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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: Rene Rahn <rene.rahn@fu-berlin.de>
// ==========================================================================
// Adaptor methods to transcribe a set of trace segments into the
// alignment representing structure.
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_ADAPTOR_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_ADAPTOR_H_
namespace seqan2 {
// ----------------------------------------------------------------------------
// Function _writeTraceSegmentToFile()
// ----------------------------------------------------------------------------
template <typename TFile, typename TSeq0Value, typename TSeq1Value>
inline void _writeTraceSegmentToFile(TFile & file, TSeq0Value const & seq0Val, TSeq1Value const & seq1Val)
{
file << '(' << seq0Val << ',' << seq1Val << ")\n";
}
// ----------------------------------------------------------------------------
// Function _adaptTraceSegmentsTo() [Gaps]
// ----------------------------------------------------------------------------
template <typename TSourceHorizontal, typename TGapsSpecHorizontal, typename TSourceVertical,
typename TGapsSpecVertical, typename TPosition, typename TSize, typename TStringSpec>
void
_adaptTraceSegmentsTo(Gaps<TSourceHorizontal, TGapsSpecHorizontal> & gapsHorizontal,
Gaps<TSourceVertical, TGapsSpecVertical> & gapsVertical,
String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments)
{
typedef Gaps<TSourceHorizontal, TGapsSpecHorizontal> TGapsHorizontal;
typedef Gaps<TSourceVertical, TGapsSpecVertical> TGapsVertical;
typedef typename Iterator<TGapsHorizontal>::Type TIteratorHorizontal;
typedef typename Iterator<TGapsVertical>::Type TIteratorVertical;
typedef TraceSegment_<TPosition, TSize> TTraceSegment;
typedef typename Iterator<String<TTraceSegment, TStringSpec> const>::Type TTraceIterator;
clearGaps(gapsHorizontal);
clearClipping(gapsHorizontal);
clearGaps(gapsVertical);
clearClipping(gapsVertical);
// Set clipping to 0
if (empty(traceSegments))
{
setClippedBeginPosition(gapsHorizontal, 0);
setClippedEndPosition(gapsHorizontal, 0);
setClippedBeginPosition(gapsVertical, 0);
setClippedEndPosition(gapsVertical, 0);
return;
}
TTraceIterator srcIter = end(traceSegments) - 1;
TTraceIterator srcEnd = begin(traceSegments) - 1;
// we build the gap structure here.
// set the clipped begin position of the alignment.
setBeginPosition(gapsHorizontal, _getBeginHorizontal(value(srcIter))); // begin of source
setBeginPosition(gapsVertical, _getBeginVertical(value(srcIter)));
TIteratorHorizontal it0 = begin(gapsHorizontal);
TIteratorVertical it1 = begin(gapsVertical);
while (srcIter != srcEnd)
{
TSize segmentSize = value(srcIter)._length;
switch (value(srcIter)._traceValue)
{
case TraceBitMap_<>::HORIZONTAL:
insertGaps(it1, segmentSize);
break;
case TraceBitMap_<>::VERTICAL:
insertGaps(it0, segmentSize);
break;
}
goFurther(it0, segmentSize);
goFurther(it1, segmentSize);
--srcIter;
}
setClippedEndPosition(gapsHorizontal, position(it0) + clippedBeginPosition(gapsHorizontal));
setClippedEndPosition(gapsVertical, position(it1) + clippedBeginPosition(gapsVertical));
}
// ----------------------------------------------------------------------------
// Function _adaptTraceSegmentsTo() [AlignmentGraph]
// ----------------------------------------------------------------------------
template <typename TStringSet, typename TCargo, typename TSpec, typename TSequenceIdH, typename TSequenceIdV,
typename TPosition, typename TSize, typename TStringSpec>
inline void
_adaptTraceSegmentsTo(Graph<Alignment<TStringSet, TCargo, TSpec> > & g,
TSequenceIdH const & seqHId,
TSequenceIdV const & seqVId,
String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments)
{
typedef TraceSegment_<TPosition, TSize> TTraceSegment;
// check begin and end positions of the graph.
