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/dports/biology/seqan1/seqan-1.3.1/seqan/align/
H A Dalign_trace.h49 String<TSize> data_lengths;
50 String<TSize> data_factors;
64 typedef TSize Type;
91 inline TSize
93 TSize _dim)
104 TSize _length)
132 TSize _size;
166 TSize & position_,
193 TSize position_,
208 TSize coor_ = position_ / factor_;
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/dports/x11-toolkits/mygui-dummy/mygui-MyGUI3.4.0/MyGUIEngine/include/
H A DMyGUI_TSize.h18 struct TSize struct
23 TSize() : in TSize() argument
35 TSize(TSize const& _obj) : in TSize() argument
41 TSize& operator -= (TSize const& _obj)
48 TSize& operator += (TSize const& _obj)
55 TSize operator - (TSize const& _obj) const
60 TSize operator + (TSize const& _obj) const
65 TSize& operator = (TSize const& _obj)
73 TSize& operator = (TSize<U> const& _obj)
103 TSize tmp = _value; in swap()
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/dports/x11-toolkits/mygui/mygui-MyGUI3.4.0/MyGUIEngine/include/
H A DMyGUI_TSize.h18 struct TSize struct
23 TSize() : in TSize() argument
35 TSize(TSize const& _obj) : in TSize() function
41 TSize& operator -= (TSize const& _obj)
48 TSize& operator += (TSize const& _obj)
55 TSize operator - (TSize const& _obj) const
60 TSize operator + (TSize const& _obj) const
65 TSize& operator = (TSize const& _obj)
73 TSize& operator = (TSize<U> const& _obj)
103 TSize tmp = _value; in swap()
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/dports/x11-toolkits/mygui-opengl/mygui-MyGUI3.4.0/MyGUIEngine/include/
H A DMyGUI_TSize.h18 struct TSize struct
23 TSize() : in TSize() function
35 TSize(TSize const& _obj) : in TSize() argument
41 TSize& operator -= (TSize const& _obj)
48 TSize& operator += (TSize const& _obj)
55 TSize operator - (TSize const& _obj) const
60 TSize operator + (TSize const& _obj) const
65 TSize& operator = (TSize const& _obj)
73 TSize& operator = (TSize<U> const& _obj)
103 TSize tmp = _value; in swap()
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/dports/x11-toolkits/mygui-ogre/mygui-MyGUI3.4.0/MyGUIEngine/include/
H A DMyGUI_TSize.h18 struct TSize struct
23 TSize() : in TSize() function
35 TSize(TSize const& _obj) : in TSize() function
41 TSize& operator -= (TSize const& _obj)
48 TSize& operator += (TSize const& _obj)
55 TSize operator - (TSize const& _obj) const
60 TSize operator + (TSize const& _obj) const
65 TSize& operator = (TSize const& _obj)
73 TSize& operator = (TSize<U> const& _obj)
103 TSize tmp = _value; in swap()
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/dports/biology/seqan1/seqan-1.3.1/seqan/graph_types/
H A Dgraph_impl_fragment.h129 TSize begin1;
131 TSize begin2;
132 TSize len;
150 Fragment(TId sqId1, TSize beg1, TId sqId2, TSize beg2, TSize l) :
169 TSize begin1;
172 TSize len;
177 Fragment(TId_ sqId1, TSize beg1, TId_ sqId2, TSize beg2, TSize l) :
189 Fragment(TId_ sqId1, TSize beg1, TId_ sqId2, TSize beg2, TSize l, bool rev) :
251 inline TSize&
263 inline TSize&
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/
H A Dfragment.h146 TSize begin1;
148 TSize begin2;
149 TSize len;
167 Fragment(TId sqId1, TSize beg1, TId sqId2, TSize beg2, TSize l) :
224 TSize begin1;
227 TSize len;
248 Fragment(TId_ sqId1, TSize beg1, TId_ sqId2, TSize beg2, TSize l) :
252 Fragment(TId_ sqId1, TSize beg1, TId_ sqId2, TSize beg2, TSize l, bool rev) :
372 inline TSize&
383 inline TSize&
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H A Ddp_trace_segment.h60 template <typename TPosition, typename TSize>
111 template <typename TPosition, typename TSize>
117 template <typename TPosition, typename TSize>
125 template <typename TPosition, typename TSize>
126 struct Size<TraceSegment_<TPosition, TSize> >
128 typedef TSize Type;
131 template <typename TPosition, typename TSize>
215 inline TSize
228 _setLength(TraceSegment_<TPosition, TSize> & traceSegment, TSize newLength)
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 Dfragment.h146 TSize begin1;
148 TSize begin2;
149 TSize len;
167 Fragment(TId sqId1, TSize beg1, TId sqId2, TSize beg2, TSize l) :
224 TSize begin1;
227 TSize len;
