This alphabet is used to deal NumericAlphabet. More...

Classes
class	AAChargeIndex
	Charge of each amino acid. More...

class	AAChenGuHuangHydrophobicityIndex
	Hydrophobicity of each amino acid, according to Table 1 in Chen, Gu and Huang, BMC Bioinformatics 2006. More...

class	AAChouFasmanAHelixIndex
	A-Helix score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm. More...

class	AAChouFasmanBSheetIndex
	B-sheet score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm. More...

class	AAChouFasmanTurnIndex
	Turn score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm. More...

class	AAIndex1Entry
	Create a AlphabetIndex1 object from an AAIndex2 entry. More...

class	AAIndex2Entry
	Create a AlphabetIndex2 object from an AAIndex2 entry. More...

class	AAMassIndex
	Mass (dalton) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html. More...

class	AASEA1030Index
	Percentage of amino acids having a Solvent Exposed Area between 10 and 30 Angström^2 for each type of amino acid, according to http://prowl.rockefeller.edu/aainfo/access.htm. More...

class	AASEAInf10Index
	Percentage of amino acids having a Solvent Exposed Area below 10 Angström^2 for each type of amino acid, according to http://prowl.rockefeller.edu/aainfo/access.htm. More...

class	AASEASup30Index
	Percentage of amino acids having a Solvent Exposed Area above 30 Angström^2 for each type of amino acid, according to http://prowl.rockefeller.edu/aainfo/access.htm. More...

class	AASurfaceIndex
	Surface (Angström^2) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html. More...

class	AAVolumeIndex
	Volume (Angström^3) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html. More...

class	AbstractAlphabet
	A partial implementation of the Alphabet interface. More...

class	AbstractIAlignment
	Partial implementation of the IAlignment interface, dedicated to alignment readers. More...

class	AbstractISequence
	Partial implementation of the ISequence interface. More...

class	AbstractOAlignment
	Partial implementation of the OAlignment interface. More...

class	AbstractOSequence
	Partial implementation of the OSequence and OAlignment interfaces. More...

class	AbstractReverseTransliterator
	Partial implementation of the ReverseTransliterator interface. More...

class	AbstractSequenceContainer
	Partial implementation of the OrderedSequenceContainer interface. More...

class	AbstractSequenceContainerIterator
	Partial implementation of the SequenceIterator interface, allowing to loop over an ordered sequence container. More...

class	AbstractSequencePositionIterator
	Partial implementation of the SequencePositionIterator interface. More...

class	AbstractSiteContainerIterator
	Partial implementation of the SiteIterator interface, allowing to loop over a site container. More...

class	AbstractTransliterator
	Partial implementation of the Transliterator interface. More...

class	AlignedSequenceContainer
	Aligned sequences container. More...

class	Alphabet
	The Alphabet interface. More...

class	AlphabetException
	The alphabet exception base class. More...

class	AlphabetIndex1
	One dimensionnal alphabet index interface. More...

class	AlphabetIndex2
	Two dimensionnal alphabet index interface. More...

class	AlphabetMismatchException
	Exception thrown when two alphabets do not match. More...

class	AlphabetNumericState
	States that do have a double value. More...

class	AlphabetState
	This is the base class to describe states in an Alphabet. More...

class	AlphabetTools
	Utilitary functions dealing with alphabets. More...

class	AscidianMitochondrialGeneticCode
	This class implements the ascidian mitochondrial genetic code as describe on the NCBI web site: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG13. More...

class	BadCharException
	An alphabet exception thrown when trying to specify a bad char to the alphabet. More...

class	BadIntException
	An alphabet exception thrown when trying to specify a bad int to the alphabet. More...

class	BasicSequence
	A basic implementation of the Sequence interface. More...

class	BasicSymbolList
	A basic SymbolList object. More...

class	BinaryAlphabet
	The BinaryAlphabet class, letters are 0 and 1. More...

class	BLOSUM50
	BLOSUM 50 Substitution Matrix. More...

class	BowkerTest
	Bowker's homogeneity test results class. More...

class	BppOAlignmentReaderFormat
	Sequence I/O in BppO format. More...

class	BppOAlignmentWriterFormat
	Sequence I/O in BppO format. More...

class	BppOAlphabetIndex1Format
	AlphabetIndex1 I/O in BppO format. More...

class	BppOAlphabetIndex2Format
	AlphabetIndex2 I/O in BppO format. More...

class	BppOSequenceReaderFormat
	Sequence I/O in BppO format. More...

class	BppOSequenceStreamReaderFormat
	Sequence I/O in BppO format. More...

class	BppOSequenceWriterFormat
	Sequence I/O in BppO format. More...

class	CaseMaskedAlphabet
	Case-sensitive letter alphabet. More...

class	CharStateNotSupportedException
	Exception thrown in case no character is available for a certain state in an alphabet. More...

class	Clustal
	The clustal sequence file format. More...

class	CodonAlphabet
	Codon alphabet class. More...

class	CodonSiteTools
	Utilitary functions for codon sites. More...

class	CompleteSiteContainerIterator
	Loop over all complete sites in a SiteContainer (i.e. sites without gap and unresolved characters). More...

