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Model

class Base64Coder
A Base64 encoder/decoder. This class is used to encode and decode data in Base64 for...
class CmdLineParser
Largely GNU-compatible command -line options parser. Has sho rt (-v) and long-form (--...
class Ascii
This class implements some bas ic ASCII character handling f unctions.
class HttpDate
This class can be used to effi ciently parse and write an RF C 1123 formatted date in ...
class DirectoryManager
class Globals
User: jrobinso Date: Feb 3, 20 10
Annotation
class? ForTesting
Indicates that class/field/met hod/whatever exists only to s upport testing User: jaco...
class IGVS3Object
UI
class S3LoadDialog
class S3Object
class S3TreeNode
class BatchRunner
class CommandExecutor
class CommandListener
class Exec
Created by IntelliJ IDEA. User : jrobinso Date: Apr 29, 2010 Time: 1:29:50 PM To chan...
class TestClient
class BBFileHeader
class BBFileReader
class BBTotalSummaryBlock
Created by IntelliJ IDEA. User : martind Date: Jan 18, 2010 Time: 12:51:25 PM To chan...
class BBZoomLevelFormat
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class BBZoomLevelHeader
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class BBZoomLevels
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class BPTree
Created by IntelliJ IDEA. User : martind Date: Dec 17, 2009 Time: 12:28:30 PM To chan...
class BPTreeChildNode
Created by IntelliJ IDEA. User : martind Date: Jan 13, 2010 Time: 11:33:41 AM To chan...
class BPTreeChildNodeItem
Created by IntelliJ IDEA. User : martind Date: Dec 20, 2009 Time: 10:50:26 PM To chan...
class BPTreeHeader
Created by IntelliJ IDEA. User : martind Date: Jan 8, 2010 T ime: 3:50:08 PM To change...
class BPTreeLeafNode
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class BPTreeLeafNodeItem
Interface
interface BPTreeNode
Created by IntelliJ IDEA. User : martind Date: Jan 13, 2010 Time: 11:30:36 AM To chan...
Interface
interface BPTreeNodeItem
class BedFeature
Created by IntelliJ IDEA. User : martind Date: Mar 18, 2010 Time: 3:36:10 PM To chang...
class BigBedDataBlock
Created by IntelliJ IDEA. User : martind Date: Jan 26, 2010 Time: 12:18:32 PM To chan...
class BigBedIterator
Created by IntelliJ IDEA. User : martind Date: Apr 5, 2010 T ime: 3:10:26 PM To change...
class BigWigDataBlock
Created by IntelliJ IDEA. User : martind Date: Apr 16, 2010 Time: 10:32:51 AM To chan...
class BigWigIterator
Created by IntelliJ IDEA. User : martind Date: Apr 13, 2010 Time: 12:34:16 PM To chan...
class BigWigSection
Created by IntelliJ IDEA. User : Owner Date: May 3, 2010 Tim e: 12:32:17 AM To change ...
class BigWigSectionHeader
Created by IntelliJ IDEA. User : martind Date: Jan 6, 2010 T ime: 3:00:11 PM To change...
class RPChromosomeRegion
Created by IntelliJ IDEA. User : martind Date: Jan 22, 2010 Time: 3:37:38 PM private ...
class RPTree
Created by IntelliJ IDEA. User : martind Date: Jan 6, 2010 T ime: 4:05:31 PM To change...
class RPTreeChildNodeItem
Created by IntelliJ IDEA. User : martind Date: Jan 6, 2010 T ime: 4:35:42 PM To change...
class RPTreeHeader
Created by IntelliJ IDEA. User : martind Date: Jan 14, 2010 Time: 3:59:55 PM To chang...
class RPTreeLeafNodeItem
Container class for R+ tree le af node data locator. Note: D etermination of data item...
class RPTreeNode
Created by IntelliJ IDEA. User : martind Date: Jan 14, 2010 Time: 11:16:03 AM To chan...
Abstract
abstract class RPTreeNodeItem
Created by IntelliJ IDEA. User : martind Date: Jan 6, 2010 T ime: 4:29:53 PM To change...
class RPTreeNodeProxy
class WigItem
Created by IntelliJ IDEA. User : martind Date: Apr 5, 2010 T ime: 4:00:41 PM To change...
class ZoomDataBlock
Created by IntelliJ IDEA. User : Owner Date: May 5, 2010 Tim e: 8:27:56 PM To change t...
class ZoomDataRecord
Created by IntelliJ IDEA. User : martind Date: Jan 18, 2010 Time: 2:24:44 PM To chang...
class ZoomLevelIterator
Interface
interface BedPE
class BedPEFeature
Created by jrobinso on 6/29/18 .
class BedPEInterFeature
class BedPEParser
Created by jrobinso on 6/29/18 .
Interface
interface BedPERenderer
Interface
interface BedPEShape
For hit testing
class BedPEUtils
Created by jrobinso on 6/29/18 .
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?
Abstract
abstract class AbstractMapping
class Anchor
class BlastMapping
// TODO -- consider implementi ng feature interface
class BlastParser
Interface
interface Mapping
class Region
class Axis
UI
class AxisPanel
class ChartLayout
Layout manager for chart panel s, based loosely on BorderLay out
UI
class ChartPanel
class ScatterPlot
Renders a scatterplot
class ScatterPlotData
class ScatterPlotDemo
A demo scatter plot.