// Not safe!
if (empty(traceSegments))
return;
// insert leading gaps
TTraceSegment traceBegin = traceSegments[length(traceSegments) - 1];
if (_getBeginVertical(traceBegin) != 0)
addVertex(g, seqVId, 0, _getBeginVertical(traceBegin));
if (_getBeginHorizontal(traceBegin) != 0)
addVertex(g, seqHId, 0, _getBeginHorizontal(traceBegin));
for (TSize i = 0; i < length(traceSegments); ++i)
{
switch (traceSegments[i]._traceValue)
{
case TraceBitMap_<>::DIAGONAL:
addEdge(g, addVertex(g, seqHId, traceSegments[i]._horizontalBeginPos, traceSegments[i]._length),
addVertex(g, seqVId, traceSegments[i]._verticalBeginPos, traceSegments[i]._length));
break;
case TraceBitMap_<>::VERTICAL:
addVertex(g, seqVId, traceSegments[i]._verticalBeginPos, traceSegments[i]._length);
break;
case TraceBitMap_<>::HORIZONTAL:
addVertex(g, seqHId, traceSegments[i]._horizontalBeginPos, traceSegments[i]._length);
}
}
// insert trailing gaps
TTraceSegment traceEnd = traceSegments[0];
if (_getEndVertical(traceEnd) != length(value(stringSet(g), idToPosition(stringSet(g), seqVId))))
addVertex(g, seqVId, _getEndVertical(traceEnd),
length(value(stringSet(g), idToPosition(stringSet(g), seqVId))) - _getEndVertical(traceEnd));
if (_getEndHorizontal(traceEnd) != length(value(stringSet(g), idToPosition(stringSet(g), seqHId))))
addVertex(g, seqHId, _getEndHorizontal(traceEnd),
length(value(stringSet(g), idToPosition(stringSet(g), seqHId))) - _getEndHorizontal(traceEnd));
}
// ----------------------------------------------------------------------------
// Function _adaptTraceSegmentsTo() [File]
// ----------------------------------------------------------------------------
template <typename TFile, typename TSequenceH, typename TSequenceV, typename TPosition, typename TSize,
typename TStringSpec>
inline void
_adaptTraceSegmentsTo(TFile & file,
TSequenceH const & seqH,
TSequenceV const & seqV,
String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments)
{
for (TSize k = length(traceSegments); k > (TSize) 0; --k)
{
switch (traceSegments[k - 1]._traceValue)
{
case TraceBitMap_<>::DIAGONAL:
{
int j = traceSegments[k - 1]._verticalBeginPos;
for (int i = traceSegments[k - 1]._horizontalBeginPos; i < (int) (traceSegments[k - 1]._horizontalBeginPos + traceSegments[k - 1]._length); ++i)
{
_writeTraceSegmentToFile(file, seqH[i], seqV[j]);
++j;
}
break;
}
case TraceBitMap_<>::VERTICAL:
{
for (int i = traceSegments[k - 1]._verticalBeginPos; i < (int) (traceSegments[k - 1]._verticalBeginPos + traceSegments[k - 1]._length); ++i)
_writeTraceSegmentToFile(file, gapValue<char>(), seqV[i]);
break;
}
case TraceBitMap_<>::HORIZONTAL:
{
for (int i = traceSegments[k - 1]._horizontalBeginPos; i < (int) (traceSegments[k - 1]._horizontalBeginPos + traceSegments[k - 1]._length); ++i)
_writeTraceSegmentToFile(file, seqH[i], gapValue<char>());
}
}
}
}
// ----------------------------------------------------------------------------
// Function _adaptTraceSegmentsTo() [Fragments]
// ----------------------------------------------------------------------------
template <typename TSize, typename TFragmentSpec, typename TStringSpec, typename TSequenceH, typename TSequenceV,
typename TPosition, typename TSize2, typename TStringSpec2>
inline void
_adaptTraceSegmentsTo(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & matches,
TSequenceH const & seqHId,
TSequenceV const & seqVId,
String<TraceSegment_<TPosition, TSize2>, TStringSpec2> const & traceSegments)
{
typedef Fragment<TSize, TFragmentSpec> TFragment;
for (TSize2 i = 0; i < length(traceSegments); ++i)
if (traceSegments[i]._traceValue == TraceBitMap_<>::DIAGONAL)
appendValue(
matches,
TFragment(seqHId, traceSegments[i]._horizontalBeginPos, seqVId,
traceSegments[i]._verticalBeginPos, traceSegments[i]._length),
Generous());
}
// ----------------------------------------------------------------------------
// Function _adaptTraceSegmentsTo() [VertexDescriptor]
// ----------------------------------------------------------------------------
//// TODO (rmaerker): Check if we really need this!
