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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: Hannes Hauswedell <hauswedell@mi.fu-berlin.de>
// ==========================================================================
// This file contains routines to extend an existing Align object
// ==========================================================================
#ifndef INCLUDE_ALIGN_ALIGN_EXTEND_H
#define INCLUDE_ALIGN_ALIGN_EXTEND_H
namespace seqan2 {
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ----------------------------------------------------------------------------
// Class AliExtContext_
// ----------------------------------------------------------------------------
// Context with memory holding objects for alignment extension
// This can be reused to prevent repeated memory allocations
template <typename TGaps0, typename TGaps1, typename TDPContext>
struct AliExtContext_
{
typedef typename Size<TGaps0>::Type TSize;
typedef typename Position<TGaps0>::Type TPosition;
TGaps0 leftRow0, centerRow0, rightRow0;
TGaps1 leftRow1, centerRow1, rightRow1;
TDPContext dpContext;
String<TraceSegment_<TPosition, TSize> > traceSegment;
};
template <typename TGaps0, typename TGaps1, typename TDPContext>
inline void
clear(AliExtContext_<TGaps0, TGaps1, TDPContext> & prov)
{
// gaps don't need to be cleared, because they are always
// re-assigned before use; dpContext, too!
// trace segment always needs to be cleared
clear(prov.traceSegment);
// dpContext doesn't need to be cleared
}
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function _reverseTrace()
// ----------------------------------------------------------------------------
// Reverse a trace string and adapt internal position.
template <typename TPosition, typename TPos2, typename TSize, typename TSpec>
void _reversePartialTrace(String<TraceSegment_<TPosition,
TSize>, TSpec> & trace,
TPos2 const lengthH,
TPos2 const lengthV)
{
typedef String<TraceSegment_<TPosition, TSize>, TSpec> TTrace;
typedef typename Iterator<TTrace, Rooted>::Type TTraceIter;
if (empty(trace))
return;
for (TTraceIter it = begin(trace, Rooted()); !atEnd(it); goNext(it))
{
it->_horizontalBeginPos = lengthH - _getEndHorizontal(*it);
it->_verticalBeginPos = lengthV - _getEndVertical(*it);
}
reverse(trace);
}
// ----------------------------------------------------------------------------
// Function _setUpAndRunAlignImpl()
// ----------------------------------------------------------------------------
template <typename TAliExtContext_, typename TString0, typename TString1, typename TScoreValue,
typename TScoreSpec, typename TTracebackConfig>
inline TScoreValue
_setUpAndRunAlignImpl(TAliExtContext_ & alignContext,
TString0 const & str0,
TString1 const & str1,
Score<TScoreValue, TScoreSpec> const & scoreScheme,
int const /*lowerDiag*/,
int const /*upperDiag*/,
TScoreValue const /*xDrop*/,
TTracebackConfig const & /*gapOrientation*/,
False const & /*TBoolBanded*/,
False const & /*TBoolXDrop*/)
{
typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps;
typedef AlignConfig2<AlignExtend_<>, DPBandConfig<BandOff>, TFreeEndGaps,
TracebackOn<TracebackConfig_<CompleteTrace, GapsLeft> > > TAlignConfig;
DPScoutState_<Default> scoutState;
return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, str1, scoreScheme,
TAlignConfig());
}
template <typename TAliExtContext_, typename TString0, typename TString1, typename TScoreValue,
typename TScoreSpec, typename TTracebackConfig>
inline TScoreValue
