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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