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/dports/biology/seqan1/seqan-1.3.1/seqan/seeds/
H A Dseed_multi.h64 std::list<Triple<TPosition, TPosition, TPosition> > seedSet;
203 inline const std::list<Triple<TPosition, TPosition, TPosition> >&
210 inline std::list<Triple<TPosition, TPosition, TPosition> >&
231 Triple<TPosition, TPosition, TPosition> diag) in appendDiag() argument
238 Triple<TPosition, TPosition, TPosition>&
245 const Triple<TPosition, TPosition, TPosition>&
252 Triple<TPosition, TPosition, TPosition>&
259 const Triple<TPosition, TPosition, TPosition>&
355 Triple <TPosition, TPosition, TPosition> tmpSeed = _getLastDiag(firstSeed); in _mergeTwoSeeds()
543 seed.seedSet.push_front(Triple<TPosition, TPosition, TPosition> in _setExtendedSeedDimensions()
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H A Dseed_base.h132 …Seed(TPosition leftDim0, TPosition leftDim1, TPosition length):leftDim0(leftDim0),leftDim1(leftDim… in Seed()
198 inline TPosition
216 inline TPosition
236 inline TPosition
256 inline TPosition
279 inline TPosition
300 inline TPosition
336 inline TPosition
354 inline TPosition
372 inline TPosition
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H A Dseeds_generated_forwards.h337 template <typename TPosition> inline const std::list<Triple<TPosition, TPosition, TPosition> >& _ge…
338 template <typename TPosition> inline std::list<Triple<TPosition, TPosition, TPosition> >& _getDiagS…
343 template <typename TPosition> Triple<TPosition, TPosition, TPosition>& _getFirstDiag(Seed<TPosition…
344 template <typename TPosition> const Triple<TPosition, TPosition, TPosition>& _getFirstDiag(Seed<TPo…
349 template <typename TPosition> Triple<TPosition, TPosition, TPosition>& _getLastDiag(Seed<TPosition,…
350 template <typename TPosition> const Triple<TPosition, TPosition, TPosition>& _getLastDiag(Seed<TPos…
380 template <typename TPosition> void _mergeTwoSeeds(Seed<TPosition, ChainedSeed> &firstSeed, TPositio…
388 …ate <typename TPosition, typename TSpecSeed> void _mergeTwoSeeds(Seed<TPosition, TSpecSeed> &first…
389 … <typename TPosition> void _mergeTwoSeeds(Seed<TPosition, SimpleSeed> &firstSeed, TPosition qlPos,…
529 template <typename TPosition> void appendDiag(Seed<TPosition,ChainedSeed> & seed, Triple<TPosition,…
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/dports/biology/seqan1/seqan-1.3.1/apps/rep_sep/
H A Drgraph_base.h37 typedef Pair< TPosition , TColumnAlphabet> TColumnInfo;
55 id(GraphCargo<TColumnAlphabet, TAlignedReadStoreElement,TPosition> & me) in id()
62 id(GraphCargo<TColumnAlphabet, TAlignedReadStoreElement,TPosition> const & me) in id()
79 void addColumn(GraphCargo<TColumnAlphabet, TAlignedReadStoreElement,TPosition> & me, TPosition pos,… in addColumn()
142 …phabet,TAlignedReadStoreElement, TPosition> & me, typename ReadGraph<TColumnAlphabet,TAlignedReadS…
150 inline GraphCargo<TColumnAlphabet,TAlignedReadStoreElement, TPosition> &
151 …phabet,TAlignedReadStoreElement, TPosition> & me, typename ReadGraph<TColumnAlphabet,TAlignedReadS…
160 …phabet,TAlignedReadStoreElement, TPosition> & me, typename ReadGraph<TColumnAlphabet,TAlignedReadS…
175 inline GraphCargo<TColumnAlphabet,TAlignedReadStoreElement, TPosition> &
176 …phabet,TAlignedReadStoreElement, TPosition> & me, typename ReadGraph<TColumnAlphabet,TAlignedReadS…
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/rep_sep/