_setUpAndRunAlignImpl(TAliExtContext_ & alignContext,
TString0 const & str0,
TString1 const & str1,
Score<TScoreValue, TScoreSpec> const & scoreScheme,
int const lowerDiag,
int const upperDiag,
TScoreValue const /*xDrop*/,
TTracebackConfig const & /*gapOrientation*/,
True const & /*TBoolBanded*/,
False const & /*TBoolXDrop*/)
{
typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps;
typedef AlignConfig2<AlignExtend_<>, DPBandConfig<BandOn>, TFreeEndGaps,
TracebackOn<TracebackConfig_<CompleteTrace, GapsLeft> > > TAlignConfig;
DPScoutState_<Default> scoutState;
return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, str1, scoreScheme,
TAlignConfig(lowerDiag, upperDiag));
}
template <typename TAliExtContext_, typename TString0, typename TString1, typename TScoreValue,
typename TScoreSpec, typename TTracebackConfig>
inline TScoreValue
_setUpAndRunAlignImpl(TAliExtContext_ & alignContext,
TString0 const & str0,
TString1 const & str1,
Score<TScoreValue, TScoreSpec> const & scoreScheme,
int const /*lowerDiag*/,
int const /*upperDiag*/,
TScoreValue const xDrop,
TTracebackConfig const & /*gapOrientation*/,
False const & /*TBoolBanded*/,
True const & /*TBoolXDrop*/)
{
typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps;
typedef AlignConfig2<AlignExtend_<XDrop_<TScoreValue> >, DPBandConfig<BandOff>, TFreeEndGaps,
TracebackOn<TracebackConfig_<CompleteTrace, GapsLeft> > > TAlignConfig;
DPScoutState_<Terminator_<XDrop_<TScoreValue> > > scoutState(xDrop);
return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, str1, scoreScheme,
TAlignConfig());
}
template <typename TAliExtContext_, typename TString0, typename TString1, typename TScoreValue,
typename TScoreSpec, typename TTracebackConfig>
inline TScoreValue
_setUpAndRunAlignImpl(TAliExtContext_ & alignContext,
TString0 const & str0,
TString1 const & str1,
Score<TScoreValue, TScoreSpec> const & scoreScheme,
int const lowerDiag,
int const upperDiag,
TScoreValue const xDrop,
TTracebackConfig const & /*gapOrientation*/,
True const & /*TBoolBanded*/,
True const & /*TBoolXDrop*/)
{
typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps;
typedef AlignConfig2<AlignExtend_<XDrop_<TScoreValue> >, DPBandConfig<BandOn>, TFreeEndGaps,
TracebackOn<TracebackConfig_<CompleteTrace, GapsLeft> > > TAlignConfig;
DPScoutState_<Terminator_<XDrop_<TScoreValue> > > scoutState(xDrop);
return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, str1, scoreScheme,
TAlignConfig(lowerDiag, upperDiag));
}
// ----------------------------------------------------------------------------
// Function _extendAlignmentImpl()
// ----------------------------------------------------------------------------
template <typename TSource0, typename TSource1, typename TGapsSpec0, typename TGapsSpec1,
typename TString0, typename TString1, typename TPos, typename TScoreValue, typename TScoreSpec,
typename TBoolBanded, typename TBoolXDrop, typename TAliExtContext_>
inline TScoreValue
_extendAlignmentImpl(Gaps<TSource0, TGapsSpec0> & row0,
Gaps<TSource1, TGapsSpec1> & row1,
TScoreValue const & origScore,
TString0 const & hSeq,
TString1 const & vSeq,
Tuple<TPos, 4> const & positions,
ExtensionDirection const & direction,
int const lowerDiag,
int const upperDiag,
TScoreValue const & xDrop,
Score<TScoreValue, TScoreSpec> const & scoreScheme,
TBoolBanded const & /**/,
TBoolXDrop const & /**/,
TAliExtContext_ & alignContext)
{
typedef typename Infix<TSource0 const>::Type TInf0;
typedef typename Infix<TSource1 const>::Type TInf1;
TPos const hBeginPos = positions[0];
