Mauve Class List

Here are the classes, structs, unions and interfaces with brief descriptions:
org::gel::mauve::summary::output::AbstractIslandWriter
org::gel::mauve::summary::output::AbstractMatchDataWriter
org::gel::mauve::gui::sequence::AbstractSequencePanel
org::gel::mauve::summary::output::AbstractTabbedDataWriterUsed to provide base functionality to print files largely made up of rows of tab- separated data
org::gel::mauve::dcjx::Adjacency
org::gel::mauve::dcjx::AdjacencyGraph
org::gel::mauve::summary::output::AlignedSequenceWriterWrites out fastas for each genome containing only those sections that aligned to a part of the specified genome
org::gel::mauve::gui::AlignFrameA dialog box implementing a graphical interface to the command-line mauveAligner tool
org::gel::mauve::gui::AlignmentProcessListener
org::gel::mauve::gui::AlignWorker
org::gel::mauve::gui::AnalysisDisplayWindow
org::gel::mauve::gui::AnalysisDisplayWindow::ContentManager
org::gel::mauve::summary::AnalysisModuleFrame
org::gel::mauve::gui::navigation::AnnotationContainsFilterAllows features to be filtered based on whether they contain an annotation of a particular type with an either exact or partial value match
org::gel::mauve::AsapXrefHandler
org::gel::mauve::assembly::AssemblyScorer
org::gel::mauve::backbone::Backbone
org::gel::mauve::summary::output::BackboneCompareFileOutputs data from Match objects stored in Genome objects in Mauve in a format compatible with the .backbone file to see if the two match
org::gel::mauve::color::BackboneLcbColor
org::gel::mauve::backbone::BackboneList
org::gel::mauve::backbone::BackboneList::BbComparatorCompares LCB ids and left-columns of backbone segments
org::gel::mauve::backbone::BackboneList::BbLeftEndComparatorCompares LCB ids and left-columns of backbone segments
org::gel::mauve::backbone::BackboneListBuilder
org::gel::mauve::color::BackboneMultiplicityColor
org::gel::mauve::format::BaseFormat
org::gel::mauve::BaseViewerModel
org::gel::mauve::dcjx::Block
org::gel::mauve::dcjx::BlockEnd
org::gel::mauve::analysis::BrokenCDS
org::gel::mauve::BrowserLauncherBrowserLauncher is a class that provides one static method, openURL, which opens the default web browser for the current user of the system to the given URL
org::gel::mauve::analysis::CDSErrorExporterA class for extracting broken CDS features from a draft genome
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::ColorSchemeInterface for objects that can apply a color scheme to the elements of a model
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
org::gel::mauve::contigs::ContigGrouper::ContigGroup
org::gel::mauve::contigs::ContigHandler
org::gel::mauve::contigs::ContigInverter
org::gel::mauve::contigs::ContigMauveAlignFrame
org::gel::mauve::contigs::ContigOrderer
org::gel::mauve::contigs::ContigRenamer
org::gel::mauve::contigs::ContigReorderer
org::gel::mauve::contigs::ContigReorderer::ReordererMauveFrame
org::gel::mauve::gui::sequence::ControlPanel
org::gel::mauve::chado::DBUtils
org::gel::mauve::DbXrefFactoryA factory class that tracks databases known to have a GenBank xref Use this class to map a GenBank db_xref to a URL
org::gel::mauve::DbXrefFactory::UnknownDatabaseException
org::gel::mauve::DbXrefHandlerAn interface classes that map a GenBank db_xref to a web database URL
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::contigs::DefaultContigHandler
org::gel::mauve::format::DelegatingSequence
org::gel::mauve::format::DelegatingSequence::DelegatingSublist
org::gel::mauve::gui::dnd::DnDListAn extension of JListthat supports drag and drop to rearrange its contents and to move objects in and out of the list