H A Drgraph_base.h37 typedef Pair< TPosition , TColumnAlphabet> TColumnInfo;
55 id(GraphCargo<TColumnAlphabet, TAlignedReadStoreElement,TPosition> & me) in id()
62 id(GraphCargo<TColumnAlphabet, TAlignedReadStoreElement,TPosition> const & me) in id()
79 void addColumn(GraphCargo<TColumnAlphabet, TAlignedReadStoreElement,TPosition> & me, TPosition pos,… in addColumn()
142 …phabet,TAlignedReadStoreElement, TPosition> & me, typename ReadGraph<TColumnAlphabet,TAlignedReadS…
150 inline GraphCargo<TColumnAlphabet,TAlignedReadStoreElement, TPosition> &
151 …phabet,TAlignedReadStoreElement, TPosition> & me, typename ReadGraph<TColumnAlphabet,TAlignedReadS…
160 …phabet,TAlignedReadStoreElement, TPosition> & me, typename ReadGraph<TColumnAlphabet,TAlignedReadS…
175 inline GraphCargo<TColumnAlphabet,TAlignedReadStoreElement, TPosition> &
176 …phabet,TAlignedReadStoreElement, TPosition> & me, typename ReadGraph<TColumnAlphabet,TAlignedReadS…
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/
H A Ddp_trace_segment.h60 template <typename TPosition, typename TSize>
80 …TraceSegment_(TPosition const & horizontalBeginPos, TPosition const & verticalBeginPos, TSize cons… in TraceSegment_()
111 template <typename TPosition, typename TSize>
114 typedef TPosition Type;
117 template <typename TPosition, typename TSize>
145 inline TPosition
157 inline TPosition
169 inline TPosition
185 inline TPosition
283 inline bool operator==(TraceSegment_<TPosition, TSize> const & left, TraceSegment_<TPosition, TSize…
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/
H A Ddp_trace_segment.h60 template <typename TPosition, typename TSize>
80 …TraceSegment_(TPosition const & horizontalBeginPos, TPosition const & verticalBeginPos, TSize cons… in TraceSegment_()
111 template <typename TPosition, typename TSize>
114 typedef TPosition Type;
117 template <typename TPosition, typename TSize>
145 inline TPosition
157 inline TPosition
169 inline TPosition
186 inline TPosition
283 inline bool operator==(TraceSegment_<TPosition, TSize> const & left, TraceSegment_<TPosition, TSize…
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/
H A Ddp_trace_segment.h60 template <typename TPosition, typename TSize>
80 …TraceSegment_(TPosition const & horizontalBeginPos, TPosition const & verticalBeginPos, TSize cons… in TraceSegment_()
111 template <typename TPosition, typename TSize>
114 typedef TPosition Type;
117 template <typename TPosition, typename TSize>
145 inline TPosition
157 inline TPosition
169 inline TPosition
186 inline TPosition
283 inline bool operator==(TraceSegment_<TPosition, TSize> const & left, TraceSegment_<TPosition, TSize…
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/
H A Dseeds_seed_diagonal.h86 template <typename TPosition, typename TSize>
90 TPosition beginPositionH;
91 TPosition beginPositionV;
97 SeedDiagonal(TPosition _beginPositionH, TPosition _beginPositionV, TSize _length) : in SeedDiagonal()
121 template <typename TPosition, typename TSize>
124 typedef TPosition Type;
127 template <typename TPosition, typename TSize>
128 struct Position<SeedDiagonal<TPosition, TSize> const> : Position<SeedDiagonal<TPosition, TSize> >
147 struct Size<SeedDiagonal<TPosition, TSize> >
153 struct Size<SeedDiagonal<TPosition, TSize> const> : Size<SeedDiagonal<TPosition, TSize> >
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H A Dseeds_seed_simple.h81 typedef typename TConfiguration::TPosition TPosition; typedef