TPos const vBeginPos = positions[1];
TPos const hEndPos = positions[2];
TPos const vEndPos = positions[3];
SEQAN_ASSERT_EQ(infix(source(row0), beginPosition(row0), endPosition(row0)),
infix(hSeq, hBeginPos, hEndPos));
SEQAN_ASSERT_EQ(infix(source(row1), beginPosition(row1), endPosition(row1)),
infix(vSeq, vBeginPos, vEndPos));
bool extendLeft = ((direction & EXTEND_LEFT) && (hBeginPos > 0u) && (vBeginPos > 0u));
bool extendRight = ((direction & EXTEND_RIGHT) && (hEndPos < length(hSeq)) && (vEndPos < length(vSeq)));
clear(alignContext);
alignContext.centerRow0 = row0;
alignContext.centerRow1 = row1;
TScoreValue leftScore = 0;
TScoreValue centerScore = origScore;
TScoreValue rightScore = 0;
TPos newAlignLen = length(row0);
// centerScore was set to "compute yourself" by interface function without score parameter
if (centerScore == std::numeric_limits<TScoreValue>::min())
{
centerScore = 0;
for (TPos i = 0; i < length(row0); ++i)
{
if ( ( isGap(row0, i)) || ( isGap(row1, i)) )
{
if (( i==0 ) ||
(isGap(row0, i-1) != isGap(row0, i)) ||
(isGap(row1, i-1) != isGap(row1, i)) )
{
centerScore += scoreGapOpen(scoreScheme);
}
else
{
centerScore += scoreGapExtend(scoreScheme);
}
}
else
{
centerScore += score(scoreScheme, row0[i], row1[i]);
}
}
}
// "reset" original alignment to full length on sequences and no gaps
assignSource(row0, infix(hSeq, 0, length(hSeq)));
assignSource(row1, infix(vSeq, 0, length(vSeq)));
// left
if (extendLeft)
{
TInf0 inf0 = infix(hSeq, 0, hBeginPos);
TInf1 inf1 = infix(vSeq, 0, vBeginPos);
// reverse input
ModifiedString<TInf0, ModReverse> const r_inf0(inf0);
ModifiedString<TInf1, ModReverse> const r_inf1(inf1);
leftScore = _setUpAndRunAlignImpl(alignContext, r_inf0, r_inf1, scoreScheme, lowerDiag, upperDiag, xDrop,
TracebackConfig_<CompleteTrace, GapsRight>(), TBoolBanded(), TBoolXDrop());
// un-reverve
_reversePartialTrace(alignContext.traceSegment, length(inf0), length(inf1));
setSource(alignContext.leftRow0, inf0);
setSource(alignContext.leftRow1, inf1);
_adaptTraceSegmentsTo(alignContext.leftRow0, alignContext.leftRow1, alignContext.traceSegment);
if (length(alignContext.leftRow0) > 0)
{
integrateGaps(row0, alignContext.leftRow0);
integrateGaps(row1, alignContext.leftRow1);
setClippedBeginPosition(row0, clippedBeginPosition(alignContext.leftRow0));
setClippedBeginPosition(row1, clippedBeginPosition(alignContext.leftRow1));
newAlignLen += length(alignContext.leftRow0);
}
else
{
extendLeft = false;
}
}
// center
if (extendLeft)
{
integrateGaps(row0, alignContext.centerRow0, length(alignContext.leftRow0));
integrateGaps(row1, alignContext.centerRow1, length(alignContext.leftRow1));
}
else
{
integrateGaps(row0, alignContext.centerRow0, hBeginPos);
integrateGaps(row1, alignContext.centerRow1, vBeginPos);
TPos leadGaps0 = countGaps(begin(alignContext.centerRow0));
TPos leadGaps1 = countGaps(begin(alignContext.centerRow1));
TPos sourceBeginPos0 = toSourcePosition(alignContext.centerRow0, leadGaps0) + hBeginPos -
beginPosition(alignContext.centerRow0);
TPos sourceBeginPos1 = toSourcePosition(alignContext.centerRow1, leadGaps1) + vBeginPos -
beginPosition(alignContext.centerRow1);
setClippedBeginPosition(row0, toViewPosition(row0, sourceBeginPos0) - leadGaps0);
setClippedBeginPosition(row1, toViewPosition(row1, sourceBeginPos1) - leadGaps1);
}
// right
if (extendRight)
{
TInf0 inf0 = infix(hSeq, hEndPos, length(hSeq));
TInf1 inf1 = infix(vSeq, vEndPos, length(vSeq));
clear(alignContext.traceSegment);