UI
class ScatterPlotFrame
class ScatterPlotUtils
class SelectionPath
Simple geometric class to supp ort lasso selection
class XYDataModel
class XYDataPoint
class XYSeries
class AbstractDataParser
Abstract
abstract class AbstractDataSource
class BasicScore
Interface
interface Bin
class CharArrayList
class ChromosomeData
Container for a block of data for a chromosome
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 DataStatistics
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 SummaryTile2D
Represents a chunk of data ove r a fixed window span (defaul t == 1)
class WiggleDataset
class WiggleParser
Parser for wiggle and "wiggle- like" formats.
class ZipUtils
Abstract
abstract class CufflinksCodec
class CufflinksDataSource
class CufflinksParser
Parses various cufflinks (and cuffdiff) output files as des cribed here: http://cuffl...
class CufflinksTrack
Abstract
abstract class CufflinksValue
class ExpDiffCodec
Codec for cufflinks .exp_diff files
class ExpDiffValue
class FPKMSampleValue
Represents a value from a cuff links file for a single sampl e
class FPKMTrackingCodec
Codec for Cufflinks FPKM files , extension fpkm_tracking
class FPKMTrackingSampleCodec
Wrapper class to make it easy to just extract the first sam ple from an fpkm_tracking...
class FPKMValue
Represents a cufflinks value f rom any of a fpkm tracking fi le as described here http...
class ExpressionDataset
class ExpressionFileParser
TODO -- handle case with probe file
class GeneToLocusHelper
class ProbeToLocusMap
class FreqData
Interface
interface SegFileParser
User: jrobinso Date: Feb 18, 2 010
class Segment
class SegmentFileParser
Example CCLE_name chrom loc.st art loc.end num.mark seg.mean A2780_OVARY 1 51598 8846...
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 AlignmentTrackEvent
class DataLoadedEvent
User: jacob Date: 2013-Feb-06
class GenomeChangeEvent
Created by jrobinso on 1/7/17.
class GenomeResetEvent
Created by jrobinso on 2/7/17.
class IGVEventBus
Ludicrously simple event bus - - its all we need.
Interface
interface IGVEventObserver
Created by jrobinson on 6/3/16 .
class ReferenceFrameEvent
Created by jrobinson on 6/3/16 .
class RefreshEvent
Created by jrobinso on 6/24/17 .
class RepaintEvent
Event signalling need to repai nt a track or collection of t racks with existing data....
class ShiftEvent
Created by jrobinso on 2/26/17 . Represents view shift left or right, e.g. moving via...
class StopEvent
Created by jrobinso on 6/24/17 .
class TrackGroupEvent
class ViewChange
Events corresponding to a chan ge in viewed area (chromosome , position, and/or zoom)....
class ZoomChange
Events which either cause or a re the result of changes in t he zoom level User: jacob...
class DataLoadException
Author: nazaire Date: Jul 8, 2 009
class HttpResponseException
Class for converting HTTP erro r response codes to exception s
class LoadResourceFromServerException
User: nazaire
class ParserException
Created by IntelliJ IDEA. User : nazaire Date: Jul 13, 2009
class ProbeMappingException
User: nazaire
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
class BasePairData
class BasePairFeature
Created by jrobinson on 3/1/16 .
class BasePairFileParser
class BasePairRenderer
class BasePairTrack
Show base-pairing arcs
class SMAPFeature
class SMAPPairedFeature
Created by jrobinson on 2/25/1 6.
class SMAPParser
For the time being we bypass t ribble and just use a parser
class SMAPRenderer
Created by jrobinson on 9/17/1 5.
class CytobandTrack
class DRangerFeature
class DRangerParser
class DRangerRenderer
class DSICodec
Created by jrobinson on 7/19/1 6.
class DSIFeature
Created by jrobinson on 7/19/1 6. Chr - Number of chromosome Position - Start positio...
class DSIRenderer
Created by jrobinson on 7/19/1 6.
class DSITrack
Created by jrobinson on 7/19/1 6.
class ChromSizesParser
class ChromosomeComparator
For comparing chromosomes. We order by "important" vs "unim portant". The idea being ...
class ChromosomeCoordinate
class ChromosomeNameComparator
Comparator for chromosome name s. All pure string comparison s are case insensitive. I...
class ColorSpaceSequence
Created with IntelliJ IDEA. Us er: jrobinso Date: 6/25/12 Ti me: 11:00 AM To change th...
class GenbankParser
Sequence defined by a Genbank (.gbk) file. These files cont ain a single sequence/chr...
class Genome
Simple model of a genome. Keep s an ordered list of Chromoso mes, an alias table, and ...
UI
class GenomeBuilderDialog
UI
class GenomeBuilderPane
Abstract
abstract class GenomeDescriptor
class GenomeException
class GenomeImporter
/
class GenomeListItem
A container for specific genom e information which can be us ed to manage loaded genom...
class GenomeManager
class GenomeServerException
class GenomeUtils
Static utility functions for g enome data-wrangling.
class GenomeZipDescriptor
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.
UI
class RemoveGenomesDialog
Interface
interface Sequence
class SequenceInterval
Created by jrobinso on 1/7/17.