86 TPosition _beginPositionH;
87 TPosition _beginPositionV;
88 TPosition _endPositionH;
89 TPosition _endPositionV;
98 Seed(TPosition beginPositionH, TPosition beginPositionV, TPosition seedLength) : in Seed()
106 …Seed(TPosition beginPositionH, TPosition beginPositionV, TPosition endPositionH, TPosition endPosi… in Seed()
189 template <typename TConfig, typename TPosition>
211 template <typename TConfig, typename TPosition>
233 template <typename TConfig, typename TPosition>
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H A Dseeds_combination.h248 TPosition minGap = _min(gapDim0, gapDim1); in _combineSeeds()
250 TPosition remainingGap = maxGap - minGap; in _combineSeeds()
255 TPosition posLeft0 = endPositionH(seed); in _combineSeeds()
256 TPosition posLeft1 = endPositionV(seed); in _combineSeeds()
259 for (TPosition i = 0; i < minGap; ++i) in _combineSeeds()
273 for (TPosition i = 1; i < minGap; ++i) { in _combineSeeds()
404 TPosition remainingGap = maxGap - minGap; in _combineSeeds()
409 TPosition posLeft0 = endPositionH(seed); in _combineSeeds()
410 TPosition posLeft1 = endPositionV(seed); in _combineSeeds()
413 for (TPosition i = 0; i < minGap; ++i) in _combineSeeds()
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/dports/biology/seqan1/seqan-1.3.1/seqan/seeds2/
H A Dseeds_seed_diagonal.h56 template <typename TPosition, typename TSize>
63 TPosition beginDim0;
67 TPosition beginDim1;
77 SeedDiagonal(TPosition _beginDim0, TPosition _beginDim1, TSize _length) in SeedDiagonal()
87 template <typename TPosition, typename TSize>
90 typedef TPosition Type;
93 template <typename TPosition, typename TSize>
98 template <typename TPosition, typename TSize>
99 struct Size<SeedDiagonal<TPosition, TSize> >
104 template <typename TPosition, typename TSize>
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H A Dseeds_combination.h247 TPosition minGap = _min(gapDim0, gapDim1); in _combineSeeds()
249 TPosition remainingGap = maxGap - minGap; in _combineSeeds()
254 TPosition posLeft0 = getEndDim0(seed); in _combineSeeds()
255 TPosition posLeft1 = getEndDim1(seed); in _combineSeeds()
258 for (TPosition i = 0; i < minGap; ++i) in _combineSeeds()
272 for (TPosition i = 1; i < minGap; ++i) { in _combineSeeds()
407 TPosition remainingGap = maxGap - minGap; in _combineSeeds()
412 TPosition posLeft0 = getEndDim0(seed); in _combineSeeds()
413 TPosition posLeft1 = getEndDim1(seed); in _combineSeeds()
416 for (TPosition i = 0; i < minGap; ++i) in _combineSeeds()
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H A Dalign_dynprog_linear.h83 typedef typename Position<TMatrix>::Type TPosition; in _alignInitGutter() typedef
92 for (TPosition i = 0, iend = length(matrix, 0); i < iend; ++i) { in _alignInitGutter()
139 typedef typename Position<TMatrix>::Type TPosition; in _alignInitGutterFromBanded() typedef
289 TPosition origPos0 = pos0; in _alignTraceback()
291 TPosition origPos1 = pos1; in _alignTraceback()
305 TPosition altPos1 = pos1; in _alignTraceback()
317 TPosition altPos0 = pos0; in _alignTraceback()
345 if (pos0 == static_cast<TPosition>(0) || pos1 == static_cast<TPosition>(0)) in _alignTraceback()
350 …ic_cast<TPosition>(1) || pos1 <= static_cast<TPosition>(1)) || (pos0 < static_cast<TPosition>(uppe… in _alignTraceback()
426 for (TPosition i = 0; i < pos0; ++i) { in _alignTraceback()
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H A Dseeds_seed_simple.h76 typedef typename TConfiguration::TPosition TPosition; typedef
