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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: David Weese <david.weese@fu-berlin.de>
// ==========================================================================
#ifndef SEQAN_HEADER_PIPE_EDIT_ENVIRONMENT_H
#define SEQAN_HEADER_PIPE_EDIT_ENVIRONMENT_H
namespace seqan2
{
//namespace seqan2_NAMESPACE_PIPELINING
//{
template < typename TDistanceSpec, unsigned STEP_SIZE = 1 >
struct EditEnvironment;
/*!
* @class EditEnvironment
* @extends Pipe
* @headerfile <seqan/pipe.h>
* @brief Outputs tuples of the <tt>tupleLen</tt> consecutive elements of the input stream.
*
* @signature template <typename TInput, unsigned TUPLE_LEN, bool OMIT_LAST>
* class Pipe<TInput, Tupler<TUPLE_LEN, OMIT_LAST> >;
*
* @tparam OMIT_LAST Omit half filled tuples. If <tt>true</tt>, the output stream is <tt>tupleLen-1</tt> elements
* shorter than the input stream. If <tt>false</tt>, the lengths are identical and the last
* tuples are filled with blanks (default constructed elements) for undefined entries.
* @tparam TInput The type of the pipeline module this module reads from.
* @tparam TUPLE_LEN The tuple length.The tuples contain elements <tt>in[i]in[i+1]...in[i+(tupleLen-1)]</tt>.
*
* The output type is a @link Tuple @endlink of input elements and length <tt>tupleLen</tt> (i.e.
* <tt>Tuple<Value<TInput>::Type, tupleLen></tt>).
*
* The tuples are sequences of the form <tt>in[i]in[i-1]in[i-2]..in[i-tupleLen+1]</tt>. For <tt>omitLast=false</tt>
* <tt>i</tt> begins with 0 and for <tt>omitLast=true</tt> <tt>i</tt> begins with <tt>tupleLen-1</tt>.
*/
//////////////////////////////////////////////////////////////////////////////
// pipe to enumerate the hamming 1-environment
template < typename TInput, unsigned STEP_SIZE >
struct Pipe< TInput, EditEnvironment< Tag<HammingDistance_>, STEP_SIZE > >
{
typedef typename Value< typename Value<TInput>::Type, 2 >::Type TTuple;
typedef typename Value<TTuple>::Type TValue;
TInput ∈
typename Value<Pipe>::Type tmp, orig;
unsigned errorPos; // position of substitution
unsigned character; // replacement character
unsigned skipChar; // skip the original character
Pipe(TInput& _in):
in(_in) {}
inline typename Value<Pipe>::Type const & operator*() const {
return tmp;
}
inline Pipe& operator++() {
do {
if (++character < ValueSize<TValue>::VALUE)
// next replacement value
assignValue(tmp.i2, errorPos, (TValue) character);
else {
// next error position
assignValue(tmp.i2, errorPos, orig.i2[errorPos]);
character = 0;
if (++errorPos < length(tmp.i2)) {
skipChar = (unsigned) orig.i2[errorPos];
assignValue(tmp.i2, errorPos, (TValue) 0);
} else {
// next tuple
errorPos = 0;
++in;
for(unsigned i = 1; i < STEP_SIZE && !eof(in); ++i)
++in;
if (!eof(in)) {
tmp = orig = *in;
assignValue(tmp.i2, 0, (TValue) 0);
}
}
}
// output the original tuple only once
} while ((errorPos > 0) && (character == skipChar));
return *this;
}
};
//////////////////////////////////////////////////////////////////////////////
// pipe to enumerate the levenshtein 1-environment
template < typename TInput, unsigned STEP_SIZE >
struct Pipe< TInput, EditEnvironment< Tag<LevenshteinDistance_>, STEP_SIZE > >
