Mauve Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

• org::gel::mauve::summary::output::AbstractTabbedDataWriter
  • org::gel::mauve::summary::output::AbstractMatchDataWriter
    • org::gel::mauve::summary::output::AbstractIslandWriter
      • org::gel::mauve::summary::output::IslandCoordinateWriter
      • org::gel::mauve::summary::output::IslandFeatureWriter
        • org::gel::mauve::summary::output::IslandGeneFeatureWriter
    • org::gel::mauve::summary::output::TroubleMatchWriter
  • org::gel::mauve::summary::output::OverviewFileWriter
• org::gel::mauve::dcjx::Adjacency
• org::gel::mauve::dcjx::AdjacencyGraph
• org::gel::mauve::summary::output::AlignedSequenceWriter
• org::gel::mauve::gui::AlignmentProcessListener
  • org::gel::mauve::gui::AlignFrame
    • org::gel::mauve::gui::MauveAlignFrame
    • org::gel::mauve::gui::ProgressiveMauveAlignFrame
• org::gel::mauve::gui::AnalysisDisplayWindow
• org::gel::mauve::gui::AnalysisDisplayWindow::ContentManager
• org::gel::mauve::summary::AnalysisModuleFrame
• org::gel::mauve::gui::navigation::AnnotationContainsFilter
• org::gel::mauve::assembly::AssemblyScorer
• org::gel::mauve::backbone::Backbone
• org::gel::mauve::summary::output::BackboneCompareFile
• org::gel::mauve::backbone::BackboneList
• org::gel::mauve::backbone::BackboneList::BbComparator
• org::gel::mauve::backbone::BackboneList::BbLeftEndComparator
• org::gel::mauve::backbone::BackboneListBuilder
• org::gel::mauve::BaseViewerModel
  • org::gel::mauve::LcbViewerModel
    • org::gel::mauve::XmfaViewerModel
• org::gel::mauve::dcjx::Block
• org::gel::mauve::dcjx::BlockEnd
  • org::gel::mauve::dcjx::Head
  • org::gel::mauve::dcjx::Tail
• org::gel::mauve::analysis::BrokenCDS
• org::gel::mauve::BrowserLauncher
• org::gel::mauve::analysis::CDSErrorExporter
• org::gel::mauve::chado::ChadoDB
• org::gel::mauve::chado::ChadoFeatureLoader
• org::gel::mauve::chado::ChadoReader
• org::gel::mauve::chado::ChadoWriter
• org::gel::mauve::contigs::ChangedFastaFormat
• org::gel::mauve::contigs::ChangedFeatureWriter
• org::gel::mauve::Chromosome
• org::gel::mauve::color::ColorMenu
• org::gel::mauve::ColorScheme
  • org::gel::mauve::color::BackboneLcbColor
  • org::gel::mauve::color::BackboneMultiplicityColor
  • org::gel::mauve::color::LCBColorScheme
  • org::gel::mauve::color::MultiplicityColorScheme
  • org::gel::mauve::color::MultiplicityTypeColorScheme
  • org::gel::mauve::color::NormalizedMultiplicityTypeColorScheme
  • org::gel::mauve::color::NormalizedOffsetColorScheme
  • org::gel::mauve::color::OffsetColorScheme
• org::gel::mauve::gui::ConsoleDialog
• org::gel::mauve::dcjx::Constants
• org::gel::mauve::dcjx::Contig
• org::gel::mauve::contigs::ContigFeatureWriter
• org::gel::mauve::contigs::ContigGrouper::ContigGroup
• org::gel::mauve::contigs::ContigHandler
  • org::gel::mauve::contigs::DefaultContigHandler
• org::gel::mauve::contigs::ContigMauveAlignFrame
• org::gel::mauve::contigs::ContigReorderer::ReordererMauveFrame
• org::gel::mauve::chado::DBUtils