org::gel::mauve::format::EmblFormat
org::gel::mauve::EricXrefHandler
org::gel::mauve::gui::ExportFrame
org::gel::mauve::gui::ExportMenu
org::gel::mauve::dcjx::FastAccessTable
org::gel::mauve::contigs::FastAContigChangeWriter
org::gel::mauve::format::FastaFormat
org::gel::mauve::gui::sequence::FeatureFiltererAllows a user to select which features should be viewable by feature type
org::gel::mauve::contigs::FeatureFixer
org::gel::mauve::gui::sequence::FeaturePanel
org::gel::mauve::gui::sequence::FeaturePanel::ClickListener
org::gel::mauve::gui::sequence::FeaturePanel::DbXrefMenuAction
org::gel::mauve::gui::sequence::FeaturePanel::DbXrefMenuItemBuilder
org::gel::mauve::gui::sequence::FeaturePanel::FeatureMenuItemBuilder
org::gel::mauve::gui::sequence::FeaturePanel::FeaturePopupMenuBuilder
org::gel::mauve::gui::sequence::FeaturePanel::GenbankMenuAction
org::gel::mauve::gui::sequence::FeaturePanel::GenbankMenuItemBuilder
org::gel::mauve::gui::sequence::FeaturePanel::ToolTipMotionListener
org::gel::mauve::gui::dnd::FileDropThis class makes it easy to drag and drop files from the operating system to a Java program
org::gel::mauve::gui::dnd::FileDrop::ListenerImplement this inner interface to listen for when files are dropped
org::gel::mauve::format::FileFinder
org::gel::mauve::tree::FileKey
org::gel::mauve::gui::FillLayout
org::gel::mauve::FilterCacheSpec
org::gel::mauve::gui::sequence::FlatFileFeatureConstants
org::gel::mauve::gui::sequence::FlatFileFeatureImporter
org::gel::mauve::gui::FrameLoader
org::gel::mauve::analysis::Gap
org::gel::mauve::tree::GapKey
org::gel::mauve::format::GenbankEmblFormat
org::gel::mauve::format::GenbankFileFormat
org::gel::mauve::gui::GenericActionGeneric class to propagate action events to a listener
org::gel::mauve::Genome
org::gel::mauve::GenomeBuilder
org::gel::mauve::gui::GenomeCellRenderer
org::gel::mauve::tree::GISTreeRecords a mapping between gapped sequence coordinates and ungapped sequence coordinates
org::gel::mauve::GiXrefHandler
org::gel::air::util::GroupHelpers
org::gel::mauve::dcjx::Head
org::gel::mauve::HighlightListener
org::gel::mauve::gui::sequence::HighlightPanel
org::gel::mauve::gui::HintMessageEvent
org::gel::mauve::gui::HintMessageListener
org::gel::mauve::histogram::HistogramBuilder
org::gel::mauve::histogram::HistogramBuilder::HistogramLine
org::gel::mauve::gui::sequence::HistogramPanel
org::gel::mauve::format::INSDseqFormat
org::gel::mauve::tree::IntervalSequenceTree
org::gel::air::util::IOUtils
org::gel::mauve::summary::output::IslandCoordinateWriter
org::gel::mauve::summary::output::IslandFeatureWriter
org::gel::mauve::summary::output::IslandGeneFeatureWriter
org::gel::mauve::tree::IstIterator
org::gel::mauve::tree::IstNode
org::gel::mauve::tree::KeyKey specifies the interface allowed for intervals that can be stored in an interval sequence tree
org::gel::mauve::LCBThe LCB class tracks locally collinear blocks: regions of homologous sequence that do not contain rearrangements
org::gel::mauve::color::LCBColorSchemeColor matches by their LCB number
org::gel::mauve::LcbIdComparatorCompares LCB ids
org::gel::mauve::LCBLeftComparatorCompares left end of LCBs
org::gel::mauve::gui::LcbLinePanelThis class is intended to overlay a RearrangementPanel with lines that connect each locally collinear block
org::gel::mauve::LCBlistClass implementing manipulation and analysis functions for LCBs
org::gel::mauve::gui::LCBStatusBarThis class displays statistics about LCBs in a status bar
org::gel::mauve::LcbViewerModel
org::gel::mauve::contigs::ListSequenceIterator
org::gel::mauve::analysis::LiteWeightFeature
org::gel::mauve::MatchRecords an ungapped local alignment among multiple sequences
