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/*
Author: Scott Kuehn, Shane Neph
Date: Wed Sep 5 09:40:33 PDT 2007
*/
//
// BEDOPS
// Copyright (C) 2011-2022 Shane Neph, Scott Kuehn and Alex Reynolds
//
// This program 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 2 of the License, or
// (at your option) any later version.
//
// This program 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 this program; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
//
#ifndef OVR_AGGREGATE_VISITOR_HPP
#define OVR_AGGREGATE_VISITOR_HPP
#include <set>
#include "data/bed/BedCompare.hpp"
namespace Visitors {
namespace BedSpecific {
// Collect the total number of overlapping positions
template <
typename ProcessType,
typename BaseVisitor
>
struct OvrAggregate : BaseVisitor {
typedef BaseVisitor BaseClass;
typedef typename BaseClass::RefType RefType;
typedef typename BaseClass::MapType MapType;
OvrAggregate(const ProcessType& pt = ProcessType()) : ovr_(0), refItem_(0), pt_(pt)
{ /* */ }
inline void SetReference(RefType* t) {
refItem_ = t;
ovr_ = 0;
if ( !cache_.empty() ) {
for ( cacheI i = cache_.begin(); i != cache_.end(); ++i )
ovr_ += coordCompare(refItem_, *i);
}
}
inline void Delete(MapType* v) {
cacheI iter = cache_.find(v);
if ( iter != cache_.end() )
ovr_ -= coordCompare(refItem_, v);
cache_.erase(v);
}
inline void Add(MapType* v) {
cache_.insert(v);
ovr_ += coordCompare(refItem_, v);
}
inline void DoneReference() {
pt_.operator()(ovr_);
}
virtual ~OvrAggregate() { }
protected:
inline unsigned long coordCompare(RefType* t, MapType* v) {
if ( t->start() >= v->start() ) {
if ( v->end() > t->start() ) {
if( v->end() > t->end() )
return (t->end() - t->start());
else
return (v->end() - t->start());
}
else
return 0;
} else { // t->start() < v->start()
if ( t->end() > v->start() ) {
if ( v->end() < t->end() )
return (v->end() - v->start());
else
return (t->end() - v->start());
}
else
return 0;
}
}
protected:
typedef Bed::GenomicRestAddressCompare<MapType, MapType> Comp;
typedef std::set<MapType*, Comp> SType;
typedef typename SType::const_iterator cacheI;
unsigned long ovr_;
RefType* refItem_;
ProcessType pt_;
SType cache_;
};
} // namespace BedSpecific
} // namespace Visitors
#endif // OVR_AGGREGATE_VISITOR_HPP
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