• org::gel::mauve::DbXrefFactory
• org::gel::mauve::DbXrefFactory::UnknownDatabaseException
• org::gel::mauve::DbXrefHandler
  • org::gel::mauve::AsapXrefHandler
  • org::gel::mauve::EricXrefHandler
  • org::gel::mauve::GiXrefHandler
• org::gel::mauve::dcj::DCJ
• org::gel::mauve::dcjx::DCJ
• org::gel::mauve::dcj::DCJ::SB
• org::gel::mauve::dcj::DCJ::Vert
• org::gel::mauve::dcjx::DCJDistance
• org::gel::mauve::dcjx::DCJDistance::DistanceFunction
• org::gel::mauve::dcj::DCJWindow
• org::gel::mauve::dcj::DCJWindow::ChangeCards
• org::gel::mauve::dcj::DCJWindow::ClearData
• org::gel::mauve::dcj::DCJWindow::SubmitData
• org::gel::mauve::format::DelegatingSequence
  • org::gel::mauve::format::RichDelegatingSequence
• org::gel::mauve::format::DelegatingSequence::DelegatingSublist
• org::gel::mauve::gui::dnd::DnDList
• org::gel::mauve::gui::ExportFrame
• org::gel::mauve::gui::ExportMenu
• org::gel::mauve::dcjx::FastAccessTable
• org::gel::mauve::gui::sequence::FeatureFilterer
• org::gel::mauve::gui::sequence::FeaturePanel::ClickListener
• org::gel::mauve::gui::sequence::FeaturePanel::DbXrefMenuAction
• org::gel::mauve::gui::sequence::FeaturePanel::FeatureMenuItemBuilder
  • org::gel::mauve::gui::sequence::FeaturePanel::DbXrefMenuItemBuilder
  • org::gel::mauve::gui::sequence::FeaturePanel::GenbankMenuItemBuilder
• org::gel::mauve::gui::sequence::FeaturePanel::FeaturePopupMenuBuilder
• org::gel::mauve::gui::sequence::FeaturePanel::GenbankMenuAction
• org::gel::mauve::gui::sequence::FeaturePanel::ToolTipMotionListener
• org::gel::mauve::gui::dnd::FileDrop
• org::gel::mauve::gui::dnd::FileDrop::Listener
• org::gel::mauve::format::FileFinder
• org::gel::mauve::gui::FillLayout
• org::gel::mauve::FilterCacheSpec
• org::gel::mauve::gui::FrameLoader
• org::gel::mauve::analysis::Gap
• org::gel::mauve::gui::GenericAction
• org::gel::mauve::Genome
• org::gel::mauve::GenomeBuilder
• org::gel::mauve::gui::GenomeCellRenderer
• org::gel::mauve::tree::GISTree
• org::gel::air::util::GroupHelpers
• org::gel::mauve::HighlightListener
  • org::gel::mauve::gui::LCBStatusBar
  • org::gel::mauve::gui::sequence::HighlightPanel
  • org::gel::mauve::gui::sequence::MatchPanel
  • org::gel::mauve::gui::sequence::RangeHighlightPanel
  • org::gel::mauve::remote::WargDisplayCommunicator
• org::gel::mauve::gui::HintMessageEvent
• org::gel::mauve::gui::HintMessageListener
  • org::gel::mauve::gui::LCBStatusBar
• org::gel::mauve::histogram::HistogramBuilder
• org::gel::mauve::histogram::HistogramBuilder::HistogramLine
• org::gel::mauve::tree::IntervalSequenceTree
• org::gel::air::util::IOUtils
• org::gel::mauve::tree::IstIterator
• org::gel::mauve::tree::IstNode
• org::gel::mauve::tree::Key
  • org::gel::mauve::tree::FileKey
  • org::gel::mauve::tree::GapKey
• org::gel::mauve::LCB
• org::gel::mauve::LcbIdComparator
• org::gel::mauve::LCBLeftComparator
• org::gel::mauve::LCBlist
• org::gel::mauve::contigs::ListSequenceIterator
• org::gel::mauve::analysis::LiteWeightFeature
• org::gel::mauve::Match
