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/*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Bowtie 2 is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef REF_COORD_H_
#define REF_COORD_H_
#include <stdint.h>
#include <iostream>
#include <limits>
#include "assert_helpers.h"
typedef int64_t TRefId;
typedef int64_t TRefOff;
/**
* Encapsulates a reference coordinate; i.e. identifiers for
* (a) a reference sequence, and
* (b) a 0-based offset into that sequence.
*/
class Coord {
public:
Coord() { reset(); }
Coord(const Coord& c) { init(c); }
Coord(TRefId rf, TRefOff of, bool fw) { init(rf, of, fw); }
/**
* Copy given fields into this Coord.
*/
void init(TRefId rf, TRefOff of, bool fw) {
ref_ = rf;
off_ = of;
orient_ = (fw ? 1 : 0);
}
/**
* Copy contents of given Coord into this one.
*/
void init(const Coord& c) {
ref_ = c.ref_;
off_ = c.off_;
orient_ = c.orient_;
}
/**
* Return true iff this Coord is identical to the given Coord.
*/
bool operator==(const Coord& o) const {
assert(inited());
assert(o.inited());
return ref_ == o.ref_ && off_ == o.off_ && fw() == o.fw();
}
/**
* Return true iff this Coord is less than the given Coord. One Coord is
* less than another if (a) its reference id is less, (b) its orientation is
* less, or (c) its offset is less.
*/
bool operator<(const Coord& o) const {
if(ref_ < o.ref_) return true;
if(ref_ > o.ref_) return false;
if(orient_ < o.orient_) return true;
if(orient_ > o.orient_) return false;
if(off_ < o.off_) return true;
if(off_ > o.off_) return false;
return false;
}
/**
* Return the opposite result from operator<.
*/
bool operator>=(const Coord& o) const {
return !((*this) < o);
}
/**
* Return true iff this Coord is greater than the given Coord. One Coord
* is greater than another if (a) its reference id is greater, (b) its
* orientation is greater, or (c) its offset is greater.
*/
bool operator>(const Coord& o) const {
if(ref_ > o.ref_) return true;
if(ref_ < o.ref_) return false;
if(orient_ > o.orient_) return true;
if(orient_ < o.orient_) return false;
if(off_ > o.off_) return true;
if(off_ < o.off_) return false;
return false;
}
/**
* Return the opposite result from operator>.
*/
bool operator<=(const Coord& o) const {
return !((*this) > o);
}
/**
* Reset this coord to uninitialized state.
*/
void reset() {
ref_ = std::numeric_limits<TRefId>::max();
off_ = std::numeric_limits<TRefOff>::max();
orient_ = -1;
}
/**
* Return true iff this Coord is initialized (i.e. ref and off have both
* been set since the last call to reset()).
*/
bool inited() const {
if(ref_ != std::numeric_limits<TRefId>::max() &&
off_ != std::numeric_limits<TRefOff>::max())
{
assert(orient_ == 0 || orient_ == 1);
return true;
}
return false;
}
/**
* Get orientation of the Coord.
*/
bool fw() const {
assert(inited());
assert(orient_ == 0 || orient_ == 1);
return orient_ == 1;
}
#ifndef NDEBUG
/**
* Check that coord is internally consistent.
*/
bool repOk() const {
if(ref_ != std::numeric_limits<TRefId>::max() &&
off_ != std::numeric_limits<TRefOff>::max())
{
assert(orient_ == 0 || orient_ == 1);
}
return true;
}
#endif
/**
* Check whether an interval defined by this coord and having
* length 'len' is contained within an interval defined by
* 'inbegin' and 'inend'.
*/
bool within(int64_t len, int64_t inbegin, int64_t inend) const {
return off_ >= inbegin && off_ + len <= inend;
}
inline TRefId ref() const { return ref_; }
inline TRefOff off() const { return off_; }
inline int orient() const { return orient_; }
inline void setRef(TRefId id) { ref_ = id; }
inline void setOff(TRefOff off) { off_ = off; }
inline void adjustOff(TRefOff off) { off_ += off; }
protected:
TRefId ref_; // which reference?
TRefOff off_; // 0-based offset into reference
int orient_; // true -> Watson strand
};
std::ostream& operator<<(std::ostream& out, const Coord& c);
/**
* Encapsulates a reference interval, which consists of a Coord and a length.
*/
class Interval {
public:
Interval() { reset(); }
explicit Interval(const Coord& upstream, TRefOff len) {
init(upstream, len);
}
explicit Interval(TRefId rf, TRefOff of, bool fw, TRefOff len) {
init(rf, of, fw, len);
}
void init(const Coord& upstream, TRefOff len) {
upstream_ = upstream;
len_ = len;
}
void init(TRefId rf, TRefOff of, bool fw, TRefOff len) {
upstream_.init(rf, of, fw);
len_ = len;
}
/**
* Set offset.