//template <typename TVertexDescriptor, typename TSpec, typename TSequence0, typename TSequence1, typename TPosition,
// typename TSize, typename TStringSpec>
//inline void
//_adaptTraceSegmentsTo(String<String<TVertexDescriptor, TSpec> > & /*nodeString*/,
// TSequence0 const & /*seq0*/,
// TSequence1 const & /*seq1*/,
// String<TraceSegment_<TPosition, TSize>, TStringSpec> const & /*traceSegments*/)
//{
// typedef String<TVertexDescriptor, TSpec> TVertexDescriptorString;
// typedef typename Size<TSource>::Type TSize;
// typedef typename Iterator<TVertexDescriptorString>::Type TStringIter;
// TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();
// TODO (rmaerker): see how to adapt this code here for the new structure.
// // TraceBack values
// TTraceValue Diagonal = 0; TTraceValue Horizontal = 1; TTraceValue Vertical = 2;
//
// if (segLen == 0) return;
// // Number of vertex descriptors in the first string at any position (e.g., group of 5 sequences = group of 5 vertex descriptors)
// TSize len1 = length(getValue(getValue(str,0), 0));
// // Number of vertex descriptors in the second string at any position (e.g., group of 5 sequences = group of 5 vertex descriptors)
// TSize len2 = length(getValue(getValue(str,1), 0));
//
// // Resize the node string
// TSize index = length(nodeString);
// resize(nodeString, index + segLen);
//
// if (tv == Horizontal) {
// for (int i = pos1 + segLen - 1; i>= (int) pos1;--i) {
// resize(value(nodeString, index), len1 + len2, nilVertex);
// TStringIter it = begin(value(nodeString, index));
// for(TPos all = 0;all<len1;++all) {
// *it = getValue(getValue(getValue(str,0),i), all);
// goNext(it);
// }
// ++index;
// }
// }
// else if (tv == Vertical) {
// for (int i = pos2 + segLen - 1; i>= (int) pos2;--i) {
// resize(value(nodeString, index), len1 + len2, nilVertex);
// TStringIter it = begin(value(nodeString, index));
// it+=len1;
// for(TPos all = 0;all<len2;++all) {
// *it = getValue(getValue(getValue(str,1),i), all);
// goNext(it);
// }
// ++index;
// }
// }
// else if (tv == Diagonal) {
// int j = pos2 + segLen - 1;
// for (int i = pos1 + segLen - 1; i>= (int) pos1;--i) {
// resize(value(nodeString, index), len1 + len2);
// TStringIter it = begin(value(nodeString, index));
// for(TPos all = 0;all<len1;++all) {
// *it = getValue(getValue(getValue(str,0),i), all);
// goNext(it);
// }
// for(TPos all = 0;all<len2;++all) {
// *it = getValue(getValue(getValue(str,1),j), all);
// goNext(it);
// }
// ++index;
// --j;
// }
// }
//}
} // namespace seqan2
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_TRACEBACK_ADAPTOR_H_
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