org::gel::mauve::gui::sequence::MatchPanel
org::gel::mauve::gui::sequence::MatchPanel::EditLcbMenuItemBuilder
org::gel::mauve::gui::sequence::MatchPanel::MatchDisplayMenuItemBuilder
org::gel::mauve::gui::sequence::MatchPanel::MatchPopupMenuBuilder
org::gel::mauve::gui::sequence::MatchPanel::MatchPopupMenuItemBuilder
org::gel::mauve::gui::sequence::MatchPanel::SetReferenceMenuItemBuilder
org::gel::mauve::gui::sequence::MatchPopupMenuA popup menu showing the sequence coordinates covered by an ungapped alignment
org::gel::mauve::MatchStartComparatorCompare the start coordinates of ungapped local alignments in a particular sequence Note: this comparator imposes orderings that are inconsistent with the equals operator
org::gel::air::util::MathUtils
org::gel::mauve::gui::Mauve
org::gel::mauve::gui::Mauve::UpdateCheckChecks the Mauve web server for a newer version of this software
org::gel::mauve::gui::MauveAlignFrame
org::gel::mauve::MauveConstants
org::gel::mauve::remote::MauveDisplayCommunicator
org::gel::mauve::MauveFormatException
org::gel::mauve::gui::MauveFrameThe window frame for a Mauve application, containing a menu bar, a tool bar and a RearrangementPanel to display genome alignments
org::gel::mauve::gui::MauveFrame::GenericAction
org::gel::mauve::MauveHelperFunctionsFile writing routines and variables useful to multiple classes
org::gel::mauve::remote::MauveInterface
org::gel::mauve::remote::MauveInterfaceImpl
org::gel::mauve::summary::MauveInterfacerThis class interfaces between Mauve's existing code and modules that may or may not become a part of Mauve, but require it's base classes to run
org::gel::mauve::module::MauveModule
org::gel::mauve::module::MauveModuleFrame
org::gel::mauve::gui::MauveRenderingHints
org::gel::mauve::gui::MauveRenderingHints::SimilarityDensityKey
org::gel::mauve::ModelBuilderMethods to parse data files into models
org::gel::mauve::ModelEvent
org::gel::mauve::ModelListener
org::gel::mauve::ModelProgressListener
org::gel::mauve::module::ModuleListener
org::gel::mauve::gui::sequence::MultiGenomeRectangularBeadRenderer
org::gel::mauve::color::MultiplicityColorSchemeColors the matches based on their multiplicity
org::gel::mauve::color::MultiplicityTypeColorSchemeColor matches by their multiplicity and the sequences they match in
org::gel::mauve::MyConsole
org::gel::mauve::gui::MySymbolSequenceRendererA slightly revised version of Biojava's SymbolSequenceRenderer, which prints symbols near center of range for location, and offset a little further down
org::gel::mauve::gui::navigation::NavigationPanelA panel that allows a user to set up a constraint for searching features
org::gel::mauve::color::NormalizedMultiplicityTypeColorSchemeColor matches by their multiplicity and the sequences they match in
org::gel::mauve::color::NormalizedOffsetColorSchemeColors the matches based on their generalized offsets using the entire color spectrum evenly
org::gel::mauve::color::OffsetColorSchemeColors the matches based on their generalized offsets
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::OverviewFileWriter
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::PrintUtilitiesA couple of utilities
org::gel::mauve::summary::ProcessBackboneFile
org::gel::mauve::gui::ProgressiveMauveAlignFrame
org::gel::mauve::gui::QualifierPanel
org::gel::mauve::gui::sequence::RangeHighlightPanel
org::gel::mauve::format::RawFastaBridgeFilterReader
org::gel::mauve::format::RawFormat
org::gel::mauve::gui::RearrangementPanelThe primary container class for the visualization interface
org::gel::mauve::gui::RearrangementPanel::CtrlKeyDetectorCtrlKeyDetector is used to capture the press and release of the Ctrl key so that the cursor for zooming in and out can be changed