*/
void setOff(TRefOff of) {
upstream_.setOff(of);
}
/**
* Set length.
*/
void setLen(TRefOff len) {
len_ = len;
}
/**
* Reset this interval to uninitialized state.
*/
void reset() {
upstream_.reset();
len_ = 0;
}
/**
* Return true iff this Interval is initialized.
*/
bool inited() const {
if(upstream_.inited()) {
assert_gt(len_, 0);
return true;
} else {
return false;
}
}
/**
* Return true iff this Interval is equal to the given Interval,
* i.e. if they cover the same set of positions.
*/
bool operator==(const Interval& o) const {
return upstream_ == o.upstream_ &&
len_ == o.len_;
}
/**
* Return true iff this Interval is less than the given Interval.
* One interval is less than another if its upstream location is
* prior to the other's or, if their upstream locations are equal,
* if its length is less than the other's.
*/
bool operator<(const Interval& o) const {
if(upstream_ < o.upstream_) return true;
if(upstream_ > o.upstream_) return false;
if(len_ < o.len_) return true;
return false;
}
/**
* Return opposite result from operator<.
*/
bool operator>=(const Interval& o) const {
return !((*this) < o);
}
/**
* Return true iff this Interval is greater than than the given
* Interval. One interval is greater than another if its upstream
* location is after the other's or, if their upstream locations
* are equal, if its length is greater than the other's.
*/
bool operator>(const Interval& o) const {
if(upstream_ > o.upstream_) return true;
if(upstream_ < o.upstream_) return false;
if(len_ > o.len_) return true;
return false;
}
/**
* Return opposite result from operator>.
*/
bool operator<=(const Interval& o) const {
return !((*this) > o);
}
/**
* Set upstream Coord.
*/
void setUpstream(const Coord& c) {
upstream_ = c;
}
/**
* Set length.
*/
void setLength(TRefOff l) {
len_ = l;
}
inline TRefId ref() const { return upstream_.ref(); }
inline TRefOff off() const { return upstream_.off(); }
inline TRefOff dnoff() const { return upstream_.off() + len_; }
inline int orient() const { return upstream_.orient(); }
/**
* Return a Coord encoding the coordinate just past the downstream edge of
* the interval.
*/
inline Coord downstream() const {
return Coord(
upstream_.ref(),
upstream_.off() + len_,
upstream_.orient());
}
/**
* Return true iff the given Coord is inside this Interval.
*/
inline bool contains(const Coord& c) const {
return
c.ref() == ref() &&
c.orient() == orient() &&
c.off() >= off() &&
c.off() < dnoff();
}
/**
* Return true iff the given Coord is inside this Interval, without
* requiring orientations to match.
*/
inline bool containsIgnoreOrient(const Coord& c) const {
return
c.ref() == ref() &&
c.off() >= off() &&
c.off() < dnoff();
}
/**
* Return true iff the given Interval is inside this Interval.
*/
inline bool contains(const Interval& c) const {
return
c.ref() == ref() &&
c.orient() == orient() &&
c.off() >= off() &&
c.dnoff() <= dnoff();
}
/**
* Return true iff the given Interval is inside this Interval, without
* requiring orientations to match.
*/
inline bool containsIgnoreOrient(const Interval& c) const {
return
c.ref() == ref() &&
c.off() >= off() &&
c.dnoff() <= dnoff();
}
/**
* Return true iff the given Interval overlaps this Interval.
*/
inline bool overlaps(const Interval& c) const {
return
c.ref() == upstream_.ref() &&
c.orient() == upstream_.orient() &&
((off() <= c.off() && dnoff() > c.off()) ||
(off() <= c.dnoff() && dnoff() > c.dnoff()) ||
(c.off() <= off() && c.dnoff() > off()) ||
(c.off() <= dnoff() && c.dnoff() > dnoff()));
}
/**
* Return true iff the given Interval overlaps this Interval, without
* requiring orientations to match.
*/
inline bool overlapsIgnoreOrient(const Interval& c) const {
return
c.ref() == upstream_.ref() &&
((off() <= c.off() && dnoff() > c.off()) ||
(off() <= c.dnoff() && dnoff() > c.dnoff()) ||
(c.off() <= off() && c.dnoff() > off()) ||
(c.off() <= dnoff() && c.dnoff() > dnoff()));
}
inline const Coord& upstream() const { return upstream_; }
inline TRefOff len() const { return len_; }
#ifndef NDEBUG
/**
* Check that the Interval is internally consistent.
*/
bool repOk() const {
assert(upstream_.repOk());
assert_geq(len_, 0);
return true;
}
#endif
inline void adjustOff(TRefOff off) { upstream_.adjustOff(off); }
protected:
Coord upstream_;
TRefOff len_;
};
std::ostream& operator<<(std::ostream& out, const Interval& c);
#endif /*ndef REF_COORD_H_*/
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