rightScore = _setUpAndRunAlignImpl(alignContext, inf0, inf1, scoreScheme, lowerDiag, upperDiag, xDrop,
TracebackConfig_<CompleteTrace, GapsLeft>(), TBoolBanded(), TBoolXDrop());
setSource(alignContext.rightRow0, inf0);
setSource(alignContext.rightRow1, inf1);
_adaptTraceSegmentsTo(alignContext.rightRow0, alignContext.rightRow1, alignContext.traceSegment);
if (length(alignContext.rightRow0) > 0)
{
integrateGaps(row0, alignContext.rightRow0);
integrateGaps(row1, alignContext.rightRow1);
newAlignLen += length(alignContext.rightRow0);
}
}
setClippedEndPosition(row0, clippedBeginPosition(row0) + newAlignLen);
setClippedEndPosition(row1, clippedBeginPosition(row1) + newAlignLen);
return leftScore + centerScore + rightScore;
}
// get rows from align object
template <typename TStringInfix, typename TAlignSpec, typename TString,
typename TPos, typename TScoreValue, typename TScoreSpec,
typename TBoolBanded, typename TBoolXDrop, typename TAliExtContext_>
inline TScoreValue
_extendAlignmentImpl(Align<TStringInfix, TAlignSpec> & align,
TScoreValue const & origScore,
TString const & hSeq,
TString const & vSeq,
Tuple<TPos, 4> const & positions,
ExtensionDirection const & direction,
int const lowerDiag,
int const upperDiag,
TScoreValue const & xDrop,
Score<TScoreValue, TScoreSpec> const & scoreScheme,
TBoolBanded const & /**/,
TBoolXDrop const & /**/,
TAliExtContext_ & alignContext)
{
SEQAN_ASSERT_EQ_MSG(length(rows(align)), 2u, "Only works with pairwise alignments.");
SEQAN_ASSERT_EQ_MSG(length(row(align, 0)), length(row(align, 1)), "Invalid alignment!");
return _extendAlignmentImpl(row(align, 0), row(align, 1), origScore, hSeq, vSeq, positions, direction, lowerDiag,
upperDiag, xDrop, scoreScheme, TBoolBanded(), TBoolXDrop(), alignContext);
}
// create AlignContext
template <typename TStringInfix, typename TAlignSpec, typename TString,
typename TPos, typename TScoreValue, typename TScoreSpec,
typename TBoolBanded, typename TBoolXDrop>
inline TScoreValue
_extendAlignmentImpl(Align<TStringInfix, TAlignSpec> & align,
TScoreValue const & origScore,
TString const & hSeq,
TString const & vSeq,
Tuple<TPos, 4> const & positions,
ExtensionDirection const & direction,
int const lowerDiag,
int const upperDiag,
TScoreValue const & xDrop,
Score<TScoreValue, TScoreSpec> const & scoreScheme,
TBoolBanded const & /**/,
TBoolXDrop const & /**/)
{
if (scoreGapOpen(scoreScheme) == scoreGapExtend(scoreScheme))
{
typedef DPContext<DPCell_<TScoreValue, LinearGaps>, typename TraceBitMap_<TScoreValue>::Type> TDPContext;
typedef AliExtContext_<Gaps<TStringInfix, TAlignSpec>,
Gaps<TStringInfix, TAlignSpec>,
TDPContext> TAliExtContext_;
TAliExtContext_ alignContext;
return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, lowerDiag, upperDiag, xDrop,
scoreScheme, TBoolBanded(), TBoolXDrop(), alignContext);
}
else
{
typedef DPContext<DPCell_<TScoreValue, AffineGaps>, typename TraceBitMap_<TScoreValue>::Type> TDPContext;
typedef AliExtContext_<Gaps<TStringInfix, TAlignSpec>,
Gaps<TStringInfix, TAlignSpec>,
TDPContext> TAliExtContext_;
TAliExtContext_ alignContext;
return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, lowerDiag, upperDiag, xDrop,
scoreScheme, TBoolBanded(), TBoolXDrop(), alignContext);
}
}
// ----------------------------------------------------------------------------
// Function extendAlignment()
// ----------------------------------------------------------------------------
/*!
* @fn extendAlignment
* @headerfile <seqan/align_extend.h>
* @brief X-Drop extension for alignment objects.
