base.hpp

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#ifndef ALGO_COBALT___BASE__HPP
#define ALGO_COBALT___BASE__HPP
 
/* $Id: base.hpp 35542 2007-09-24 15:34:03Z papadopo $
* ===========================================================================
*
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*               National Center for Biotechnology Information
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*  terms of the United States Copyright Act.  It was written as part of
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/*****************************************************************************
 
File name: base.hpp
 
Author: Jason Papadopoulos
 
Contents: Definitions used by all COBALT aligner components
 
******************************************************************************/
 
/// @file base.hpp
/// Definitions used by all COBALT aligner components
 
#include <util/range.hpp>
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(cobalt)
 
/// Basic data type for offsets into a sequence. By
/// convention, all offsets are zero-based
typedef int TOffset;
 
/// Basic type specifying a range on a sequence
typedef pair<TOffset, TOffset> TOffsetPair;
 
/// Sufficient extra functionality is needed from CRange
/// that it justifies extending the class
template<class Position>
class CLocalRange : public CRange<Position>
{
public:
    typedef CRange<Position> TParent;                       ///< parent class
    typedef typename TParent::position_type position_type;  ///< underlying type
    typedef CLocalRange<Position> TThisType;                ///< shorthand
 
    /// default constructor
    CLocalRange() {}
 
    /// convert offsets into a range
    /// @param from Start offset
    /// @param to End offset
    ///
    CLocalRange(position_type from, position_type to)
        : TParent(from, to) {}
 
    /// convert parent class to a range
    /// @param range Reference to an object of the parent class
    ///
    CLocalRange(const TParent& range)
        : TParent(range) {}
 
    /// Test whether 'this' completely envelops
    /// a given sequence range
    /// @param r Range to test for containment
    /// @return true if 'this' envelops r, false otherwise
    ///
    bool Contains(const TThisType& r)
    {
        return !TParent::Empty() && 
               TParent::GetFrom() <= r.GetFrom() &&
               TParent::GetToOpen() >= r.GetFrom() &&
               TParent::GetFrom() <= r.GetToOpen() &&
               TParent::GetToOpen() >= r.GetToOpen();
    }
 
    /// Test whether 'this' represents a sequence range
    /// strictly less than a given sequence range
    /// @param r Range to test for disjointness
    /// @return true if offsets of 'this' are strictly
    ///         below the offsets of r, false otherwise
    ///
    bool StrictlyBelow(const TThisType& r)
    {
        return TParent::GetToOpen() <= r.TParent::GetFrom();
    }
 
    /// Initialize an empty range
    ///
    void SetEmpty()
    {
        TParent::Set(TParent::GetPositionMax(), TParent::GetPositionMin());
    }
};
 
/// define for the fundamental building block
/// of sequence ranges
typedef CLocalRange<TOffset> TRange;
 
/// The aligner internally works only with the 
/// ncbistdaa alphabet
static const int kAlphabetSize = 28;
 
END_SCOPE(cobalt)
END_NCBI_SCOPE
 
#endif // ALGO_COBALT___BASE__HPP