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// Copyright 2008 Martin C. Frith
// This struct holds alignments, and includes a procedure to
// non-redundantize alignments that share endpoints.
#ifndef ALIGNMENTPOT_HH
#define ALIGNMENTPOT_HH
#include "Alignment.hh"
#include <algorithm> // sort
#include <vector>
namespace cbrc{
struct AlignmentPot{
typedef std::vector<Alignment>::iterator iterator;
// add an alignment to the pot
void add( const Alignment& aln ) { items.push_back(aln); }
// the number of alignments in the pot
size_t size() const { return items.size(); }
// if several alignments share an endpoint, erase all but one
// highest-scoring alignment
void eraseSuboptimal();
// sort the alignments in ascending order of score
void sort() { std::sort(items.begin(), items.end(), lessScore); }
// data:
std::vector<Alignment> items;
static bool lessScore(const Alignment &x, const Alignment &y) {
// Try to break ties, so that alignments come in a consistent
// order. This makes it easier to compare different results.
return x.score != y.score ? x.score < y.score : !lessBeg(x, y);
}
static bool lessBeg( const Alignment& x, const Alignment& y ){
if( x.beg1() != y.beg1() ) return x.beg1() < y.beg1();
if( x.beg2() != y.beg2() ) return x.beg2() < y.beg2();
if( x.score != y.score ) return x.score > y.score;
// arbitrary (but systematic) order:
const SegmentPair& a = x.seed;
const SegmentPair& b = y.seed;
return a.beg1() != b.beg1() ? a.beg1() < b.beg1() : a.beg2() < b.beg2();
}
static bool lessEnd( const Alignment& x, const Alignment& y ){
if( x.end1() != y.end1() ) return x.end1() < y.end1();
if( x.end2() != y.end2() ) return x.end2() < y.end2();
if( x.score != y.score ) return x.score > y.score;
// arbitrary (but systematic) order:
const SegmentPair& a = x.seed;
const SegmentPair& b = y.seed;
return a.beg1() != b.beg1() ? a.beg1() < b.beg1() : a.beg2() < b.beg2();
}
static void mark( Alignment& a ) { a.blocks[0].score = -1; }
static bool isMarked( Alignment& a ) { return a.blocks[0].score == -1; }
};
} // end namespace cbrc
#endif // ALIGNMENTPOT_HH
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