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NCBI C++ ToolKit: include/algo/cobalt/base.hpp Source File

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1 #ifndef ALGO_COBALT___BASE__HPP 2 #define ALGO_COBALT___BASE__HPP 56 

template<class Position>

88

TParent::GetFrom() <=

r

.GetFrom() &&

89

TParent::GetToOpen() >=

r

.GetFrom() &&

90

TParent::GetFrom() <=

r

.GetToOpen() &&

91

TParent::GetToOpen() >=

r

.GetToOpen();

102  return

TParent::GetToOpen() <=

r

.TParent::GetFrom();

109

TParent::Set(TParent::GetPositionMax(), TParent::GetPositionMin());

static const int kAlphabetSize

The aligner internally works only with the ncbistdaa alphabet.

int TOffset

Basic data type for offsets into a sequence.

CLocalRange< TOffset > TRange

define for the fundamental building block of sequence ranges

pair< TOffset, TOffset > TOffsetPair

Basic type specifying a range on a sequence.

Sufficient extra functionality is needed from CRange that it justifies extending the class.

CLocalRange()

default constructor

TParent::position_type position_type

underlying type

CLocalRange< Position > TThisType

shorthand

bool StrictlyBelow(const TThisType &r)

Test whether 'this' represents a sequence range strictly less than a given sequence range.

CRange< Position > TParent

parent class

CLocalRange(position_type from, position_type to)

convert offsets into a range

CLocalRange(const TParent &range)

convert parent class to a range

bool Contains(const TThisType &r)

Test whether 'this' completely envelops a given sequence range.

void SetEmpty()

Initialize an empty range.

bool Empty(const CNcbiOstrstream &src)

TParent::position_type position_type

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

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