class	CompressedVectorSiteContainer
	A low memory, yet restricted, version of the VectorSiteContainer class. More...

class	ConstSequenceIterator
	Generic const sequence iterator interface, allowing to loop over const sequences. More...

class	ConstSequenceWithQualityIterator
	Generic const sequence iterator interface, allowing to loop over const sequences with quality scores. More...

class	ConstSiteIterator
	Generic const site iterator interface, allowing to loop over const sites. More...

class	DCSE
	Support for the Dedicated Comparative Sequence Editor format. More...

class	DefaultAlphabet
	The DefaultAlphabet class. More...

class	DefaultNucleotideScore
	Default Substitution Matrix for nucleotide alignments. More...

class	DistanceMatrix
	A Matrix class to store phylogenetic distances. More...

class	DNA
	This alphabet is used to deal with DNA sequences. More...

class	DNAToRNA
	Reverse iterator to convert RNA to DNA. More...

class	EchinodermMitochondrialGeneticCode
	This class implements the Echinoderm and Faltworms Mitochondrial genetic code as describe on the NCBI website: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG9. More...

class	EdSymbolList
	A event-driven SymbolList object. More...

class	EmptyContainerException
	Exception thrown when an empty container is found. More...

class	EmptySequenceException
	Exception thrown when a sequence is found to be empty and it should not. More...

class	EmptySiteException
	Exception sent when a empty site is found. More...

class	Fasta
	The fasta sequence file format. More...

class	GenBank
	The GenBank sequence file format. More...

class	GeneticCode
	Partial implementation of the Transliterator interface for genetic code object. More...

class	GranthamAAChemicalDistance
	Grantham (1974) Amino-Acid chemical distance. More...

class	GranthamAAPolarityIndex
	Polarity index used in Grantham (1974). More...

class	GranthamAAVolumeIndex
	Volume index used in Grantham (1974). More...

class	IAlignment
	The IAlignment interface. More...

class	IntegerAlphabet
	The Integer Alphabet class, letters are from 0 to a given number, MAX. More...

class	InvertebrateMitochondrialGeneticCode
	This class implements the Invertebrate Mitochondrial genetic code as describe on the NCBI website: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG5. More...

class	IOSequence
	The IOSequence interface. More...

class	IoSequenceFactory
	Utilitary class for creating sequence readers and writers. More...

class	IOSequenceStream
	The IOSequenceStream interface. More...

class	ISequence
	The ISequence interface. More...

class	ISequenceStream
	The ISequenceStream interface. More...

class	KleinAANetChargeIndex
	Charge of each amino acid. More...

class	LetterAlphabet
	Specialized partial implementation of Alphabet using single letters. More...

class	MapSequenceContainer
	MapSequenceContainer class. More...

class	Mase
	The mase sequence file format. More...

class	MaseHeader
	A class to store information from the header of Mase files. More...

class	MaseTools
	Utilitary methods that deal with the Mase format. More...

class	MiyataAAChemicalDistance
	Miyata et al. (1979) Amino-Acid chemical distance. More...

class	MoldMitochondrialGeneticCode
	This class implements the mold, protozoan, and coelenterate mitochondrial code and the Mycoplasma/Spiroplasma code as describe on the NCBI website: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG4. More...

class	NexusIOSequence
	The Nexus format reader for sequences. More...

class	NexusTools
	Tools for parsing Nexus files. More...

class	NoGapSiteContainerIterator
	Loop over all sites without gaps in a SiteContainer. More...

class	NucleicAcidsReplication
	Replication between to nucleic acids. More...

class	NucleicAlphabet
	The abstract base class for nucleic alphabets. More...

class	NucleicAlphabetState
	This is the base class to describe states in a NucleicAlphabet. More...

class	NumericAlphabet

class	OAlignment
	The OAlignment interface. More...

class	OrderedSequenceContainer
	The OrderedSequenceContainer interface. More...

class	OSequence
	The OSequence interface. More...

class	OSequenceStream
	The OSequenceStream interface. More...

class	PhredPhd
	The phd sequence file format from phred software. More...

class	PhredPoly
	The poly sequence file format from phred software. More...

class	Phylip
	The Phylip & co format. More...

class	ProteicAlphabet
	This alphabet is used to deal with proteins. More...

class	ProteicAlphabetState
	This is the base class to describe states in a ProteicAlphabet. More...

class	ReverseTransliterator
	The same as previous, but can perform the reverse translation, eg: RNA -> DNA and DNA -> RNA;. More...

class	RNA
	This alphabet is used to deal with RNA sequences. More...

class	RNY

class	Sequence
	The sequence interface. More...

class	SequenceAnnotation
	Interface for sequence annotations. More...

class	SequenceApplicationTools
	This class provides some common tools for applications. More...

class	SequenceContainer
	The SequenceContainer interface. More...

class	SequenceContainerTools
	Utilitary methods dealing with sequence containers. More...

class	SequenceException
	The sequence exception base class. More...

class	SequenceFileIndex
	Index to retrieve Sequence in a file. More...