* @signature TScoreValue extendAlignment(align, [origScore,] hSeq, vSeq, positions, extensionDirection,
* [lowerDiag, upperDiag,] [xDrop,] scoreScheme);
*
* @param[in,out] align The @link Align @endlink object to work on. Must be an alignment over the
* @link InfixSegment infix @endlink of the <i>const</i> type of <tt>hSeq</tt>
* and <tt>vSeq</tt>. Also see section "Returned Alignment".
* @param[in] origScore Original score value of the alignment (optional; computed if not provided).
* @param[in] hSeq Full horizontal sequence.
* @param[in] vSeq Full vertical sequence.
* @param[in] positions A @link Tuple @endlink of length 4 with the begin and end position of the
* infixes in align.
* @param[in] extensionDirection
* The extension direction (@link ExtensionDirection @endlink).
* @param[in] lowerDiag Lower alignment diagonal to use (<tt>int</tt>).
* @param[in] upperDiag Upper alignment diagonal to use (<tt>int</tt>).
* @param[in] xDrop The X-drop value to use (integral value). It only limits computation of new
* columns in the DP-Matrix and has no influence on the diagonals (but can be combined with them).
* @param[in] scoringScheme
* The @link Score @endlink to use.
*
* @return TScoreValue
* The score of the new alignment. <tt>TScoreValue</tt> is the value type of
* <tt>scoringScheme</tt>.
*
* @section Returned Alignment
*
* The resulting alignment has the infixes extended to the whole underlying sequence. The alignment
* is clipped to give the parts of the aligned sequences.
*
* @section Example
*
* @include demos/dox/align_extend/extend_alignment.cpp
*
* The output is as follows:
*
* @include demos/dox/align_extend/extend_alignment.cpp.stdout
*
* @section Remarks
*
* It is necessary to explicitly pass hSeq, vSeq and the positions, because the
* original hSeq and vSeq (that Align was created on), might have been infixes,
* (especially if they are members of a ConcatDirect set) in which cases their
* actual begin and end positions cannot be inferred from the Align object's
* rows' source().
*/
// NO BAND, NO XDROP
template <typename TStringInfix, typename TAlignSpec, typename TString,
typename TPos, typename TScoreValue, typename TScoreSpec>
inline TScoreValue
extendAlignment(Align<TStringInfix, TAlignSpec> & align,
TString const & hSeq,
TString const & vSeq,
Tuple<TPos, 4> const & positions,
ExtensionDirection const & direction,
Score<TScoreValue, TScoreSpec> const & scoreScheme)
{
return _extendAlignmentImpl(align, std::numeric_limits<TScoreValue>::min(), hSeq, vSeq, positions, direction, 0, 0, 0, scoreScheme,
False(), False());
}
template <typename TStringInfix, typename TAlignSpec, typename TString,
typename TPos, typename TScoreValue, typename TScoreSpec>
inline TScoreValue
extendAlignment(Align<TStringInfix, TAlignSpec> & align,
TScoreValue const & origScore,
TString const & hSeq,
TString const & vSeq,
Tuple<TPos, 4> const & positions,
ExtensionDirection const & direction,
Score<TScoreValue, TScoreSpec> const & scoreScheme)
{
return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, 0, 0, 0, scoreScheme, False(),
False());
}
// BAND, NO XDROP
template <typename TStringInfix, typename TAlignSpec, typename TString,
typename TPos, typename TScoreValue, typename TScoreSpec>
inline TScoreValue
extendAlignment(Align<TStringInfix, TAlignSpec> & align,
TString const & hSeq,
TString const & vSeq,
Tuple<TPos, 4> const & positions,
ExtensionDirection const & direction,
int const lowerDiag,
int const upperDiag,
Score<TScoreValue, TScoreSpec> const & scoreScheme)
{
return _extendAlignmentImpl(align, std::numeric_limits<TScoreValue>::min(), hSeq, vSeq, positions, direction, lowerDiag, upperDiag,
0, scoreScheme, True(), False());
}
