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/*
Author: Shane Neph & Scott Kuehn
Date: Dec. 7, 2009
*/
//
// 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 _BED_BASE_VISITOR_HPP
#define _BED_BASE_VISITOR_HPP
#include <list>
#include <set>
#include <type_traits>
#include "algorithm/WindowSweep.hpp"
#include "data/bed/BedCompare.hpp"
#include "data/bed/BedDistances.hpp"
#include "utility/Assertion.hpp"
#include "utility/Exception.hpp"
/*
Bed types are not sequences of simple numbers. WindowSweep::sweep() can
be used with both types, but there are inherent difficulties with BED.
Take, for instance, the properly ordered coordinates:
Problem 1:
chr1 0 100
chr1 23 25
chr1 23 107
chr1 30 45
chr1 31 32
chr1 99 100
chr1 101 107
When the first element is evaluated, everything but the last row is part
of the current window. When you change to the second row, chr1 99 100 is
no longer part of the current window. Then it is for the 3rd row, then
not for the 4th. We do not account for such possibilities within sweep()
or the main Visitor baseclass via events.
BedBaseVisitor implements logic to deal with these problems, and issues
events to subclasses appropriately. Bed type visitors should inherit
from BedBaseVisitor and use its public interface.
The same sort of issue exists on the left end.
Problem 2:
chr1 0 100
chr1 23 25
chr1 39 100
When the 3rd row is the current item, row 2 does not make up its window,
but row 1 does. Once row 2 is behind and out of scope relative to the
current item; it never comes back into play.
I believe memory management can no longer be passed down to derived classes
due to buffering that goes on within this class. I haven't thought about
it much yet as no Visitor has yet needed its own memory management.
I have tried optimizing things when the overlap method is based upon bp's and
not percentages and received much better runtimes. Unfortunately, my assumptions
were wrong. The bottom line is that you need to look at every element in the
current window, both going out of range to the left and coming into range on
the right in fixWindow(). Here is the case that fails:
chr1 1 200 a 1
chr1 10 20 b 3
chr1 50 150 c 4
when used with bedmap --bp-ovr 11 --count -
row 2 has no hits, but row 1 goes with row 3's output. Cannot assume that once
row 2 is out of range that everything to the left of it is out of range too,
even when looking at straight bp's. The main issue shown here is that the
--bp-ovr 11 is larger than row 2's range. It can never qualify but row 1 can.
All of the problems mentioned can be attributed to fully nested elements. There
are scenarios without fully nested elements that are problematic too without this
BedBaseVisitor. For example, consider using Visitors.hpp as base class with the
bedmap application under the following scenario:
bedmap --fraction-map 0.1 --echo --count with the following file:
chr1 564622 564633
chr1 564629 564637
chr1 564634 564677
chr1 564673 564681
chr1 564974 565006
chr1 564978 565023
chr1 565007 565040
chr1 565256 565294
When at line 2, line 3 does not map b/c 0.1*43nt = 4nt while line 2 and line 3
overlap by 3 nt. But, when we go to line 3 as the reference, line 2 is an
overlapping element that qualifies since its size is 8 nt (0.1*8nt -> any
overlap satisfies). Unfortunately, sweep() has already flushed out line 2
since it has the inherent symmetry assumption: dist(a,b) == dist(b,a).
BedBaseVisitor deals with this scenario properly.
*/
namespace Visitors {
template <typename BedDist, typename Ref, typename Map = Ref>
struct BedBaseVisitor {
typedef BedDist DistType;
typedef Ref RefType;
typedef Map MapType;
protected:
// typedefs
typedef std::set<MapType*, Bed::CoordRestAddressCompare<MapType>> OrderLesser;
typedef OrderLesser OrderCache;
typedef OrderLesser OrderWin;
public:
// Interface for sweep()
inline bool ManagesOwnMemory() const { return(false); }
inline void OnStart(RefType* t) {
// Give derived class the new reference
ref_ = t;
SetReference(t);
}
inline void OnAdd(MapType* u) {
// Add(u); Do not add until deletions done in fixWindow()
cache_.insert(u);
}
inline void OnDelete(MapType* u) {
static typename OrderWin::iterator winIter;
winIter = win_.find(u);
if ( winIter != win_.end() ) { // update
Delete(u);
win_.erase(winIter);
} else {
cache_.erase(u);
}
}
void OnDone() {
fixWindow(); // deletions before insertions
DoneReference();
}
inline void OnEnd() {
End();
win_.clear();
cache_.clear();
}
inline void OnPurge() {
// bed types can violate sweep's OnPurge() checks and they aren't really needed
}
explicit BedBaseVisitor(const DistType& d = DistType()) : dist_(d)
{ /* */ }
virtual ~BedBaseVisitor() { /* */ }
// Derived Class interface : Must be public due to MultiVisitor-type usage
virtual void Delete(MapType*) = 0;
virtual void Add(MapType*) = 0;
virtual void DoneReference() = 0;
virtual inline void SetReference(RefType*) { /* */ }
virtual inline void End() { /* */ }
private:
void fixWindow() {
// Deletions must come before insertions for consistency with sweep()
// Realize that, at a minimum, ref_ has changed -> all time-consuming
// checks are necessary
// Are any items in the window really out of range of 't'? See problem 2.
static std::list<MapType*> lst;
auto winIter = win_.begin();
while ( winIter != win_.end() ) {
if ( dist_.Map2Ref(*winIter, ref_) != 0 ) {
Delete(*winIter);
lst.push_back(*winIter);
win_.erase(winIter++);
} else {
++winIter;
}
} // while
auto cacheIter = cache_.begin();
while ( cacheIter != cache_.end() ) {
if ( 0 == dist_.Map2Ref(*cacheIter, ref_) ) {
Add(*cacheIter);
win_.insert(*cacheIter);
cache_.erase(cacheIter++);
} else {
++cacheIter;
}
} // while
cache_.insert(lst.begin(), lst.end());
lst.clear();
}
private:
// MUST use a set with value/address compare here instead of a std::multiset
// This is for deleting elements and making sure multiple rows with the
// same coordinates each receive Delete() calls to derived classes.
DistType dist_;
RefType* ref_;
OrderCache cache_;
OrderWin win_;
};
} // namespace Visitors
#endif // _BED_BASE_VISITOR_HPP
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