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 FastaSequenceParser
A sequence created by reading an entire fasta file (i.e. no t an indexed file).
class FastaUtils
class Cluster
Created by jrobinso on 6/30/18 .
class ClusterParser
Created by jrobinso on 6/30/18 .
class ClusterTrack
Created by jrobinso on 6/30/18 .
class BCF2WrapperCodec
class CachingFeatureReader
class CodecFactory
A factory class for Tribble co decs. implements a single, st atic, public method to re...
class DGVCodec
class EMBLTableCodec
class EncodePeakCodec
Codec for UCSC / ENCDOE "broad and narrow peak" files (http ://genome.ucsc.edu/FAQ/FA...
class FeatureFileHeader
Created by IntelliJ IDEA. User : jrobinso Date: May 22, 2010 Time: 7:10:59 PM To chan...
class GFFCodec
Notes from GFF3 spec http://ww w.sequenceontology.org/gff3.s html These tags have pred...
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 IntervalListCodec
Created by jrobinso on 8/13/18 .
class Locus
A minimal representation of a Feature.
class MUTCodec
Codec for .mut and .maf mutati on files
class PAFCodec
Created by jrobinso on 10/31/1 7. reference: https://github. com/lh3/miniasm/blob/mast...
class PAFFeature
Created by jrobinso on 10/31/1 7.
class PSLCodec
class REPMaskCodec
Basically BED format with some columns rearranged Columns, from UCSC documentation 0...
class TribbleIndexNotFoundException
Thrown when an index is not fo und, but required. This class extends Exception, as op...
class TribbleReaderWrapper
Abstract
abstract class UCSCCodec
class UCSCGeneTableCodec
class UCSCSnpCodec
Created by jrobinso on 5/26/15 .
class VCFFeature
class VCFWrapperCodec
class IGVComponentMethods
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 Ga4ghAPIHelper
Helper class for Google API pr ototype Created by jrobinso o n 8/15/14.
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 GoogleUtils
Created by jrobinson on 7/15/1 6.
class OAuthProvider
class OAuthUtils
Created by jrobinso on 11/19/1 4.
class DescriptionCache
Created by IntelliJ IDEA. User : jussi Date: 2/7/11 Time: 1: 32 PM To change this temp...
class EQTLCodec
CODEC for GTex project eQTL fi les SNP SNP_Chr SNP_Pos Gen_I D Gene_Name Gene_Pos T_St...
class EQTLFeature
Represents an eQTL value SNP S NP_Chr SNP_Pos Gen_ID Gene_Na me Gene_Pos T_Stat P_Val ...
class EqtlPreprocessor
Class for experimenting with b inary EQTL formats. SNP SNP_C hr SNP_Pos Gen_ID Gene_Na...
class GWASFeature
class GWASParser
Parses GWAS PLINK result files
class GWASTrack
class GtexJunctionExtractor
Created by jrobinso on 3/12/15 .
class GeneList
UI
class GeneListEditDialog
class GeneListGroup
class GeneListManager
UI
class GeneListManagerUI
UIAbstract
abstract class AbstractMultipleAlignmentDialog
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 MAFTile
class MAFTileCodec
class MAFUtils
class MAFtoSAM
Created by jrobinson on 5/5/16 . Parses a MAF file for Align ment records, as opposed ...
class MafChunk
class MultipleAlignmentBlock
UI
class MultipleAlignmentDialog
class MultipleAlignmentTrack
UI
class Multiz44ConfigurationDialog
NOTE: This is hardcoded for th e human 44-way files.
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 Constants
Created by jrobinso on 1/20/17 .
class IGVPreferences
Manages user preferences.
class PreferencesChangeEvent
Created by jrobinso on 1/22/17 .
class PreferencesEditor
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 ColorScaleFactory
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 GraphicUtils
class HeatmapRenderer
class IGVExomeFeatureRenderer
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...
UI
class TestGraphicUtils
Abstract
abstract class XYPlotRenderer
class RepeatMaskSplitter
Splits a repeat mask file down loaded from UCSC into multipl e files, one per repeat c...
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 AlignmentPacker
Packs alignments such that the re is no overlap
class AlignmentRenderer
class AlignmentTileLoader
A wrapper for an AlignmentQuer yReader that caches query res ults
class AlignmentTrack
class AlignmentUtils
Abstract
abstract class BaseAlignmentCounts
class BisulfiteBaseInfo
class BisulfiteBaseInfoNOMeseq
class BisulfiteCounts
class CoverageTrack
class DenseAlignmentCounts
class DotAlignedAlignment
class DownsampledInterval
Genomic interval showing which areas have had reads removed (downsampled)
class EWigTrack
Developmental track to explore display of conservation scor es.
class EmptyAlignmentIterator
class ExperimentTypeChangeEvent
Created by jrobinso on 2/10/17 .
class FeatureWrappedAlignment
Some alignment formats are par sed as Features. This is all getting rather circular, ...
class Gap
Created by jrobinso on 3/22/16 .
class HaplotypeUtils
Experimental class for phasing alignments for high ploidy r egions.
class InsertionManager
Created by jrobinso on 12/22/1 6. Experimental class to test strategies for drawing i...
class InsertionMarker
Created by jrobinso on 1/13/17 .
class InsertionSelectionEvent
Created by jrobinso on 1/12/17 .
class LinkedAlignment
Class for experimenting with 1 0X linked reads.
