polya.hpp File Reference

#include <corelib/ncbistd.hpp>
#include <util/range.hpp>

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Classes
class	CRevComp_It< Iterator >
	Implementation [in header because of templates]. More...

Enumerations
enum	EPolyTail { ePolyTail_None , ePolyTail_A3 , ePolyTail_T5 }

Functions
template<typename Iterator >
TSignedSeqPos	FindPolyA (Iterator begin, Iterator end)
	PRE : two random access iterators pointing to sequence data [begin, end) POST: poly-A tail cleavage site, if any (-1 if not) More...
template<typename Iterator >
EPolyTail	FindPolyTail (Iterator begin, Iterator end, TSignedSeqPos &cleavageSite, TSeqPos min_length=1)
	PRE : two random access iterators pointing to sequence data [begin, end); minimum length for tail POST: cleavageSite (if any) and whether we found a poly-A tail, a poly-T head, or neither. More...
template<typename Iterator >
TSeqRange	FindPolyARange (Iterator begin, Iterator end, TSeqPos max_following_bases)
	PRE : two random access iterators pointing to sequence data [begin, end); maximum number of non-A bases that are allowed to follow the tail POST: poly-A tail range, if any (empty range if not) More...
template<typename Iterator >
EPolyTail	FindPolyTail (Iterator begin, Iterator end, TSeqRange &tail, TSeqPos min_length=1, TSeqPos max_following_bases=0)
	PRE : two random access iterators pointing to sequence data [begin, end); minimum length for tail; maximum number of non-A bases that are allowed to follow the tail POST: poly-tail range (if any) and whether we found a poly-A tail, a poly-T head, or neither. More...
template<typename ForwardIterator1 , typename ForwardIterator2 >
ForwardIterator1	ItrSearch (ForwardIterator1 first1, ForwardIterator1 last1, ForwardIterator2 first2, ForwardIterator2 last2)

Enumeration Type Documentation

EPolyTail

enum EPolyTail

Enumerator
ePolyTail_None
ePolyTail_A3
ePolyTail_T5

Definition at line 40 of file polya.hpp.

Function Documentation

FindPolyA()

template<typename Iterator >

TSignedSeqPos FindPolyA	(	Iterator	begin,
		Iterator	end
	)

PRE : two random access iterators pointing to sequence data [begin, end) POST: poly-A tail cleavage site, if any (-1 if not)

Definition at line 211 of file polya.hpp.

References COpenRange< Position >::Empty(), FindPolyARange(), and CRange_Base::GetFrom().

FindPolyARange()

template<typename Iterator >

TSeqRange FindPolyARange	(	Iterator	begin,
		Iterator	end,
		TSeqPos	max_following_bases
	)

PRE : two random access iterators pointing to sequence data [begin, end); maximum number of non-A bases that are allowed to follow the tail POST: poly-A tail range, if any (empty range if not)

PRE : two random access iterators pointing to sequence data [begin, end) POST: poly-A tail range, if any (empty range if not)

Definition at line 222 of file polya.hpp.

References ItrSearch().

Referenced by FindPolyA(), and FindPolyTail().

FindPolyTail() [1/2]

template<typename Iterator >

EPolyTail FindPolyTail	(	Iterator	begin,
		Iterator	end,
		TSeqRange &	tail,
		TSeqPos	min_length = 1,
		TSeqPos	max_following_bases = 0
	)

PRE : two random access iterators pointing to sequence data [begin, end); minimum length for tail; maximum number of non-A bases that are allowed to follow the tail POST: poly-tail range (if any) and whether we found a poly-A tail, a poly-T head, or neither.

PRE : two random access iterators pointing to sequence data [begin, end); minimum length for tail POST: poly-tail range (if any) and whether we found a poly-A tail, a poly-T head, or neither.

Definition at line 317 of file polya.hpp.

References ePolyTail_A3, ePolyTail_None, ePolyTail_T5, FindPolyARange(), CRange_Base::GetFrom(), COpenRange< Position >::GetLength(), CRange_Base::GetTo(), and COpenRange< Position >::Set().

FindPolyTail() [2/2]

template<typename Iterator >

EPolyTail FindPolyTail	(	Iterator	begin,
		Iterator	end,
		TSignedSeqPos &	cleavageSite,
		TSeqPos	min_length = 1
	)

PRE : two random access iterators pointing to sequence data [begin, end); minimum length for tail POST: cleavageSite (if any) and whether we found a poly-A tail, a poly-T head, or neither.

Definition at line 297 of file polya.hpp.

References ePolyTail_A3, ePolyTail_T5, CRange_Base::GetFrom(), CRange_Base::GetTo(), and type.

Referenced by BOOST_AUTO_TEST_CASE().

ItrSearch()

template<typename ForwardIterator1 , typename ForwardIterator2 >

ForwardIterator1 ItrSearch	(	ForwardIterator1	first1,
		ForwardIterator1	last1,
		ForwardIterator2	first2,
		ForwardIterator2	last2
	)

Definition at line 178 of file polya.hpp.

Referenced by FindPolyARange().