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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
// ==========================================================================
#ifndef SEQAN_HEADER_FIND_SHIFTAND_H
#define SEQAN_HEADER_FIND_SHIFTAND_H
namespace seqan2
{
//////////////////////////////////////////////////////////////////////////////
// ShiftAnd
//////////////////////////////////////////////////////////////////////////////
/*!
* @class ShiftAndPattern
* @extends Pattern
* @headerfile <seqan/find.h>
* @brief Exact string matching using bit parallelism.
*
* The Shift-And algorithm is applicable to search small patterns in texts using a small alphabet.
*
* @signature template <typename TNeedle>
* class Pattern<TNeedle, ShiftAnd>;
*
* @tparam TNeedle The needle type. Types: String
*
* The types of the needle and the haystack have to match.
*/
struct ShiftAnd_;
typedef Tag<ShiftAnd_> ShiftAnd;
//////////////////////////////////////////////////////////////////////////////
template <typename TNeedle>
class Pattern<TNeedle, ShiftAnd>
{
//____________________________________________________________________________
public:
typedef unsigned int TWord;
enum { MACHINE_WORD_SIZE = sizeof(TWord) * 8 };
Holder<TNeedle> data_host;
String<TWord> bitMasks; // Look up table for each character in the alphabet (called B in "Navarro")
String<TWord> prefSufMatch; // Set of all the prefixes of needle that match a suffix of haystack (called D in "Navarro")
TWord needleLength; // e.g., needleLength=33 --> blockCount=2 (iff w=32 bits)
TWord blockCount; // #unsigned ints required to store needle
Pattern()
{}
// Custom c'tor setting a needle.
template <typename TNeedle2>
Pattern(TNeedle2 && ndl, SEQAN_CTOR_DISABLE_IF(IsSameType<typename std::remove_reference<TNeedle2>::type const &, Pattern const &>))
{
setHost(*this, std::forward<TNeedle2>(ndl));
ignoreUnusedVariableWarning(dummy);
}
};
//////////////////////////////////////////////////////////////////////////////
// Functions
//////////////////////////////////////////////////////////////////////////////
template <typename TNeedle>
inline void
_reinitPattern(Pattern<TNeedle, ShiftAnd> & me)
{
typedef unsigned int TWord;
typedef typename Value<TNeedle>::Type TValue;
TNeedle& ndl = needle(me);
me.needleLength = length(ndl);
if (me.needleLength < 1)
me.blockCount = 1;
else
me.blockCount = (me.needleLength - 1) / BitsPerValue<TWord>::VALUE + 1;
clear(me.bitMasks);
resize(me.bitMasks, me.blockCount * ValueSize<TValue>::VALUE, 0, Exact());
for (TWord j = 0; j < me.needleLength; ++j)
me.bitMasks[
me.blockCount * ordValue(convert<TValue>(getValue(ndl, j)))
+ j / me.MACHINE_WORD_SIZE
] |= (TWord)1 << (j % me.MACHINE_WORD_SIZE);
// setValue(me.data_host, needle);
/*
// Debug code
std::cout << "Alphabet size: " << ValueSize<TValue>::VALUE << std::endl;
std::cout << "Needle length: " << me.needleLength << std::endl;
std::cout << "Block count: " << me.blockCount << std::endl;
for(unsigned int i=0;i<ValueSize<TValue>::VALUE;++i) {
if ((i<97) || (i>122)) continue;
std::cout << static_cast<char>(i) << ": ";
for(int j=0;j<me.blockCount;++j) {
for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
std::cout << ((me.bitMasks[me.blockCount*i+j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
}
}
std::cout << std::endl;
}
*/
}
//____________________________________________________________________________
template <typename TNeedle>
inline void
_patternInit (Pattern<TNeedle, ShiftAnd> & me)
{
clear(me.prefSufMatch);
resize(me.prefSufMatch, me.blockCount, 0, Exact());
}
//____________________________________________________________________________
template <typename TFinder, typename TNeedle>
inline bool
_findShiftAndSmallNeedle(TFinder & finder, Pattern<TNeedle, ShiftAnd> & me)
{
typedef typename Value<TNeedle>::Type TValue;
typedef unsigned int TWord;
TWord compare = (TWord)1 << (me.needleLength - 1);
while (!atEnd(finder))
{
TWord pos = ordValue(convert<TValue>(*finder));
me.prefSufMatch[0] = ((me.prefSufMatch[0] << 1) | (TWord)1) & me.bitMasks[pos];
if ((me.prefSufMatch[0] & compare) != 0)
{
_setFinderEnd(finder);
finder -= me.needleLength - 1;
return true;
}
goNext(finder);
}
return false;
}
template <typename TFinder, typename TNeedle>
inline bool
_findShiftAndLargeNeedle(TFinder & finder, Pattern<TNeedle, ShiftAnd> & me)
{
typedef typename Value<TNeedle>::Type TValue;
typedef unsigned int TWord;
TWord compare = (TWord)1 << ((me.needleLength - 1) % BitsPerValue<TWord>::VALUE);
while (!atEnd(finder))
{
TWord pos = ordValue(convert<TValue>(*finder));
TWord carry = 1;
for(TWord block = 0; block < me.blockCount; ++block)
{
bool newCarry = (me.prefSufMatch[block] & ((TWord)1<< (BitsPerValue<TWord>::VALUE - 1))) != 0;
me.prefSufMatch[block] <<= 1;
me.prefSufMatch[block] |= carry;
carry = newCarry;
}
for(TWord block = 0; block < me.blockCount; ++block)
me.prefSufMatch[block] &= me.bitMasks[me.blockCount * pos + block];
if ((me.prefSufMatch[me.blockCount-1] & compare) != 0)
{
_setFinderEnd(finder);
finder -= me.needleLength - 1;
return true;
}
/*
// Debug code
std::cout << " ";
for(int j=0;j<me.blockCount;++j) {
for(int bit_pos=0;bit_pos<BitsPerValue<unsigned int>::VALUE;++bit_pos) {
std::cout << ((me.prefSufMatch[j] & (1<<(bit_pos % BitsPerValue<unsigned int>::VALUE))) !=0);
}
}
std::cout << std::endl;
*/
goNext(finder);
}
return false;
}
template <typename TFinder, typename TNeedle>
inline bool find(TFinder & finder, Pattern<TNeedle, ShiftAnd> & me) {
if (empty(finder)) {
_patternInit(me);
_setFinderLength(finder, me.needleLength);
_finderSetNonEmpty(finder);
} else
finder += me.needleLength;
// Fast algorithm for needles < machine word?
if (me.blockCount == 1)
return _findShiftAndSmallNeedle(finder, me);
else
return _findShiftAndLargeNeedle(finder, me);
}
}// namespace seqan2
#endif //#ifndef SEQAN_HEADER_FIND_SHIFTAND_H
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