class PEStats
class PackedAlignments
Convenience class for storing map from group -> list of ali gnments packed into rows ...
class PairedAlignment
class PicardAlignment
class PositionCache
Stores objects by position so they can be looked up by inex act position (contains)
class ReadMate
class ReadStats
Created by jrobinso on 12/20/1 6. Some simple statistics to distinguish dna, rna, and...
class ReducedMemoryAlignment
class Row
A row of alignments, packed to minimize empty space
Abstract
abstract class SAMAlignment
class SAMWriter
Write SAM/BAM Alignments to a file or stream
class SparseAlignmentCounts
class SpliceGap
Created by jrobinso on 3/31/16 .
class SpliceJunctionHelper
A helper class for computing s plice junctions from alignmen ts. Junctions are filtere...
class SpliceJunctionTrack
class IGVReferenceSource
Provide a reference sequence f or CRAM decompression. Note t he rule for MD5 calculati...
class ReferenceDiskCache
Created by jrobinso on 6/25/17 . Some static methods for man aging the CRAM reference ...
class BAMAlignment
Created by jrobinso on 3/13/17 .
class BAMIndex
Created by jrobinso on 3/9/17.
class BAMReader
Created by jrobinso on 3/9/17.
class BGUnzip
Created by jrobinso on 3/10/17 .
class CigarOperator
Created by jrobinso on 3/14/17 .
Abstract
abstract class AlignmentIndexer
Interface
interface AlignmentParser
Interface
interface AlignmentReader
class AlignmentReaderFactory
class BAMReader
Created by IntelliJ IDEA. User : jrobinso Date: Sep 22, 2009 Time: 2:21:04 PM
class CGIAlignmentReader
Reader for querying a CGI serv ice for SAM (note not BAM) fi les.
class DotAlignedCodec
private String chromosome; pri vate int start; private int e nd; boolean negativeStrand;
class DotAlignedIndexer
Created by IntelliJ IDEA.
class DotAlignedParser
class FeatureIndex
class GeraldReader
A wrapper for SamTextReader th at supports query by interval .
class IndexLoadException
Created by IntelliJ IDEA. User : jrobinso Date: Nov 2, 2009 Time: 9:45:22 PM To chang...
class IndexNotFoundException
class MergedAlignmentReader
Performs a logical merge of ba m files. User: jrobinso Date: Apr 25, 2010
class PSLAlignmentParser
class ReadGroupFilter
Created by IntelliJ IDEA. User : jrobinso Date: Oct 1, 2009 Time: 7:09:37 PM To chang...
class SAMQueryIterator
class SAMReader
A wrapper for SamTextReader th at supports query by interval .
class SamIndexer
Created by IntelliJ IDEA.
class SamUtils
class SolexaQualityConverter
Optimized method for convertin g Solexa ASCII qualities into Phred scores. Pre-comput...
class UnsortedFileException
class WrappedIterator
class SashimiJunctionRenderer
Renderer for splice junctions. Draws a filled-in arc for ea ch junction, with the wid...
UI
class SashimiPlot
Window for displaying sashimi style junction plot See http: //genes.mit.edu/burgelab/...
class History
class IGVSessionReader
Class to parse an IGV session file
class IndexAwareSessionReader
Class to parse an index aware session file
Interface
interface Persistable
Interface for a session persis table object.
class RendererFactory
Maps between renderer type nam e and renderer class. Used fo r saving and restoring se...
class Session
class SessionAttribute
Session Attribute types
class SessionElement
Session Element types
Interface
interface SessionReader
class SessionWriter
class UCSCSessionReader
Class to parse a UCSC session file
class Accumulator
Accumulator for a single windo w function. Estimating percen tiles -- weighted average...
class BufferedByteWriter
class IBFAttributes
Interface
interface IBFBin
Interface
interface IBFIndex
class LinearIndex
class TDFBedTile
class TDFDataSource
class TDFDataset
Represents the data for a part icular chromosome and zoom le vel
class TDFEntity
class TDFFixedTile
class TDFGroup
class TDFReader
Interface
interface TDFTile
class TDFUtils
class TDFVaryTile
class TDFWriter
Assumptions Little endian is u sed throughout Strings are nu ll terminated ascii (sing...
class TileFactory
Abstract
abstract class AbstractConsensusCalculator
Calculates the consensus seque nce based on alignments The r ules for defining a conse...
class CavenerConsensusCalculator
Rules taken from Cavener, Nucl eic Acids Res. 15, 1353-1361, 1987. Also used by CisRE...
class CommandLineStatusMonitor
class CoverageCounter
Class to compute coverage on a n alignment or feature file. This class is designed to...
class FeatureSearcher
Used for searching for the nex t feature, given a source. We simply call getFeature o...
class GenomeDesc
class IgvTools
Command accessories for IGV.
UI
class IgvToolsGui
class ListAccumulator
Estimating percentiles -- weig hted average of multiple esti mates
class PFMExporter
Export the consensus of alignm ent counts. Format is similar to http://lgsun.grc.nia....
class PairedEndStats
class PairedUtils
Created by jrobinso on 10/6/15 .
class PreprocessingException
class Preprocessor
class RepeatMaskSplitter
Splits a repeat mask file down loaded from UCSC into multipl e files, one per repeat c...
