seqan-dev 1.3.1-1 / usr / include / seqan / find / find_bom.h

// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2010, Knut Reinert, FU Berlin
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// ==========================================================================
// Author: Tobias Rausch <rausch@embl.de>
// ==========================================================================

#ifndef SEQAN_HEADER_FIND_BOM_H
#define SEQAN_HEADER_FIND_BOM_H

namespace SEQAN_NAMESPACE_MAIN
{

//////////////////////////////////////////////////////////////////////////////
// BomAlgo
//////////////////////////////////////////////////////////////////////////////

/**
.Spec.Bfam:
..summary:Backward Factor Automaton Matching algorithm.
..general:Class.Pattern
..cat:Searching
..signature:Pattern<TNeedle, Bfam<TAutomaton> >
..param.TNeedle:The needle type.
...type:Class.String
..param.TAutomaton:A tag that specifies the used automaton.
...default:@Spec.Bfam<Oracle>@
..remarks.text:To be used in combination with the default specialization of @Class.Finder@.
..include:seqan/find.h
*/

/**
.Spec.Bfam<Oracle>:
..summary:Backward Oracle Matching algorithm.
..general:Spec.Bfam
..cat:Searching
..signature:Pattern<TNeedle, Bfam<Oracle> >
..param.TNeedle:The needle type.
...type:Class.String
..remarks.text:To be used in combination with the default specialization of @Class.Finder@.
..see:Spec.Bfam<Trie>
..include:seqan/find.h
*/
/**
.Spec.Bfam<Trie>:
..summary:Backward Suffix Trie Matching algorithm.
..general:Spec.Bfam
..cat:Searching
..signature:Pattern<TNeedle, Bfam<Trie> >
..param.TNeedle:The needle type.
...type:Class.String
..remarks.text:To be used in combination with the default specialization of @Class.Finder@.
..see:Spec.Bfam<Oracle>
..include:seqan/find.h
*/

///.Class.Pattern.param.TSpec.type:Spec.Bfam

struct Oracle; //Oracle Tag => "BOM"
struct Trie; //Trie Tag => "BTM"

template <typename TSpec = Oracle>
struct Bfam; //backward factor automaton searching

typedef Bfam<Oracle> BomAlgo; //deprecated, still there for compatibility reasons

//////////////////////////////////////////////////////////////////////////////

template <typename TNeedle, typename TSpec>
class Pattern<TNeedle, Bfam<TSpec> > {
//____________________________________________________________________________
public:
	typedef typename Value<TNeedle>::Type TAlphabet;
	typedef typename Size<TNeedle>::Type TSize;
	Holder<TNeedle> data_host;
	TSize needleLength;
	TSize haystackLength;
	TSize step;
	Graph<Automaton<TAlphabet, void, WithoutEdgeId> > automaton;

//____________________________________________________________________________

	Pattern() {
	}

	template <typename TNeedle2>
	Pattern(TNeedle2 const & ndl)
	{
SEQAN_CHECKPOINT
		setHost(*this, ndl);
	}

	~Pattern() {
		SEQAN_CHECKPOINT
	}
//____________________________________________________________________________
};

//////////////////////////////////////////////////////////////////////////////
// Host Metafunctions
//////////////////////////////////////////////////////////////////////////////

template <typename TNeedle>
struct Host< Pattern<TNeedle, BomAlgo> >
{
	typedef TNeedle Type;
};

template <typename TNeedle>
struct Host< Pattern<TNeedle, BomAlgo> const>
{
	typedef TNeedle const Type;
};


//////////////////////////////////////////////////////////////////////////////
// Functions
//////////////////////////////////////////////////////////////////////////////

//Bfam<Oracle>: BOM Algorithm
template <typename TNeedle, typename TNeedle2>
inline void 
setHost (Pattern<TNeedle, Bfam<Oracle> > & me, TNeedle2 const& needle) 
{
	SEQAN_CHECKPOINT
	me.needleLength = length(needle);
	clear(me.automaton);
	createOracleOnReverse(me.automaton,needle);
	setValue(me.data_host, needle);
}

//Bfam<Trie>: BTM Algorithm (the same as BOM, but with an trie)
template <typename TNeedle, typename TNeedle2>
inline void 
setHost (Pattern<TNeedle, Bfam<Trie> > & me, TNeedle2 const& needle) 
{
	SEQAN_CHECKPOINT;
	typedef typename Position<TNeedle>::Type TPosition;
	me.needleLength = length(needle);
	clear(me.automaton);

	String<String<TPosition> > terminal_state_map; //dummy
	typedef typename Value<TNeedle2 const>::Type TValue;
	String<TValue> reverse_string = needle;
	reverse(reverse_string);

	createSuffixTrie(me.automaton, terminal_state_map, reverse_string);

	setValue(me.data_host, needle);
}

template <typename TNeedle, typename TNeedle2, typename TSpec>
inline void 
setHost (Pattern<TNeedle, Bfam<TSpec> > & me, TNeedle2 & needle)
{
	setHost(me, reinterpret_cast<TNeedle2 const &>(needle));
}

//____________________________________________________________________________


template <typename TNeedle, typename TSpec>
inline void _patternInit (Pattern<TNeedle, Bfam<TSpec> > & me) 
{
SEQAN_CHECKPOINT
	me.step = 0;
}


//____________________________________________________________________________


template <typename TFinder, typename TNeedle, typename TSpec>
inline bool 
find(TFinder & finder, Pattern<TNeedle, Bfam<TSpec> > & me) 
{
	SEQAN_CHECKPOINT
	
	if (empty(finder)) {
		_patternInit(me);
		_setFinderLength(finder, length(needle(me)));
		_finderSetNonEmpty(finder);
		me.haystackLength = length(container(finder));
	} else
		finder+=me.step;

	if (me.haystackLength < me.needleLength) return false;
	typedef typename Value<TNeedle>::Type TAlphabet;
	typedef Graph<Automaton<TAlphabet> > TOracle;
	typedef typename Size<TNeedle>::Type TSize;
	typedef typename VertexDescriptor<TOracle>::Type TVertexDescriptor;
	typedef typename EdgeDescriptor<TOracle>::Type TEdgeDescriptor;
	TVertexDescriptor nilVal = getNil<TVertexDescriptor>();
	while (position(finder) <= me.haystackLength - me.needleLength) {
		TVertexDescriptor current = getRoot(me.automaton);
		TSize j = me.needleLength;
		while ((j>0) &&	(current != nilVal))
		{
			TAlphabet c = *(finder+(j-1));
			current = targetVertex(me.automaton, findEdge(me.automaton, current, c));
			--j;
		}
		if (current != nilVal) {
			me.step = j + 1;
			_setFinderEnd(finder, position(finder) + me.needleLength);
			return true;
		}
		finder += j + 1;
	}
	return false;
}

}// namespace SEQAN_NAMESPACE_MAIN

#endif //#ifndef SEQAN_HEADER_FIND_SHIFTAND_H