{
typedef typename Value< typename Value<TInput>::Type, 2 >::Type TTuple;
typedef typename Value<TTuple>::Type TValue;
enum TState { SUBST_, DELETE_, INSERT_, INSERT_LAST_, Eof_, INSERT_EOS_ };
TInput ∈
typename Value<Pipe>::Type tmp, orig, prev;
unsigned errorPos; // position of substitution
unsigned character; // replacement character
unsigned skipChar; // skip the original character
TState state;
Pipe(TInput& _in):
in(_in),
state(Eof_) {}
inline typename Value<Pipe>::Type const & operator*() const {
return tmp;
}
inline Pipe& operator++() {
switch (state) {
case SUBST_:
// before SUBST_ (tmp[1..] == orig[1..] and tmp[0] == 0) holds
do {
if (++character < ValueSize<TValue>::VALUE) {
// next replacement value
assignValue(tmp.i2, errorPos, (TValue) character);
} else {
// next substitution position
assignValue(tmp.i2, errorPos, orig.i2[errorPos]);
character = 0;
if (++errorPos < length(tmp.i2)) {
skipChar = (unsigned) orig.i2[errorPos];
assignValue(tmp.i2, errorPos, (TValue) 0);
} else {
// NEXT TUPLE
// now (tmp == orig) holds
++in;
for(unsigned i = 1; i < STEP_SIZE && !eof(in); ++i)
++in;
if (!eos(in)) {
prev = orig;
orig = *in;
tmp.i2 = orig.i2;
assignValue(tmp.i2, 0, prev.i2[0]);
assignValue(tmp.i2, 1, prev.i2[1]);
if (length(tmp.i2) >= 4) {
errorPos = 2;
state = DELETE_;
//std::cerr << std::endl << "_DELETIONS____" << std::endl;
return *this;
}
} else {
// LAST TUPLE
shiftLeft(orig.i2);
assignValue(tmp.i2, 0, orig.i2[0]);
assignValue(tmp.i2, 1, (TValue) 0);
character = 0;
errorPos = 1;
state = INSERT_LAST_;
//std::cerr << std::endl << "_INSERTS______" << std::endl;
return *this;
}
}
}
// output the original tuple only once
} while ((errorPos > 0) && (character == skipChar));
break;
case DELETE_:
// before DELETE_ (prev=orig, ++in; tmp=orig=*in) holds
assignValue(tmp.i2, errorPos, prev.i2[errorPos]);
if (++errorPos >= length(tmp.i2) - 1) {
assignValue(tmp.i2, length(tmp.i2)-1, prev.i2[length(tmp.i2)-1]);
assignValue(tmp.i2, 0, orig.i2[0]);
assignValue(tmp.i2, 1, (TValue) 0);
character = 0;
errorPos = 1;
state = INSERT_;
//std::cerr << std::endl << "_INSERTS______" << std::endl;
}
break;
case INSERT_EOS_:
state = INSERT_;
SEQAN_FALLTHROUGH
case INSERT_:
case INSERT_LAST_:
// before INSERT_ (prev=orig, ++in; tmp=prev) holds
if (++character < ValueSize<TValue>::VALUE)
// next replacement value
assignValue(tmp.i2, errorPos, (TValue) character);
else {
// next insert position
assignValue(tmp.i2, errorPos, orig.i2[errorPos]);
character = 0;
if (++errorPos >= length(tmp.i2) - 1 && state == INSERT_) {
tmp = orig;
state = SUBST_;
//std::cerr << std::endl << "_REPLACEMENTS_" << std::endl;
errorPos = 0;
assignValue(tmp.i2, 0, (TValue) 0);
break;
}
if (errorPos >= length(tmp.i2)) {
if (eof(in))
state = Eof_;
else {
tmp = orig = *in;
// begin to insert the first char at position 0
shiftRight(tmp.i2);
assignValue(tmp.i2, 1, (TValue) 0);
errorPos = 0;
state = INSERT_EOS_;
//std::cerr << std::endl << "_INSERTS______" << std::endl;
}
break;
}
assignValue(tmp.i2, errorPos, (TValue) 0);
}
break;
default:;
}
return *this;
}
};
//////////////////////////////////////////////////////////////////////////////
// global pipe functions
