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Main Methods

play_circle_filledJava Main Methods
org.broad.igv.batch
class Exec ............................... -- Created by IntelliJ IDEA. User: jrobinso D...
main(...) ............................ source
class TestClient
main(...) ............................ source
org.broad.igv.bedpe
class BedPEUtils ......................... -- Created by jrobinso on 6/29/18.
main(...) ............................ source
org.broad.igv.charts
class ScatterPlotDemo .................... -- A demo scatter plot.
main(...) ............................ source -- Starting point for the demonstration appli...
org.broad.igv.feature
class EmblFeatureTableParser ............. -- Parses exon information from the feature t...
main(...) ............................ source -- Method description
class FeatureFileUtils
main(...) ............................ source
class GFFParser
main(...) ............................ source
org.broad.igv.feature.genome
class GenomeUtils ........................ -- Static utility functions for genome data-w...
main(...) ............................ source
org.broad.igv.google
class GoogleUtils ........................ -- Created by jrobinson on 7/15/16.
main(...) ............................ source
org.broad.igv.gwas
class EqtlPreprocessor ................... -- Class for experimenting with binary EQTL f...
main(...) ............................ source
class GWASParser ......................... -- Parses GWAS PLINK result files
main(...) ............................ source
org.broad.igv.maf
class MAFUtils
main(...) ............................ source
class MAFtoSAM ........................... -- Created by jrobinson on 5/5/16. Parses a M...
main(...) ............................ source
org.broad.igv.prefs
class PreferencesEditor
main(...) ............................ source
org.broad.igv.renderer
class TestGraphicUtils
main(...) ............................ source
org.broad.igv.repeats
class RepeatMaskSplitter ................. -- Splits a repeat mask file downloaded from ...
main(...) ............................ source
org.broad.igv.sam.reader
class CGIAlignmentReader ................. -- Reader for querying a CGI service for SAM ...
main(...) ............................ source
org.broad.igv.tdf
class TDFUtils
main(...) ............................ source
org.broad.igv.tools
class IgvTools ........................... -- Command accessories for IGV.
main(...) ............................ source -- Main method. Used to run igvtools from the...
class IgvToolsGui
main(...) ............................ source
class PairedEndStats
main(...) ............................ source
class PairedUtils ........................ -- Created by jrobinso on 10/6/15.
main(...) ............................ source
class RepeatMaskSplitter ................. -- Splits a repeat mask file downloaded from ...
main(...) ............................ source
class TestFileGenerator
main(...) ............................ source
class UCSCUtils
main(...) ............................ source
org.broad.igv.tools.converters
class CLWtoSAM ........................... -- Created by jrobinson on 5/5/16. Parses a M...
main(...) ............................ source
class ExpressionFormatter ................ -- Scales and centers expression data for dis...
main(...) ............................ source
class GFFtoBed ........................... -- Convert a GFF to a BED file, keeping the c...
main(...) ............................ source
class IlluminaToCN ....................... -- User: jrobinso Date: Apr 19, 2010
main(...) ............................ source
class MFastaToSAM ........................ -- Created by jrobinson on 5/5/16. Parses a M...
main(...) ............................ source
class WigToBed ........................... -- Converts a "wig" file to a "bed" file by a...
main(...) ............................ source
org.broad.igv.track
class TestUtils
main(...) ............................ source
org.broad.igv.ui
class AWTFrameTest
main(...) ............................ source
class AboutDialog
main(...) ............................ source
class DataRangeDialog
main(...) ............................ source
class HeatmapDialog
main(...) ............................ source
class HeatmapScaleDialog
main(...) ............................ source
class IGVMainFrame ....................... -- This class exists solely to provide backwa...
main(...) ............................ source
class Main ............................... -- Utility class for launching IGV. Provides ...
main(...) ............................ source -- Launch an igv instance as a stand-alone ap...
class ResourceFileBuilderDialog
main(...) ............................ source
class TooltipTextFrame
main(...) ............................ source
class TrackConfigurationDialog
main(...) ............................ source
org.broad.igv.ui.color
class PaletteToolFrame
main(...) ............................ source
org.broad.igv.ui.legend
class LegendDialog
main(...) ............................ source
org.broad.igv.ui.svg
class SVGTest
main(...) ............................ source
org.broad.igv.ui.util ........................ -- SnapshotUtilities.java <p> Created on Nove...
class FontChooser2 ....................... -- A font selection dialog. Note: can take a ...
main(...) ............................ source -- Simple main program to start it running
class MessageUtils ....................... -- Provides thread-safe, Swing-safe, utilitie...
main(...) ............................ source -- Test program - call all methods from both ...
class ReorderableJList
main(...) ............................ source
class SimpleFormDialog ................... -- Constructs a simple multi-field text entry...
main(...) ............................ source
class SortDialog
main(...) ............................ source
org.broad.igv.ui.util.download
class Downloader
main(...) ............................ source
org.broad.igv.util
class AsciiEcho
main(...) ............................ source
class DumpHttpHeaders .................... -- Utility class to dump headers from an http...
main(...) ............................ source
class IlluminaUtils
main(...) ............................ source
class SequenceGC
main(...) ............................ source
class TutorialUtils ...................... -- Utilities for creating compact files for t...
main(...) ............................ source
class UnzipGenomes
main(...) ............................ source
org.broad.igv.util.blat
class BlatClient ......................... -- Port of perl script blatPlot.pl http://gen...
main(...) ............................ source
org.broad.igv.util.collections
class LRUCache ........................... -- A least-recently-used cache with a maximum...
main(...) ............................ source -- Test for memory leaks
org.broad.igv.util.converters
class DensitiesToBedGraph ................ -- Converts a directory of "density" files (T...
main(...) ............................ source
class TarjeiToBedgraph ................... -- Converts a director of files of the form c...
main(...) ............................ source
org.broad.igv.util.encode
class EncodeFileBrowser
main(...) ............................ source
class UCSCEncodeUtils
main(...) ............................ source
org.broad.igv.util.stats
class KaplanMeierEstimator ............... -- Computes the Kaplan-Meier survival curve R...
main(...) ............................ source
org.broad.igv.util.stream
class IGVSeekableHTTPStream
main(...) ............................ source
org.broad.igv.variant.util
class AutismUtils
main(...) ............................ source
class VCFtoBed ........................... -- Utility class to convert a VCF to a BED fi...
main(...) ............................ source
slider
class RangeSliderDemo .................... -- Demo application panel to display a range ...
main(...) ............................ source -- Main application method.