template <typename TStringInfix, typename TAlignSpec, typename TString,
typename TPos, typename TScoreValue, typename TScoreSpec>
inline TScoreValue
extendAlignment(Align<TStringInfix, TAlignSpec> & align,
TScoreValue const & origScore,
TString const & hSeq,
TString const & vSeq,
Tuple<TPos, 4> const & positions,
ExtensionDirection const & direction,
int const lowerDiag,
int const upperDiag,
Score<TScoreValue, TScoreSpec> const & scoreScheme)
{
return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, lowerDiag, upperDiag, 0,
scoreScheme, True(), False());
}
// NO BAND, XDROP
template <typename TStringInfix, typename TAlignSpec, typename TString,
typename TPos, typename TScoreValue, typename TScoreSpec>
inline TScoreValue
extendAlignment(Align<TStringInfix, TAlignSpec> & align,
TString const & hSeq,
TString const & vSeq,
Tuple<TPos, 4> const & positions,
ExtensionDirection const & direction,
TScoreValue const & xDrop,
Score<TScoreValue, TScoreSpec> const & scoreScheme)
{
return _extendAlignmentImpl(align, std::numeric_limits<TScoreValue>::min(), hSeq, vSeq, positions, direction, 0, 0, xDrop,
scoreScheme, False(), True());
}
template <typename TStringInfix, typename TAlignSpec, typename TString,
typename TPos, typename TScoreValue, typename TScoreSpec>
inline TScoreValue
extendAlignment(Align<TStringInfix, TAlignSpec> & align,
TScoreValue const & origScore,
TString const & hSeq,
TString const & vSeq,
Tuple<TPos, 4> const & positions,
ExtensionDirection const & direction,
TScoreValue const & xDrop,
Score<TScoreValue, TScoreSpec> const & scoreScheme)
{
return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, 0, 0, xDrop, scoreScheme, False(),
True());
}
// BAND, XDROP
template <typename TStringInfix, typename TAlignSpec, typename TString,
typename TPos, typename TScoreValue, typename TScoreSpec>
inline TScoreValue
extendAlignment(Align<TStringInfix, TAlignSpec> & align,
TString const & hSeq,
TString const & vSeq,
Tuple<TPos, 4> const & positions,
ExtensionDirection const & direction,
int const lowerDiag,
int const upperDiag,
TScoreValue const & xDrop,
Score<TScoreValue, TScoreSpec> const & scoreScheme)
{
return _extendAlignmentImpl(align, std::numeric_limits<TScoreValue>::min(), hSeq, vSeq, positions, direction, lowerDiag, upperDiag,
xDrop, scoreScheme, True(), True());
}
template <typename TStringInfix, typename TAlignSpec, typename TString,
typename TPos, typename TScoreValue, typename TScoreSpec>
inline TScoreValue
extendAlignment(Align<TStringInfix, TAlignSpec> & align,
TScoreValue const & origScore,
TString const & hSeq,
TString const & vSeq,
Tuple<TPos, 4> const & positions,
ExtensionDirection const & direction,
int const lowerDiag,
int const upperDiag,
TScoreValue const & xDrop,
Score<TScoreValue, TScoreSpec> const & scoreScheme)
{
return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, lowerDiag, upperDiag, xDrop,
scoreScheme, True(), True());
}
template <typename TStringInfix, typename TAlignSpec, typename TString,
typename TPos, typename TScoreValue, typename TScoreSpec,
typename TAliExtContext>
inline TScoreValue
extendAlignment(Align<TStringInfix, TAlignSpec> & align,
TAliExtContext & alignContext,
TScoreValue const & origScore,
TString const & hSeq,
TString const & vSeq,
Tuple<TPos, 4> const & positions,
ExtensionDirection const & direction,
int const lowerDiag,
int const upperDiag,
TScoreValue const & xDrop,
Score<TScoreValue, TScoreSpec> const & scoreScheme)
{
return _extendAlignmentImpl(align, origScore, hSeq, vSeq, positions, direction, lowerDiag, upperDiag, xDrop,
scoreScheme, True(), True(), alignContext);
}
}
#endif // INCLUDE_ALIGN_ALIGN_EXTEND_H
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