameter for an x-y plot axis.
Abstract
abstract class DataRenderer
class FeatureDensityRenderer
Abstract
abstract class FeatureRenderer
class GeneTrackRenderer
class GenotypeRenderer
This class exists as a side ef fect of the fact that we set renderers by class, rathe...
class GisticTrackRenderer
class HeatmapRenderer
class IGVFeatureRenderer
Renderer for the full "IGV" fe ature interface
class LineplotRenderer
class MappedColorScale
A simple lookup color scale ba cked by a map.
class MonocolorScale
class MutationRenderer
class PointsRenderer
Interface
interface Renderer
class SelectableFeatureRenderer
User: jacob Date: 2013-Jan-28
class SequenceRenderer
class SpliceJunctionRenderer
Renderer for splice junctions. Draws a filled-in arc for ea ch junction, with the wid...
Abstract
abstract class XYPlotRenderer
Interface
interface Alignment
Interface
interface AlignmentBlock
Created by jrobinso on 9/22/15 .
class AlignmentBlockImpl
Interface
interface AlignmentCounts
class AlignmentDataManager
Manages data loading for a sin gle alignment file. Shared be tween alignment, coverage...
class AlignmentInterval
class AlignmentRenderer
class AlignmentTileLoader
A wrapper for an AlignmentQuer yReader that caches query res ults
class AlignmentTrack
Abstract
abstract class BaseAlignmentCounts
class BisulfiteCounts
class CoverageTrack
class DenseAlignmentCounts
chromosomeDataTreechromosomeIDTreefileHeadertotalSummaryBlockzoomLevelszoomLevelFormatList 0..* zoomLevelHeaders 0..* zoomLevelRPTree 0..* rootNodetreeHeaderchildItems 0..* childNodeleafItems 0..* chromosomeBoundsrootNoderpTreeHeaderchildNodechildNodeProxychromosomeBoundsitems 0..* chromosomeBoundsshapeshapewrappedFeaturegenomerenderers 0..* wgFeatures 0..* tracktracktrackbedCodeclevelsreaderwholeGenomeScores 0..* 0..* dataPoints 0..* genomedatasetgenomeSummaryDatagenomechromosomeSummaries 0..* genomeSummaryparsergenomesummaryScores 0..* genomevalues 0..* 0..* dataSourcegenomeamp 0..* 0..* datasetgenomegenomesegments 0..* 0..* 0..* chrData 0..* readersegmentsCache 0..* 0..* 0..* datasetinstanceobserverMap 0..* 0..* strandNULL_AMINO_ACIDsequence 0..* strandexons 0..* cytobands 0..* aminoAcidaminoAcidSequencestrandfeatureMap 0..* 0..* basePairDatabasePairRenderergenomepartialFeatures 0..* feature1str2chromosomeMap 0..* sequenceDOWNLOAD_ITEMcurrentGenometheInstancesequencesequenceMap 0..* indexbinnedClusters 0..* genomegenomestrandgenomeblock 0..* gapTypesiteratorproviderreadsets 0..* datasets 0..* gData 0..* 0..* genomereaderMap 0..* indexgenomereaderrendererreaderreaderstranddataSourcerenderercolorScaleCache 0..* parentgenericDefaultstheInstanceexonMap 0..* selectedExons 0..* strandalignmentTrackcoverageTrackintervalCache 0..* readeralignments 0..* countsgenometrackcoverageTrackdataManagergenomerendererbisulfiteCountsgenomealignmentTrackdataManagerdataSourcedataSourceRenderergenomeprefs