Interface
interface StatusMonitor
class TestFileGenerator
class UCSCUtils
class WigSummer
Sum the values from a list of wig files and output a new wi g file with the totals. T...
class BamToBed
Converts a bam -> a bed file b y writing each record as a be d feature. If the "proper...
class CLWtoSAM
Created by jrobinson on 5/5/16 . Parses a MAF file for Align ment records, as opposed ...
class ExpressionFormatter
Scales and centers expression data for display in IGV. 1. t ake log2 of data 2. compu...
class GCTtoIGVConverter
class GFFtoBed
Convert a GFF to a BED file, k eeping the column 9 attribute tags.
class IlluminaToCN
User: jrobinso Date: Apr 19, 2 010
class MFastaToSAM
Created by jrobinson on 5/5/16 . Parses a MAF file for Align ment records, as opposed ...
class MageTabToIGVConverter
class WigToBed
Converts a "wig" file to a "be d" file by applying a thresho ld
UI
class MotifFinderDialog
Dialog so the user can enter a pattern that can be used to search a nucleotide seque...
class MotifFinderPlugin
Search for a motif (currently can be a regex or IUPAC code)
class MotifFinderSource
Class for searching for patter n in a sequence. We recognize single letter codes, inc...
Abstract
abstract class AbstractParser
class CNParser
Interface
interface DataConsumer
class ToolsWiggleParser
Parses a wiggle file, as descr ibed by UCSC See http://genom e.ucsc.edu/goldenPath/hel...
class UnsortedException
Abstract
abstract class AsciiSorter
Created by IntelliJ IDEA. User : nazaire Date: Jun 2, 2009
class BAMSorter
class BedSorter
class CNSorter
class EQTLSorter
Created with IntelliJ IDEA. Us er: jrobinso Date: 4/26/13 Ti me: 10:03 AM To change th...
class GFFSorter
User: jrobinso Date: Jun 28, 2 010 Time: 2:37:24 PM
class GWASSorter
class GenericSorter
class InteractionSorter
class MUTSorter
class Parser
class RefgeneSorter
class SAMSorter
class SortableRecord
class SortableRecordCodec
Codec for Picard sorting class es. Used to serialize and des erialize records to disk.
Interface
interface Sorter
Created by jrobinson on 5/10/1 6.
class SorterFactory
Created by jrobinson on 5/10/1 6.
class VCFSorter
Created by IntelliJ IDEA. User : jrobinso Date: Jun 28, 2010 Time: 2:46:12 PM To chan...
UI
class CoverageGui
UI
class IndexGui
Abstract
abstract class AbstractTrack
Abstract
abstract class AttributeComparator
Sort tracks by attribute value
class AttributeManager
class BlatTrack
class CNFreqTrack
UI
class CombinedDataSourceDialog
class DataSourceTrack
Abstract
abstract class DataTrack
Represents a track of numeric data
class FeatureCollectionSource
Implementation of FeatureSourc e that wraps a list or map of features for the entire ...
class FeatureDirSource
User: jrobinso Date: Jan 31, 2 010
Interface
interface FeatureSource
A queryable source for Feature s. Used by FeatureTrack autho r: jrobinso Date: Jan 31,...
class FeatureTrack
Track which displays features, typically showing regions of the genome in a qualitat...
class FeatureTrackUtils
class GFFCombiner
The GFF spec is available at h ttp://www.sequenceontology.or g/gff3.shtml GFF Combiner...
class GFFFeatureSource
User: jacob Date: 2012-Jun-22
class GisticTrack
class LoadedDataInterval
class MergedTracks
Track to serve as a container for several tracks rendered o n top of each other
class MutationFeatureSource
class MutationTrack
class PackedFeatures
Represents a table of features , packed so there is no overl ap. Features are packed i...
class PackedFeaturesSpliceJunctions
class Range
Created by jrobinson on 5/3/16 .
Enum
enum RegionScoreType
class RenderContext
Interface
interface ScalableTrack
Created by jrobinson on 5/3/16 .
class SelectableFeatureTrack
A FeatureTrack designed for se lecting features/exons. Creat ed to support Sashimi plo...
class SequenceTrack
class TestUtils
Interface
interface Track
class TrackClickEvent
class TrackGroup
Container for a group of track s. Behaves as a single unit w hen sorting by region sco...
class TrackLoader
User: jrobinso Date: Feb 14, 2 010
Interface
interface TrackMenuItemBuilder
Interface to implement when ad ding a context menu item for track context menus
class TrackMenuUtils
class TrackProperties
This class is based on the UCS C track configuration paramet ers
Interface
interface TrackReader
class TrackSet
Enum
enum TrackType
Abstract
abstract class TribbleFeatureSource
class TribbleListFeatureSource
Wraps a collection of FeatureS ource objects, one per chromo some. The class is needed...
Enum
enum WindowFunction
class AWTFrameTest
UI
class AboutDialog
Abstract
abstract class AbstractDataPanelTool
UI
class AttributeCheckList
UI
class AttributeSelectionDialog
class Autoscaler
UI
class DataRangeDialog
class DefaultExceptionHandler
class DesktopIntegration
Java version-specific integrat ion with the platform Desktop and particularly for OS ...
UIAbstract
abstract class FilterComponent
class FontManager
class GlobalKeyDispatcher
UI
class HeatmapDialog
UI
class HeatmapScaleDialog
class IGV
Represents an IGV instance, co nsisting of a main window and associated model.