82 TPosition _beginDim0;
83 TPosition _beginDim1;
84 TPosition _endDim0;
85 TPosition _endDim1;
95 Seed(TPosition beginDim0, TPosition beginDim1, TPosition seedLength) in Seed()
108 Seed(TPosition beginDim0, TPosition beginDim1, TPosition endDim0, in Seed()
109 TPosition endDim1) in Seed()
189 TPosition newLeftPosition) in setBeginDim0()
251 TPosition newRightPosition) in setEndDim0()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/
H A Dseeds_seed_diagonal.h86 template <typename TPosition, typename TSize>
90 TPosition beginPositionH;
91 TPosition beginPositionV;
97 SeedDiagonal(TPosition _beginPositionH, TPosition _beginPositionV, TSize _length) : in SeedDiagonal()
121 template <typename TPosition, typename TSize>
124 typedef TPosition Type;
127 template <typename TPosition, typename TSize>
128 struct Position<SeedDiagonal<TPosition, TSize> const> : Position<SeedDiagonal<TPosition, TSize> >
147 struct Size<SeedDiagonal<TPosition, TSize> >
153 struct Size<SeedDiagonal<TPosition, TSize> const> : Size<SeedDiagonal<TPosition, TSize> >
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H A Dseeds_seed_simple.h81 typedef typename TConfiguration::TPosition TPosition; typedef
86 TPosition _beginPositionH;
87 TPosition _beginPositionV;
88 TPosition _endPositionH;
89 TPosition _endPositionV;
98 Seed(TPosition beginPositionH, TPosition beginPositionV, TPosition seedLength) : in Seed()
106 …Seed(TPosition beginPositionH, TPosition beginPositionV, TPosition endPositionH, TPosition endPosi… in Seed()
189 template <typename TConfig, typename TPosition>
211 template <typename TConfig, typename TPosition>
233 template <typename TConfig, typename TPosition>
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H A Dseeds_combination.h248 TPosition minGap = _min(gapDim0, gapDim1); in _combineSeeds()
250 TPosition remainingGap = maxGap - minGap; in _combineSeeds()
255 TPosition posLeft0 = endPositionH(seed); in _combineSeeds()
256 TPosition posLeft1 = endPositionV(seed); in _combineSeeds()
259 for (TPosition i = 0; i < minGap; ++i) in _combineSeeds()
273 for (TPosition i = 1; i < minGap; ++i) { in _combineSeeds()
404 TPosition remainingGap = maxGap - minGap; in _combineSeeds()
409 TPosition posLeft0 = endPositionH(seed); in _combineSeeds()
410 TPosition posLeft1 = endPositionV(seed); in _combineSeeds()
413 for (TPosition i = 0; i < minGap; ++i) in _combineSeeds()
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/
H A Dseeds_seed_diagonal.h86 template <typename TPosition, typename TSize>
90 TPosition beginPositionH;
91 TPosition beginPositionV;
97 SeedDiagonal(TPosition _beginPositionH, TPosition _beginPositionV, TSize _length) : in SeedDiagonal()
121 template <typename TPosition, typename TSize>
124 typedef TPosition Type;
127 template <typename TPosition, typename TSize>
128 struct Position<SeedDiagonal<TPosition, TSize> const> : Position<SeedDiagonal<TPosition, TSize> >
147 struct Size<SeedDiagonal<TPosition, TSize> >
153 struct Size<SeedDiagonal<TPosition, TSize> const> : Size<SeedDiagonal<TPosition, TSize> >
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H A Dseeds_seed_simple.h81 typedef typename TConfiguration::TPosition TPosition; typedef
86 TPosition _beginPositionH;
87 TPosition _beginPositionV;
88 TPosition _endPositionH;
89 TPosition _endPositionV;
98 Seed(TPosition beginPositionH, TPosition beginPositionV, TPosition seedLength) : in Seed()