• org::gel::mauve::gui::sequence::MatchPanel::MatchPopupMenuBuilder
• org::gel::mauve::gui::sequence::MatchPanel::MatchPopupMenuItemBuilder
  • org::gel::mauve::gui::sequence::MatchPanel::EditLcbMenuItemBuilder
  • org::gel::mauve::gui::sequence::MatchPanel::MatchDisplayMenuItemBuilder
  • org::gel::mauve::gui::sequence::MatchPanel::SetReferenceMenuItemBuilder
• org::gel::mauve::gui::sequence::MatchPopupMenu
• org::gel::mauve::MatchStartComparator
• org::gel::air::util::MathUtils
• org::gel::mauve::gui::Mauve
• org::gel::mauve::gui::Mauve::UpdateCheck
• org::gel::mauve::MauveConstants
  • org::gel::mauve::contigs::ContigGrouper
  • org::gel::mauve::contigs::ContigInverter
  • org::gel::mauve::contigs::ContigOrderer
  • org::gel::mauve::contigs::ContigReorderer
    • org::gel::mauve::contigs::ContigRenamer
    • org::gel::mauve::contigs::FeatureFixer
  • org::gel::mauve::contigs::DefaultContigHandler
  • org::gel::mauve::contigs::FastAContigChangeWriter
  • org::gel::mauve::gui::navigation::NavigationPanel
  • org::gel::mauve::gui::navigation::SearchResultPanel
  • org::gel::mauve::gui::sequence::FlatFileFeatureConstants
    • org::gel::mauve::gui::sequence::FlatFileFeatureImporter
    • org::gel::mauve::gui::sequence::MultiGenomeRectangularBeadRenderer
  • org::gel::mauve::gui::SequenceNavigator
  • org::gel::mauve::SeqFeatureData
  • org::gel::mauve::summary::MauveInterfacer
  • org::gel::mauve::summary::output::IslandCoordinateWriter
  • org::gel::mauve::summary::output::IslandFeatureWriter
  • org::gel::mauve::summary::output::OverviewFileWriter
  • org::gel::mauve::summary::output::SegmentDataProcessor
  • org::gel::mauve::summary::output::TroubleMatchWriter
  • org::gel::mauve::summary::ProcessBackboneFile
• org::gel::mauve::remote::MauveDisplayCommunicator
• org::gel::mauve::MauveFormatException
• org::gel::mauve::gui::MauveFrame::GenericAction
• org::gel::mauve::MauveHelperFunctions
• org::gel::mauve::remote::MauveInterface
  • org::gel::mauve::remote::MauveInterfaceImpl
• org::gel::mauve::module::MauveModule
• org::gel::mauve::module::MauveModuleFrame
• org::gel::mauve::gui::MauveRenderingHints
• org::gel::mauve::gui::MauveRenderingHints::SimilarityDensityKey
• org::gel::mauve::ModelBuilder
• org::gel::mauve::ModelEvent
• org::gel::mauve::ModelListener
  • org::gel::mauve::gui::LcbLinePanel
  • org::gel::mauve::gui::RearrangementPanel
  • org::gel::mauve::gui::sequence::AbstractSequencePanel
    • org::gel::mauve::gui::sequence::ControlPanel
    • org::gel::mauve::gui::sequence::FeaturePanel
    • org::gel::mauve::gui::sequence::HighlightPanel
    • org::gel::mauve::gui::sequence::HistogramPanel
    • org::gel::mauve::gui::sequence::MatchPanel
    • org::gel::mauve::gui::sequence::RangeHighlightPanel
    • org::gel::mauve::gui::sequence::RulerPanel
    • org::gel::mauve::gui::sequence::SeqPanel
  • org::gel::mauve::gui::sequence::ControlPanel
  • org::gel::mauve::gui::sequence::RRSequencePanel
• org::gel::mauve::ModelProgressListener
