org::gel::mauve Namespace Reference

Classes
class	AsapXrefHandler
class	BaseViewerModel
class	BrowserLauncher
	BrowserLauncher 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. More...
class	Chromosome
interface	ColorScheme
	Interface for objects that can apply a color scheme to the elements of a model. More...
class	DbXrefFactory
	A factory class that tracks databases known to have a GenBank xref Use this class to map a GenBank db_xref to a URL. More...
class	DbXrefFactory::UnknownDatabaseException
interface	DbXrefHandler
	An interface classes that map a GenBank db_xref to a web database URL. More...
class	EricXrefHandler
class	FilterCacheSpec
class	Genome
class	GenomeBuilder
class	GiXrefHandler
interface	HighlightListener
class	LCB
	The LCB class tracks locally collinear blocks: regions of homologous sequence that do not contain rearrangements. More...
class	LcbIdComparator
	Compares LCB ids. More...
class	LCBLeftComparator
	Compares left end of LCBs. More...
class	LCBlist
	Class implementing manipulation and analysis functions for LCBs. More...
class	LcbViewerModel
class	Match
	Records an ungapped local alignment among multiple sequences. More...
class	MatchStartComparator
	Compare the start coordinates of ungapped local alignments in a particular sequence Note: this comparator imposes orderings that are inconsistent with the equals operator. More...
interface	MauveConstants
class	MauveFormatException
class	MauveHelperFunctions
	contains file writing routines and variables useful to multiple classes. More...
class	ModelBuilder
	Methods to parse data files into models. More...
class	ModelEvent
interface	ModelListener
interface	ModelProgressListener
class	MyConsole
class	OptionsBuilder
class	PreferencesDump
class	SeqFeatureData
	Utility class for data specific to sequence navigator involving genomes and their features. More...
class	SeqFeatureData::FeatureComparator
	A comparator for features. More...
class	SimilarityIndex
	SimilarityIndex generates a queryable in-memory index of the similarity among a group of aligned sequences. More...
interface	SupportedFormat
	A definition of a format supported for annotation/feature reading. More...
class	ViewerMode
class	XMFAAlignment
	XMFA file class A technical cross-product of insomnia and indulgence. More...
class	XmfaViewerModel

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