248 Fragment(TId_ sqId1, TSize beg1, TId_ sqId2, TSize beg2, TSize l) :
252 Fragment(TId_ sqId1, TSize beg1, TId_ sqId2, TSize beg2, TSize l, bool rev) :
372 inline TSize&
383 inline TSize&
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H A Ddp_trace_segment.h60 template <typename TPosition, typename TSize>
111 template <typename TPosition, typename TSize>
117 template <typename TPosition, typename TSize>
125 template <typename TPosition, typename TSize>
126 struct Size<TraceSegment_<TPosition, TSize> >
128 typedef TSize Type;
131 template <typename TPosition, typename TSize>
215 inline TSize
228 _setLength(TraceSegment_<TPosition, TSize> & traceSegment, TSize newLength)
283 inline bool operator==(TraceSegment_<TPosition, TSize> const & left, TraceSegment_<TPosition, TSize…
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/
H A Dfragment.h146 TSize begin1;
148 TSize begin2;
149 TSize len;
167 Fragment(TId sqId1, TSize beg1, TId sqId2, TSize beg2, TSize l) :
224 TSize begin1;
227 TSize len;
248 Fragment(TId_ sqId1, TSize beg1, TId_ sqId2, TSize beg2, TSize l) :
252 Fragment(TId_ sqId1, TSize beg1, TId_ sqId2, TSize beg2, TSize l, bool rev) :
367 inline TSize&
379 inline TSize&
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H A Ddp_trace_segment.h60 template <typename TPosition, typename TSize>
111 template <typename TPosition, typename TSize>
117 template <typename TPosition, typename TSize>
125 template <typename TPosition, typename TSize>
126 struct Size<TraceSegment_<TPosition, TSize> >
128 typedef TSize Type;
131 template <typename TPosition, typename TSize>
213 inline TSize
226 _setLength(TraceSegment_<TPosition, TSize> & traceSegment, TSize newLength)
283 inline bool operator==(TraceSegment_<TPosition, TSize> const & left, TraceSegment_<TPosition, TSize…
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/dports/biology/seqan1/seqan-1.3.1/seqan/consensus/
H A Dconsensus_library.h46 TSize, in _getAlignmentStatistics() argument
47 TSize, in _getAlignmentStatistics()
48 TSize, in _getAlignmentStatistics()
77 TSize, in _getAlignmentStatistics()
91 public ::std::unary_function<Pair<TSize, TSize>, bool>
94 operator() (Pair<TSize, TSize> const& a1, Pair<TSize, TSize> const& a2) const { in operator()
102 public ::std::unary_function<Pair<TSize, Triple<TSize, TSize, TSize> >, bool>
105 …operator() (Pair<TSize, Triple<TSize, TSize, TSize> > const& a1, Pair<TSize, Triple<TSize, TSize, … in operator()
142 typedef Triple<TSize, TSize, TSize> TInfo; in selectPairs()
310 appendValue(ovlIndex, Pair<TSize, TSize>((TSize) (avgDiag), pairLen), Generous()); in selectPairs()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/consensus/
H A Dconsensus_library.h88 public std::unary_function<Pair<TSize, TSize>, bool>
91 operator() (Pair<TSize, TSize> const& a1, Pair<TSize, TSize> const& a2) const { in operator()
99 public std::unary_function<Pair<TSize, Triple<TSize, TSize, TSize> >, bool>
102 …operator() (Pair<TSize, Triple<TSize, TSize, TSize> > const& a1, Pair<TSize, Triple<TSize, TSize, … in operator()
138 typedef Triple<TSize, TSize, TSize> TInfo; in selectPairsAssembly()
150 typedef String<Pair<TSize, TSize> > TOverlapIndexList; in selectPairsAssembly()
306 appendValue(ovlIndex, Pair<TSize, TSize>((TSize) (avgDiag), pairLen), Generous()); in selectPairsAssembly()
345 TSize index1 = 0; in selectPairsAllAgainstAll()
486 TSize minVal = std::numeric_limits<TSize>::max(); in appendSegmentMatches()
497 for(TSize i = 0; i < (TSize) length(noFront); ++i) { in appendSegmentMatches()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/consensus/
H A Dconsensus_library.h88 public std::unary_function<Pair<TSize, TSize>, bool>
91 operator() (Pair<TSize, TSize> const& a1, Pair<TSize, TSize> const& a2) const { in operator()
99 public std::unary_function<Pair<TSize, Triple<TSize, TSize, TSize> >, bool>
102 …operator() (Pair<TSize, Triple<TSize, TSize, TSize> > const& a1, Pair<TSize, Triple<TSize, TSize, … in operator()
138 typedef Triple<TSize, TSize, TSize> TInfo; in selectPairsAssembly()
150 typedef String<Pair<TSize, TSize> > TOverlapIndexList; in selectPairsAssembly()