  • org::gel::mauve::gui::MauveFrame
• org::gel::mauve::module::ModuleListener
• org::gel::mauve::MyConsole
• org::gel::mauve::gui::MySymbolSequenceRenderer
• org::gel::mauve::analysis::OneToOneOrthologExporter
• org::gel::mauve::analysis::OneToOneOrthologExporter::CdsOverlap
• org::gel::mauve::analysis::OneToOneOrthologExporter::ExportFrame
• org::gel::mauve::analysis::OneToOneOrthologExporter::OrthologExportParameters
• org::gel::mauve::analysis::OneToOneOrthologExporter::Quad
• org::gel::mauve::OptionsBuilder
• org::gel::mauve::gui::OutStreamPrinter
• org::gel::mauve::summary::output::PartialFastaWriter
• org::gel::mauve::dcjx::Permutation
• org::gel::mauve::analysis::PermutationExporter
• org::gel::mauve::PreferencesDump
• org::gel::mauve::gui::PrintPreviewCanvas
• org::gel::mauve::gui::PrintPreviewDialog
• org::gel::mauve::gui::PrintUtilities
• org::gel::mauve::gui::QualifierPanel
• org::gel::mauve::format::RawFastaBridgeFilterReader
• org::gel::mauve::gui::RearrangementPanel::CtrlKeyDetector
• org::gel::mauve::remote::RemoteApplet
• org::gel::mauve::remote::RemoteControl
  • org::gel::mauve::remote::RemoteControlImpl
• org::gel::mauve::format::RichStrandedFeatureTemplate
• org::gel::mauve::gaggle::SampleGoose
• org::gel::mauve::assembly::ScoreAssembly
• org::gel::mauve::gui::navigation::SearchResultPanel::SignedIcon
• org::gel::mauve::analysis::Segment
• org::gel::mauve::analysis::Segment::GenomePositionComparator
• org::gel::mauve::analysis::SegmentComparator
• org::gel::mauve::SeqFeatureData::FeatureComparator
• org::gel::mauve::format::SequenceIteratorCache
• org::gel::mauve::SimilarityIndex
• org::gel::mauve::analysis::SNP
• org::gel::mauve::analysis::SnpExporter
• org::gel::mauve::gui::SplashScreen
• org::gel::air::util::StatusBox
• org::gel::mauve::gui::StyleMenu
• org::gel::mauve::SupportedFormat
  • org::gel::mauve::format::BaseFormat
    • org::gel::mauve::format::FastaFormat
      • org::gel::mauve::format::RawFormat
    • org::gel::mauve::format::GenbankEmblFormat
      • org::gel::mauve::format::EmblFormat
      • org::gel::mauve::format::GenbankFileFormat
      • org::gel::mauve::format::INSDseqFormat
• org::gel::mauve::format::SupportedFormatFactory
• org::gel::mauve::gui::SwingWorker
  • org::gel::mauve::gui::AlignWorker
• org::gel::mauve::gui::SwingWorker::ThreadVar
• org::gel::mauve::format::TestMain
• org::gel::mauve::gui::dnd::TransferableObject
• org::gel::mauve::gui::dnd::TransferableObject::Fetcher
• org::gel::mauve::analysis::TreeAnalysis
• org::gel::mauve::tree::TreeStore
• org::gel::mauve::dcjx::VestigialDCJ
• org::gel::mauve::ViewerMode
• org::gel::mauve::remote::WargInterface
• org::gel::mauve::recombination::WeakArgDataModel
• org::gel::mauve::recombination::WeakArgModelBuilder
• org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandler
• org::gel::mauve::XMFAAlignment
• org::gel::mauve::gui::sequence::ZiggyRectangularBeadRenderer
• org::gel::mauve::histogram::ZoomHistogram

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