UI
class IGVContentPane
The content pane for the IGV m ain window.
class IGVMainFrame
This class exists solely to pr ovide backward compatibility.
class IGVMenuBar
Main menu bar at top of window . File / genomes / view / etc . Singleton
UI
class InsertSizeSettingsDialog
class Main
Utility class for launching IG V. Provides a "main" method a nd an "open" method for o...
class MessageCollection
Class to hold a collection of messages for display to the u ser
Enum
enum PanelName
Identifier for each track pane l which is displayed in the I GV window
class ReadmeParser
Class used for examining our r eadme file, and presenting do cumentation to the user e...
class ResourceFileBuilder
Generate an XML resource file, suitable for loading from IG V in the "load from serve...
class ResourceFileBuilderDialog
class ResourceTree
Parses XML file of IGV resourc es, and displays them in tree format.
Enum
enum ShowDetailsBehavior
Created by jrobinso on 7/6/17.
class ShutdownThread
This thread is registered upon startup and will get execute d upon exit.
UI
class StatusWindow
UI
class TooltipTextFrame
UI
class TrackConfigurationDialog
class TrackFilter
UI
class TrackFilterComponent
class TrackFilterElement
UI
class TrackFilterPane
class UIConstants
UI
class UserDefinedGenomeCheckList
class UserPasswordPane
UI
class VersionUpdateDialog
class WaitCursorManager
Utility class for managing IGV cursors. The main purpose of the class is to centrall...
class BrowseEncodeAction
class ClearRegionsMenuAction
class ExportRegionsMenuAction
class ExportTrackNamesMenuAction
class FilterTracksMenuAction
class FitDataToWindowMenuAction
class GroupTracksMenuAction
class ImportRegionsMenuAction
class LoadFilesMenuAction
class LoadFromDatabaseAction
class LoadFromServerAction
class LoadFromURLMenuAction
class MenuAction
class NavigateRegionsMenuAction
class NewSessionMenuAction
class OpenSessionMenuAction
This menu action classes is us ed for both "Open Session ... " and load recent session...
class OverlayTracksMenuAction
class ReloadSessionMenuAction
class ReloadTracksMenuAction
class RenameTracksMenuAction
class ResetPreferencesAction
class RunScriptMenuAction
class SaveSessionMenuAction
class SearchCommand
A class for performing search actions. The class takes a vi ew context and search str...
class SetTrackHeightMenuAction
class SortTracksMenuAction
UI
class ColorChooserPanel
class ColorPalette
UI
class ColorPanel
Simple panel for displaying co lor palettes
Interface
interface ColorTable
class ColorUtilities
Miscellaneous utilities for pa rsing and manipulating colors .
class GreyscaleColorTable
Created by jrobinson on 7/5/16 .
class HSLColorTable
Experimental -- work in progre ss
class PaletteColorTable
A lookup table mapping symbols (strings) -> color. Can be i nitiated with our without...
UI
class PaletteToolFrame
UI
class ChromosomeComboBox
Created by jrobinso on 7/6/17.
UI
class GenomeComboBox
Created by jrobinso on 7/6/17.
class GenomeListManager
Created by jrobinso on 7/6/17.
UI
class GenomeSelectionDialog
Dialog box for selecting genom es. User can choose from a li st, which is filtered acc...
UI
class IGVCommandBar
class JList7
UI
class SearchTextField
Created by jrobinso on 7/6/17.
Abstract
abstract class AbstractGhostDropManager
class GhostDropAdapter
class GhostDropEvent
Interface
interface GhostDropListener
UI
class GhostGlassPane
class AlignmentFileFilter
Filters filenames to only show alignment files. This is use ful when users store a nu...
class CoverageFileFilter
Filters file names to only sho w coverage files (.tdf, .coun ts). This is useful when ...
UI
class HeatmapLegendEditor
UI
class HeatmapLegendPanel
UI
class LegendDialog
UIAbstract
abstract class LegendPanel
UI
class LohLegendPanel
UI
class MutationColorMapEditor
UI
class MutationLegendPanel
Panel to paint a legend for th e mutation tracks.
UI
class AttributeHeaderPanel
UI
class AttributePanel
class ClickTaskScheduler
A utility class for sceduling single-click actions "in the future",
UI
class CytobandPanel
UI
class DataPanel
The batch panel for displaying tracks and data. A DataPanel is always associated wit...
UI
class DataPanelContainer
class DataPanelLayout
class DataPanelPainter
class DragAndDropTransferHandler
Used by both the draggable cl ass and the target for negoti ating data. Note that thi...
UI
class FeatureTrackSelectionDialog
Dialog used for selecting a si ngle FeatureTrack
UI
class FeatureTrackSelectionPanel
Created with IntelliJ IDEA. Us er: jrobinso Date: 6/14/12 Ti me: 8:34 AM To change thi...
class FrameManager
class HeaderDropTargetListener
Listens for drops and perform s the updates. The real magic behind the drop!
UI
class HeaderPanel
The drag & drop code was modif ied from the excellent exampl e of Bryan E. Smith.
UI
class HeaderPanelContainer
The drag & drop code was modif ied from the excellent exampl e of Bryan E. Smith.