106 …Seed(TPosition beginPositionH, TPosition beginPositionV, TPosition endPositionH, TPosition endPosi… in Seed()
189 template <typename TConfig, typename TPosition>
211 template <typename TConfig, typename TPosition>
233 template <typename TConfig, typename TPosition>
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H A Dseeds_combination.h248 TPosition minGap = _min(gapDim0, gapDim1); in _combineSeeds()
250 TPosition remainingGap = maxGap - minGap; in _combineSeeds()
255 TPosition posLeft0 = endPositionH(seed); in _combineSeeds()
256 TPosition posLeft1 = endPositionV(seed); in _combineSeeds()
259 for (TPosition i = 0; i < minGap; ++i) in _combineSeeds()
273 for (TPosition i = 1; i < minGap; ++i) { in _combineSeeds()
404 TPosition remainingGap = maxGap - minGap; in _combineSeeds()
409 TPosition posLeft0 = endPositionH(seed); in _combineSeeds()
410 TPosition posLeft1 = endPositionV(seed); in _combineSeeds()
413 for (TPosition i = 0; i < minGap; ++i) in _combineSeeds()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/parse_lm/
H A Dlocal_match_store.h93 template <typename TId, typename TPosition>
99 TPosition subjectBeginPos;
100 TPosition subjectEndPos;
102 TPosition queryBeginPos;
103 TPosition queryEndPos;
117 TPosition subjectBeginPos_, in LocalMatch()
118 TPosition subjectEndPos_, in LocalMatch()
120 TPosition queryBeginPos_, in LocalMatch()
121 TPosition queryEndPos_) : in LocalMatch()
246 typedef typename TConfig::TPosition TPosition; typedef
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/parse_lm/
H A Dlocal_match_store.h93 template <typename TId, typename TPosition>
99 TPosition subjectBeginPos;
100 TPosition subjectEndPos;
102 TPosition queryBeginPos;
103 TPosition queryEndPos;
117 TPosition subjectBeginPos_, in LocalMatch()
118 TPosition subjectEndPos_, in LocalMatch()
120 TPosition queryBeginPos_, in LocalMatch()
121 TPosition queryEndPos_) : in LocalMatch()
246 typedef typename TConfig::TPosition TPosition; typedef
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/parse_lm/
H A Dlocal_match_store.h93 template <typename TId, typename TPosition>
99 TPosition subjectBeginPos;
100 TPosition subjectEndPos;
102 TPosition queryBeginPos;
103 TPosition queryEndPos;
117 TPosition subjectBeginPos_, in LocalMatch()
118 TPosition subjectEndPos_, in LocalMatch()
120 TPosition queryBeginPos_, in LocalMatch()
121 TPosition queryEndPos_) : in LocalMatch()
246 typedef typename TConfig::TPosition TPosition; typedef
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align/
H A Dtest_alignment_dp_trace_segment.h42 template <typename TPosition, typename TSize>
48 typedef TraceSegment_<TPosition, TSize> TTraceSegment; in testAlignmentTracebackTraceSegmentsConstructor()
91 template <typename TPosition, typename TSize>
97 typedef TraceSegment_<TPosition, TSize> TTraceSegment; in testAlignmentTracebackTraceSegmentsAssignment()
122 template <typename TPosition, typename TSize>
128 typedef TraceSegment_<TPosition, TSize> TTraceSegment; in testAlignmentTracebackTraceSegmentsCompare()
144 template <typename TPosition, typename TSize>
150 typedef TraceSegment_<TPosition, TSize> TTraceSegment; in testAlignmentTracebackTraceSegmentsPosition()
152 bool result = +IsSameType<TPosition_, TPosition>::VALUE; in testAlignmentTracebackTraceSegmentsPosition()
156 template <typename TPosition, typename TSize>
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