class	SequenceIterator
	Generic sequence iterator interface, allowing to loop over sequences. More...

class	SequenceMask

class	SequenceNotAlignedException
	Exception thrown when a sequence is not align with others. More...

class	SequenceNotFoundException
	Exception thrown when a sequence is not found The sequence not found exception base class. More...

class	SequencePositionIterator
	Loop over a Sequence. More...

class	SequenceQuality
	The SequenceQuality class. More...

class	SequenceTools
	SequenceTools static class. More...

class	SequenceWalker
	A helper class to easily convert coordinates between sequence and alignments. More...

class	SequenceWithAnnotation
	An implementation of the Sequence interface that supports annotation. More...

class	SequenceWithAnnotationTools
	The SequenceWithAnnotationTools static class. More...

class	SequenceWithGapException
	Exception thrown when a sequence is found to have gap and it should not. More...

class	SequenceWithQuality
	A SequenceWithAnnotation class with quality scores attached. More...

class	SequenceWithQualityIterator
	Generic sequence iterator interface, allowing to loop over sequences with quality scores. More...

class	SequenceWithQualityTools
	The SequenceWithQualityTools static class. More...

class	SimpleIndexDistance
	Simple dissimilarity distance. More...

class	SimpleScore
	Simple Substitution Matrix, with match and mismatch penalties. More...

class	SimpleSequenceContainerIterator
	Loop over all sequences in a SequenceContainer. More...

class	SimpleSequencePositionIterator
	Loop over all positions in a Sequence. More...

class	SimpleSiteContainerIterator
	Loop over all sites in a SiteContainer. More...

class	Site
	The Site class. More...

class	SiteContainer
	The SiteContainer interface. More...

class	SiteContainerTools
	Some utililitary methods to deal with site containers. More...

class	SiteException
	The site exception base class. More...

class	SiteIterator
	Generic site iterator interface, allowing to loop over sites. More...

class	SiteNotFoundException
	The site not found exception base class. More...

class	SiteTools
	Utilitary methods dealing with sites. More...

class	SiteWithGapException
	Exception sent when a site containing gap is found. More...

class	StandardGeneticCode
	This class implements the standard genetic code as describe on the NCBI web site: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG1. More...

class	Stockholm
	The Stockholm alignment file format. More...

class	StopCodonException
	Exception thrown when a stop codon is found. More...

class	StreamSequenceIterator
	A sequence iterator based on a sequence stream. More...

class	StreamSequenceWithQualityIterator
	A sequence iterator based on a sequence stream. More...

class	StringSequenceTools
	Utilitary methods working on raw string objects. More...

class	SymbolList
	The SymbolList interface. More...

class	SymbolListDeletionEvent

class	SymbolListEditionEvent

class	SymbolListInsertionEvent

class	SymbolListListener

class	SymbolListSubstitutionEvent

class	SymbolListTools
	Utilitary functions dealing with both sites and sequences. More...

class	Transliterator
	This interface is used when translating a sequence from an alphabet to another: it gives the translation rules, eg: RNA -> DNA. More...

class	UserAlphabetIndex1
	Alphabet index given by user. More...

class	VectorSequenceContainer
	The VectorSequenceContainer class. More...

class	VectorSiteContainer
	The VectorSiteContainer class. More...

class	VertebrateMitochondrialGeneticCode
	This class implements the vertebrate mitochondrial genetic code as describe on the NCBI web site: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG2. More...

class	WordAlphabet
	The base class for word alphabets. More...

class	YeastMitochondrialGeneticCode
	This class implements the Invertebrate Mitochondrial genetic code as describe on the NCBI website: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG3. More...

Typedefs
typedef std::vector< size_t >	SequenceSelection

typedef std::vector< size_t >	SiteSelection

typedef std::vector< std::string >	Comments
	Declaration of Comments type. More...

Functions
bool	operator== (const Site &site1, const Site &site2)

bool	operator< (const Site &site1, const Site &site2)

Detailed Description

This alphabet is used to deal NumericAlphabet.

Author: Laurent Guéguen

.

Triplet "---" is the only triplet defined as gap. Other triplets with "-" are defined as unresolved.

Author: Laurent Gu�guen

Typedef Documentation

◆ Comments

typedef std::vector<std::string> bpp::Comments

Declaration of Comments type.

Comments are defined as a std::vector of std::strings to allow the later creation of a full Comments class.

Definition at line 60 of file Sequence.h.

◆ SequenceSelection

typedef std::vector<size_t> bpp::SequenceSelection

Definition at line 56 of file SequenceContainerTools.h.

◆ SiteSelection

typedef std::vector< size_t > bpp::SiteSelection

Definition at line 57 of file SequenceContainerTools.h.

Function Documentation

◆ operator<()

bool bpp::operator<	(	const Site &	site1,
		const Site &	site2
	)

Definition at line 95 of file Site.cpp.

References bpp::Site::getPosition().

◆ operator==()

bool bpp::operator==	(	const Site &	site1,
		const Site &	site2
	)

Definition at line 80 of file Site.cpp.

References bpp::Site::getPosition(), and bpp::BasicSymbolList::size().

Classes

Typedefs

Functions