UI
class IGVPanel
A panel class that lays out it s components in a very specif ic way so that children (...
class IGVPopupMenu
Extension of JPopupMenu that p rovides an instance cache, an d closeAll method. Create...
UI
class MainPanel
class MouseableRegion
Regions that represent tracks
UI
class NameHeaderPanel
Name header panel. Displayed i n upper left corner
Interface
interface Paintable
class PanTool
class PanelLayoutManager
class RadioButtonSelectionList
Just like a CheckBoxList, but renders with radio buttons an d only allows single sele...
class ReferenceFrame
class RegionMenu
UI
class RegionNavigatorDialog
UI
class RegionOfInterestPanel
class RegionOfInterestTool
UI
class ReorderPanelsDialog
UI
class RulerPanel
UI
class TrackNamePanel
UI
class TrackPanel
UIAbstract
abstract class TrackPanelComponent
class TrackPanelScrollPane
UI
class TrackSelectionDialog
Dialog used for selecting one or more tracks
class TrackWrapper
UI
class ZoomSliderPanel
class SVGGraphics
This is an experimental class, its not actually used (yet)
class SVGTest
UI
class ApplicationStatusBar
class ByteSubArray
Created by jrobinson on 10/24/ 15. Class used to create a su b-array without making a ...
UI
class CancellableProgressDialog
UI
class CheckList
UI
class CheckListDialog
UI
class ConfirmDialog
A confirm dialog with a "do no t show again" checkbox. For r elease 1.5rc2 this class ...
UI
class ConvertFileDialog
Before converting .shape, .map , .ct, .db, or .dp files (ass ociated with individual R...
class ConvertOptions
Interface
interface DataPanelTool
Defines an interface for a "to ol" to be used in the data pa nel. A tool handles a sub...
class FileDialogUtils
UI
class FontChooser
UI
class FontChooser2
A font selection dialog. Note: can take a long time to star t up on systems with (lit...
class HistoryMenu
class IGVMouseEvent
class IGVMouseInputAdapter
class IconFactory
class IndefiniteProgressMonitor
UI
class IndexCreatorDialog
UI
class LinkCheckBox
UI
class LoadFromURLDialog
UI
class MagetabSignalDialog
Created by IntelliJ IDEA. User : nazaire Date: Apr 21, 2011 Time: 11:06:07 AM To chan...
class MenuAndToolbarUtils
class MessageUtils
Provides thread-safe, Swing-sa fe, utilities for interacting with JOptionPane. Accoun...
Interface
interface Packable
UI
class ProgressBar
Panel showing a progress bar, which can optionally close pa rent window when finished
class ProgressMonitor
TODO This class probably shoul dn't exist, bet we could use built-in progress monitor...
class ReorderableJList
UI
class SimpleFormDialog
Constructs a simple multi-fiel d text entry form from a list of labels. Example use: ...
class SnapshotFileChooser
class SnapshotUtilities
Utility methods for supporting saving of images as jpeg, pn g, and svg files.
UI
class SortDialog
class SwitchingLabelUI
class TracingRepaintManager
For debugging.
class UIUtilities
class VerticalLabelUI
class Downloader
class AlphaColorGradient
class AmazonS3URI
A URI wrapper that can parse o ut information about an S3 UR I.
class AmazonUtils
class ArrayHeapIntSorter
class ArrayHeapObjectSorter
class AsciiEcho
class BrowserLauncher
class ByteConverter
class ChromosomeColors
class CompressionUtils
Created by IntelliJ IDEA. User : jrobinso, mdecautis Date: D ec 13, 2009 Time: 4:16:42...
class DumpHttpHeaders
Utility class to dump headers from an http response. Used t o debug JWS update proble...
class FeatureCache
class FileUtils
Abstract
abstract class Filter
Abstract
abstract class FilterElement
class HttpUtils
Wrapper utility class... for i nteracting with HttpURLConnec tion.
class IlluminaUtils
Interface
interface IntComparator
class Interval
class IntervalTree
An implementation of an interv al tree, following the explan ation. from CLR.
class JWTParser
Utility class for all operatio ns on JWT.
class JavaAgent
Do not add any more dependenci es to this class than necessa ry. Packaged into JavaAge...
UI
class LoginDialog
class LongRunningTask
Utility class for executing lo ng running tasks in their own thread (i.e. not on the ...
class MD5Checksum
class MacroSnapshotAction
Interface
interface NamedRunnable
User: jrobinso Date: Feb 1, 20 10
class ObjectCache
class ObservableForObject
Contains an object of some typ e, and provides an accessor a nd a way of notifying obs...
class OneKGUtils
Created by jrobinso on 8/28/14 . 1-off utilties for manipula ting 1000 genomes project...
class Pair
class ParsingUtils
class ResourceLocator
Represents a data file or othe r resource, which might be lo cal file or remote resour...
