/usr/include/pbbam/Interval.h is in libpbbam-dev 0.7.4+ds-1.
This file is owned by root:root, with mode 0o644.
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//
// All rights reserved.
//
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// modification, are permitted (subject to the limitations in the
// disclaimer below) provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
//
// * Neither the name of Pacific Biosciences nor the names of its
// contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
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// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
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// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
// SUCH DAMAGE.
//
// File Description
/// \file Interval.h
/// \brief Defines the Interval class.
//
// Author: Derek Barnett
#ifndef INTERVAL_H
#define INTERVAL_H
#include "pbbam/Config.h"
#include <string>
#define BOOST_ICL_USE_STATIC_BOUNDED_INTERVALS
#include <boost/icl/discrete_interval.hpp>
#include <boost/icl/interval_traits.hpp>
namespace PacBio {
namespace BAM {
/// \brief Represents a half-open (right-open) interval [start, stop)
///
/// \note This class is agnostic whether the values are 0-based or 1-based.
/// Client code should primarily work with GenomicInterval, which does
/// enforce this distinction.
///
template<typename T>
class Interval
{
public:
typedef boost::icl::discrete_interval<T> interval_type;
public:
/// \name Constructors & Related Methods
/// \{
/// \brief Creates an empty interval [0,0)
Interval(void);
/// \brief Creates a 'singleton' interval [val,val+1)
Interval(const T val);
/// brief Creates an interval from [start, stop) */
Interval(const T start, const T stop);
Interval(const Interval<T>& other);
/// \}
public:
/// \name Comparison Operators
/// \{
/// \returns true if both intervals share the same endpoints
bool operator==(const Interval<T>& other) const;
/// \returns true if either interval's endpoints differ
bool operator!=(const Interval<T>& other) const;
/// \}
public:
/// \name Attributes
/// \{
/// \returns interval's start coordinate
T Start(void) const;
/// Sets this interval's start coordinate.
///
/// \param[in] start
/// \returns reference to this interval
///
Interval<T>& Start(const T& start);
/// \returns interval's stop coordinate
T Stop(void) const;
/// Sets this interval's stop coordinate.
///
/// \param[in] stop
/// \returns reference to this interval
///
Interval<T>& Stop(const T& stop);
/// \}
public:
/// \name Interval Operations
/// \returns true if this interval is fully covered by (or contained in) \p other
bool CoveredBy(const Interval<T>& other) const;
//// \returns true if this interval covers (or contains) \p other
bool Covers(const Interval<T>& other) const;
/// \returns true if intervals interset
bool Intersects(const Interval<T>& other) const;
/// \returns true if interval is valid (e.g. start < stop)
bool IsValid(void) const;
/// \returns interval length
size_t Length(void) const;
/// \}
private:
interval_type data_;
};
} // namespace BAM
} // namspace PacBio
#include "pbbam/internal/Interval.inl"
#endif // GENOMICINTERVAL_H
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