DNA Class Reference

#include <bioseq.h>

Inheritance diagram for DNA:

List of all members.

Public Member Functions
	DNA ()
	DNA (const DNA &s)
	DNA (const string &s)
	DNA (const string &n, const string &s)
	DNA (const string &n, const string &s, const string &t)
	DNA (const bioseq &s)
	~DNA ()
DNA &	operator= (const DNA &s)
DNA &	operator= (const string &str)
Protein	translate () const
Protein	translate (int begin, int end=-1) const
DNA	subseq (int b, int e) const
const int *	getcodeNuc () const
sequenceType	getSequenceType () const
double	GCContent () const
double	GCContent (long int &A, long int &C, long int &G, long int &T, long int &N) const
void	revcomp ()
Protein	longestORFForward (int &b, int &e) const
void	longestORFForward (Protein &p, int &b, int &e) const
Protein	longestORFReverse (int &b, int &e) const
void	longestORFReverse (Protein &p, int &b, int &e) const
Protein	longestORF (char strand, int &b, int &e) const
Protein	longestORF (int &b, int &e) const
void	longestORF (Protein &p, int &b, int &e) const
Static Public Member Functions
static const codon &	getCodonTable ()
static void	setCodonTable (const int ctid)
Static Protected Attributes
static codon	codontable = codon()

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Detailed Description

this class add a few DNA specific operations These operation can be applied to cDNA or genomic DNA

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Constructor & Destructor Documentation

DNA::DNA

(

)

[inline]

DNA::DNA

(

const DNA &

s

)

[inline]

DNA::DNA

(

const string &

s

)

[inline]

DNA::DNA	(	const string &	n,
		const string &	s
	)			[inline]

DNA::DNA	(	const string &	n,
		const string &	s,
		const string &	t
	)			[inline]

DNA::DNA

(

const bioseq &

s

)

[inline]

DNA::~DNA

(

)

[inline]

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Member Function Documentation

DNA & DNA::operator=

(

const DNA &

s

)

References bioseq::operator=().

DNA & DNA::operator=

(

const string &

str

)

replace the underlying sequece with str

Reimplemented from bioseq.

References bioseq::operator=().

Protein DNA::translate

(

)

const

this is one essential operationn with cDNA CDS features of genomic DNA also use this feature. NNN => ?, may be I should use X

References codontable, and bioseq::seq.

Referenced by longestNoStartORFPlus(), longestNoStopORFPlus(), longestORFForward(), longestORFPlus(), longestORFPlusPrefix(), longestORFPlusSuffix(), main(), GenModel::makeProtein(), and GenModel::valid().

Protein DNA::translate	(	int	begin,
		int	end = -1
	)			const

use 1-based index This operation limits the operation to a subrange of the DNA sequence. This class use only one codon table that is static.

References codontable, and bioseq::seq.

DNA DNA::subseq	(	int	b,
		int	e
	)			const [inline]

performance is very bad if sequence is long. 1-based index, inclusive [b, e]

Reimplemented from bioseq.

References bioseq::subseq().

Referenced by bufferGenomic(), buildGeneInfo(), dumpFromModel(), dumpIntronExon(), and main().

const int * DNA::getcodeNuc

(

)

const

not implemented yet, could convert bases into integers like A=>0, C=>1, ... This method is different, use a different hashing method

References bioseq::code, hashbase(), bioseq::length(), and bioseq::seq.

sequenceType DNA::getSequenceType

(

)

const [inline, virtual]

Reimplemented from bioseq.

References DNASEQ.

double DNA::GCContent

(

)

const

return the fraction of GC/Length of sequence

References at, and bioseq::seq.

Referenced by dumpFromModel(), dumpIntronExon(), and main().

double DNA::GCContent	(	long int &	A,
		long int &	C,
		long int &	G,
		long int &	T,
		long int &	N
	)			const

another version for compute the accumulative GC content for all sequences in a file Add to the counts for the four bases and N, ignoring other bases

References bioseq::seq.

void DNA::revcomp

(

)

[inline]

use the inplace global function more efficient

References reverseComplementInPlace(), and bioseq::seq.

Referenced by ESTModel::ESTModel(), and longestORFReverse().

Protein DNA::longestORFForward	(	int &	b,
		int &	e
	)			const

return the longest peptide sequence in the + strand. set b,e to the range on DNA that give rise to this translation. b,e are C style index. [b,e)

References bioseq::length(), longestORFIndex(), bioseq::subsequence(), and translate().

Referenced by ESTModel::ESTModel(), longestORF(), longestORFReverse(), testLongestORF(), and testTranslate().

void DNA::longestORFForward	(	Protein &	p,
		int &	b,
		int &	e
	)			const

more efficient version, avoiding returning a long string.

References bioseq::length(), longestORFIndex(), bioseq::subsequence(), and translate().

Protein DNA::longestORFReverse	(	int &	b,
		int &	e
	)			const

[b,e) b>e from the lower strand (-)

References bioseq::length(), longestORFForward(), and revcomp().

Referenced by longestORF(), and testTranslate().

void DNA::longestORFReverse	(	Protein &	p,
		int &	b,
		int &	e
	)			const

References bioseq::length(), longestORFForward(), and revcomp().

Protein DNA::longestORF	(	char	strand,
		int &	b,
		int &	e
	)			const

References longestORFForward(), and longestORFReverse().

Referenced by mRNA::mRNA(), and testTranslate().

Protein DNA::longestORF	(	int &	b,
		int &	e
	)			const

References longestORFForward(), and longestORFReverse().

void DNA::longestORF	(	Protein &	p,
		int &	b,
		int &	e
	)			const

References longestORFForward(), and longestORFReverse().

static const codon& DNA::getCodonTable

(

)

[inline, static]

References codontable.

Referenced by translate().

static void DNA::setCodonTable

(

const int

ctid

)

[inline, static]

References codontable, and codon::use().

Referenced by main(), and testcodon().

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Member Data Documentation

codon DNA::codontable = codon() [static, protected]

all the DNA class use one codon table This is mostly for efficiency purposes. May have to add some other function to deal with particular codon tables. Even global function use this codon table for translation.

Referenced by getCodonTable(), setCodonTable(), and translate().

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The documentation for this class was generated from the following files:

• bioseq/bioseq.h
• bioseq/bioseq.cpp