Enum
enum RunnableResult
Enum for indicating how a long running computation complete d.
class RuntimeUtils
class S3Presigner
class SOLIDUtils
User: jrobinso Date: Feb 21, 2 010
class SequenceGC
class StringUtils
Created by IntelliJ IDEA. User : jrobinso Date: Oct 30, 2009 Time: 1:51:36 AM To chan...
class TutorialUtils
Utilities for creating compact files for tutorials
class UCSCBinUtils
Created by jrobinso on 8/29/17 .
class URLDownloader
Runnable for downloading a fil e from a URL. Downloading is buffered, and can be canc...
class URLUtils
class UnzipGenomes
UI
class UserPasswordDialog
class UserPasswordInputImpl
class Utilities
class ZipArchiveWrapper
class BlatClient
Port of perl script blatPlot.p l http://genomewiki.cse.ucsc. edu/index.php/Blat_Scripts
UI
class BlatQueryWindow
class BlatTableModel
Table model for Blat results ( psl records) tChr tStart tEnd strand score match misMa...
class CI
Class for case-insensitive col lections. Needless to say, th e keys must be Strings.
class CollUtils
Utility methods which are usef ul for collections. User: jac ob Date: 2012-Aug-30
class DoubleArrayList
Author: jrobinso Date: Jul 22, 2010 ArrayList type collecti on for int types. Purpose...
class DownsampledDoubleArrayList
Collection that holds up to ma xSize doubles. Additions > ma xSize are uniformly downs...
class FloatArrayList
Author: jrobinso Date: Jul 22, 2010 ArrayList type collecti on for int types. Purpose...
class IntArrayList
Author: jrobinso Date: Jul 22, 2010 ArrayList type collecti on for int types. Purpose...
class LRUCache
A least-recently-used cache wi th a maximum size that can be altered.
class MultiMap
A "map-like" class that suppor ts multiple values for a give n key. Note this violates...
class SortingCollection
Collection to which many recor ds can be added. After all re cords are added, the coll...
class StringArrayList
class DensitiesToBedGraph
Converts a directory of "densi ty" files (Tarjei et al) to b edgraph
class TarjeiToBedgraph
Converts a director of files o f the form chr1.Brain.H3K4me2 .txt in "Tarjei" format t...
class DCCEncodeUtils
Created by jrobinso on 6/4/15.
UI
class EncodeFileBrowser
class EncodeFileRecord
class EncodeTableModel
//wgEncodeBroadHistoneGm12878H 3k4me1StdSig.bigWig // size=3 46M; // dateSubmitted=200...
class UCSCEncodeUtils
class ExtendViewClient
modified from BlatClient.java, jc 20160708
class FTPUtils
class Interval
class IntervalTree
class Distribution
class KaplanMeierEstimator
Computes the Kaplan-Meier surv ival curve Reference: http:// cancerguide.org/scurve_km...
class IGVSeekableBufferedStream
A wrapper class to provide buf fered read access to a Seekab leStream. Just wrapping s...
class IGVSeekableFTPStream
class IGVSeekableHTTPStream
class IGVSeekableStreamFactory
class IGVUrlHelper
class IGVUrlHelperFactory
class SeekableServiceStream
A SeekableStream implementatio n for the "range" webservice. The purpose of this clas...
class SeekableSplitStream
Class to support a single logi cal file split into multiple parts. Introduced to supp...
Interface
interface Genotype
Represents a genotype, that is a variant call on a single s ample
Interface
interface Variant
Represents a variant call on a collection of samples.
class VariantMenu
User: Jesse Whitworth Date: Ju l 16, 2010
class VariantRenderer
class VariantTrack
class Variant
Parser for VCF files.
class VariantCodec
Created by jrobinso on 7/29/16 .
class AutismUtils
class PedigreeUtils
class VCFtoBed
Utility class to convert a VCF to a BED file. Genotypes if any are lost in this conv...
class VCFAllele
class VCFGenotype
class VCFVariant
UI
class RangeSlider
An extension of JSlider to sel ect a range of values using t wo thumb controls. The th...
UI
class RangeSliderDemo
Demo application panel to disp lay a range slider.
class RangeSliderUI
UI delegate for the RangeSlide r component. RangeSliderUI pa ints two thumbs, one for ...
class BasicSliderUI
UI
class JPanel
UI
class JSlider
Interface
interface Allele
Represents an allele. Note: Cu rrently interface could easil y be replaced by a String...
class AsciiFeatureCodec
Interface
interface Feature
class SeekableStream
Interface
interface URLHelperFactory
Interface
interface URLHelper
Interface
interface ISeekableStreamFactory
Interface
interface Comparable
class AbstractTableModel
UI
class JDialog
Interface
interface Iterable
UI
class JFrame
Interface
interface UserPasswordInput
Interface
interface Runnable
class? Observable
Interface
interface Callable
class BasicLabelUI
class RepaintManager
Interface
interface PropertyChangeListener
class MouseInputAdapter
class MouseEvent
class JideScrollPane
Interface
interface Observer
class CheckBoxList
Interface
interface Transferable
Interface
interface DropTargetListener
Interface
interface DragSourceMotionListener
Interface
interface LayoutManager
UI
class JComponent
class FileFilter
Interface
interface FileFilter
class MouseAdapter
UI
class JTextField
UI
class JComboBox
class? Thread
Interface
interface KeyEventDispatcher
Interface
interface Thread$UncaughtExceptionHandler
Interface
interface Comparator
class? RuntimeException
Interface
interface CloseableIterator
class? Exception
Interface
interface CRAMReferenceSource
class? LinkedHashMap
class AbstractFeatureCodec
Interface
interface FeatureCodec
Interface
interface CloseableTribbleIterator
class? IOException
Interface
interface LayoutManager2
Interface
interface Locatable
Interface
interface Iterator
class DefaultMutableTreeNode