template < typename TInput, unsigned STEP_SIZE >
inline bool
control(
Pipe< TInput, EditEnvironment< Tag<HammingDistance_>, STEP_SIZE > > &me,
ControlBeginRead const &command)
{
if (!control(me.in, command)) return false;
me.tmp = me.orig = *me.in;
me.errorPos = 0;
me.character = 0;
return true;
}
template < typename TInput, unsigned STEP_SIZE >
inline bool
control(
Pipe< TInput, EditEnvironment< Tag<LevenshteinDistance_>, STEP_SIZE > > &me,
ControlBeginRead const &command)
{
if (!control(me.in, command)) return false;
if (eof(me.in)) {
me.state = me.Eof_;
return true;
}
typedef typename Value< typename Value<TInput>::Type, 2 >::Type TTuple;
typedef typename Value<TTuple>::Type TValue;
me.tmp = me.orig = *me.in;
// begin to insert the first char at position 0
shiftRight(me.tmp.i2);
assignValue(me.tmp.i2, 0, (TValue) 0);
me.character = 0;
me.errorPos = 0;
me.state = me.INSERT_;
//std::cerr << std::endl << "_INSERTS______" << std::endl;
return true;
}
template < typename TInput, unsigned STEP_SIZE >
inline bool
control(
Pipe< TInput, EditEnvironment< Tag<LevenshteinDistance_>, STEP_SIZE > > &me,
ControlEof const &)
{
return me.state == me.Eof_;
}
template < typename TInput, unsigned STEP_SIZE >
inline bool
control(
Pipe< TInput, EditEnvironment< Tag<LevenshteinDistance_>, STEP_SIZE > > &me,
ControlEos const &)
{
return me.state == me.Eof_ || me.state == me.INSERT_EOS;
}
template < typename TInput, unsigned STEP_SIZE >
inline typename Size< Pipe< TInput, Pipe< TInput, EditEnvironment< Tag<HammingDistance_>, STEP_SIZE > > > >::Type
length(Pipe< TInput, EditEnvironment< Tag<HammingDistance_>, STEP_SIZE > > const &me) {
typedef typename Value< typename Value<TInput>::Type, 2 >::Type TTuple;
typedef typename Size< Pipe< TInput, Pipe< TInput, EditEnvironment< Tag<HammingDistance_>, STEP_SIZE > > > >::Type TSize;
unsigned alphabetSize = ValueSize< typename Value<TTuple>::Type >::VALUE;
/*unsigned seqs = countSequences(me.in);*/
TSize sum = 0;
/* for(unsigned i = 0; i < seqs; ++i)
sum += (length((*me.in.in.in.in.set)[i]) / STEP_SIZE) * (1 + length(me.tmp.i2) * (alphabetSize - 1));
return sum;
*/ return (length(me.in) / STEP_SIZE) * (1 + length(me.tmp.i2) * (alphabetSize - 1));
}
template < typename TInput, unsigned STEP_SIZE >
inline typename Size< Pipe< TInput, Pipe< TInput, EditEnvironment< Tag<LevenshteinDistance_>, STEP_SIZE > > > >::Type
length(Pipe< TInput, EditEnvironment< Tag<LevenshteinDistance_>, STEP_SIZE > > const &me) {
typedef typename Value< typename Value<TInput>::Type, 2 >::Type TTuple;
unsigned alphabetSize = ValueSize< typename Value<TTuple>::Type >::VALUE;
unsigned seqs = countSequences(me.in);
// TODO: We run into problems when one sequence contains 1 or less tuples
// length should be omitted in future, but Pools or the skew algorithm needs to know the stream length
if (length(me.in) >= seqs)
return
(length(me.in) / STEP_SIZE) * (1 + length(me.tmp.i2) * (alphabetSize - 1)) + // substitutions and original
((length(me.in) / STEP_SIZE) - seqs) * (length(me.tmp.i2) - 3) + // deletions
(((length(me.in) / STEP_SIZE) + seqs) * (length(me.tmp.i2) - 2) + 2 * seqs) * alphabetSize; // insertions
else
return 0;
}
//}
}
#endif
|