org::gel::mauve::remote::RemoteApplet
org::gel::mauve::remote::RemoteControl
org::gel::mauve::remote::RemoteControlImpl
org::gel::mauve::format::RichDelegatingSequence
org::gel::mauve::format::RichStrandedFeatureTemplate
org::gel::mauve::gui::sequence::RRSequencePanel
org::gel::mauve::gui::sequence::RulerPanelAdapter class that allows use of Biojava ruler
org::gel::mauve::gaggle::SampleGooseA goose useful for testing and diagnostics and learning how to write a goose that uses the new (2007-04) API
org::gel::mauve::assembly::ScoreAssembly
org::gel::mauve::gui::navigation::SearchResultPanelA Gui component that shows the results of a given query separated by genome
org::gel::mauve::gui::navigation::SearchResultPanel::SignedIconIcon that shows whether a given node can be expanded (has children)
org::gel::mauve::analysis::Segment
org::gel::mauve::analysis::Segment::GenomePositionComparator
org::gel::mauve::analysis::SegmentComparator
org::gel::mauve::summary::output::SegmentDataProcessor
org::gel::mauve::SeqFeatureDataUtility class for data specific to sequence navigator involving genomes and their features
org::gel::mauve::SeqFeatureData::FeatureComparatorA comparator for features
org::gel::mauve::gui::sequence::SeqPanel
org::gel::mauve::format::SequenceIteratorCacheActs as a cache to allow for faster access to files with multiple contigs without creating a permanent memory commitment
org::gel::mauve::gui::SequenceNavigatorA gui that allows a user to search genome features by annotation
org::gel::mauve::SimilarityIndexSimilarityIndex generates a queryable in-memory index of the similarity among a group of aligned sequences
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::SupportedFormatA definition of a format supported for annotation/feature reading
org::gel::mauve::format::SupportedFormatFactory
org::gel::mauve::gui::SwingWorkerThis is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to perform GUI-related work in a dedicated thread
org::gel::mauve::gui::SwingWorker::ThreadVarClass to maintain reference to current worker thread under separate synchronization control
org::gel::mauve::dcjx::Tail
org::gel::mauve::format::TestMain
org::gel::mauve::gui::dnd::TransferableObjectAt last an easy way to encapsulate your custom objects for dragging and dropping in your Java programs! When you need to create a java.awt.datatransfer.Transferableobject, use this class to wrap your object
org::gel::mauve::gui::dnd::TransferableObject::FetcherInstead of passing your data directly to the TransferableObject constructor, you may want to know exactly when your data was received in case you need to remove it from its source (or do anyting else to it)
org::gel::mauve::analysis::TreeAnalysis
org::gel::mauve::tree::TreeStore
org::gel::mauve::summary::output::TroubleMatchWriter
org::gel::mauve::dcjx::VestigialDCJ
org::gel::mauve::ViewerMode
org::gel::mauve::remote::WargDisplayCommunicator
org::gel::mauve::remote::WargInterface
org::gel::mauve::recombination::WeakArgDataModel
org::gel::mauve::recombination::WeakArgModelBuilder
org::gel::mauve::recombination::WeakArgModelBuilder::WeakArgXmlHandlerClass to handle XML parse events from weak arg xml
org::gel::mauve::XMFAAlignmentXMFA file class A technical cross-product of insomnia and indulgence
org::gel::mauve::XmfaViewerModel
org::gel::mauve::gui::sequence::ZiggyRectangularBeadRenderer
org::gel::mauve::histogram::ZoomHistogramMeant to represent data that varies over a range and needs to be viewed at multiple resolutions

Generated on Mon Aug 19 06:03:44 2013 for Mauve by doxygen 1.3.6