306 appendValue(ovlIndex, Pair<TSize, TSize>((TSize) (avgDiag), pairLen), Generous()); in selectPairsAssembly()
345 TSize index1 = 0; in selectPairsAllAgainstAll()
486 TSize minVal = std::numeric_limits<TSize>::max(); in appendSegmentMatches()
497 for(TSize i = 0; i < (TSize) length(noFront); ++i) { in appendSegmentMatches()
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/consensus/
H A Dconsensus_library.h91 public std::unary_function<Pair<TSize, TSize>, bool>
94 operator() (Pair<TSize, TSize> const& a1, Pair<TSize, TSize> const& a2) const { in operator()
102 public std::unary_function<Pair<TSize, Triple<TSize, TSize, TSize> >, bool>
105 …operator() (Pair<TSize, Triple<TSize, TSize, TSize> > const& a1, Pair<TSize, Triple<TSize, TSize, … in operator()
141 typedef Triple<TSize, TSize, TSize> TInfo; in selectPairsAssembly()
153 typedef String<Pair<TSize, TSize> > TOverlapIndexList; in selectPairsAssembly()
309 appendValue(ovlIndex, Pair<TSize, TSize>((TSize) (avgDiag), pairLen), Generous()); in selectPairsAssembly()
348 TSize index1 = 0; in selectPairsAllAgainstAll()
489 TSize minVal = maxValue<TSize>(); in appendSegmentMatches()
500 for(TSize i = 0; i < (TSize) length(noFront); ++i) { in appendSegmentMatches()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/sequence_journaled/
H A Djournal_entry.h58 typedef TSize_ TSize; typedef
72 TSize length;
86 TSize length) in JournalEntry()
96 template <typename TPos, typename TSize>
110 template <typename TPos, typename TSize>
113 bool operator()(JournalEntry<TPos, TSize> const & a, JournalEntry<TPos, TSize> const & b) const in operator()
123 template <typename TPos, typename TSize>
124 struct Size<JournalEntry<TPos, TSize> >
126 typedef TSize Type;
129 template <typename TPos, typename TSize>
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/sequence_journaled/
H A Djournal_entry.h58 typedef TSize_ TSize; typedef
72 TSize length;
86 TSize length) in JournalEntry()
96 template <typename TPos, typename TSize>
110 template <typename TPos, typename TSize>
113 bool operator()(JournalEntry<TPos, TSize> const & a, JournalEntry<TPos, TSize> const & b) const in operator()
123 template <typename TPos, typename TSize>
124 struct Size<JournalEntry<TPos, TSize> >
126 typedef TSize Type;
129 template <typename TPos, typename TSize>
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/sequence_journaled/
H A Djournal_entry.h58 typedef TSize_ TSize; typedef
72 TSize length;
86 TSize length) in JournalEntry()
96 template <typename TPos, typename TSize>
110 template <typename TPos, typename TSize>
113 bool operator()(JournalEntry<TPos, TSize> const & a, JournalEntry<TPos, TSize> const & b) const in operator()
123 template <typename TPos, typename TSize>
124 struct Size<JournalEntry<TPos, TSize> >
126 typedef TSize Type;
129 template <typename TPos, typename 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>
92 TSize length;
121 template <typename TPosition, typename TSize>
127 template <typename TPosition, typename TSize>
128 struct Position<SeedDiagonal<TPosition, TSize> const> : Position<SeedDiagonal<TPosition, TSize> >
146 template <typename TPosition, typename TSize>
147 struct Size<SeedDiagonal<TPosition, TSize> >
149 typedef TSize Type;
152 template <typename TPosition, typename TSize>
153 struct Size<SeedDiagonal<TPosition, TSize> const> : Size<SeedDiagonal<TPosition, TSize> >
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/dports/biology/seqan1/seqan-1.3.1/seqan/seeds2/
H A Dseeds_seed_diagonal.h56 template <typename TPosition, typename TSize>
71 TSize length;
87 template <typename TPosition, typename TSize>
93 template <typename TPosition, typename TSize>
98 template <typename TPosition, typename TSize>
99 struct Size<SeedDiagonal<TPosition, TSize> >
101 typedef TSize Type;
104 template <typename TPosition, typename TSize>
106 : Size<SeedDiagonal<TPosition, TSize> > {};
120 template <typename TPosition, typename TSize>
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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>
92 TSize length;
121 template <typename TPosition, typename TSize>
127 template <typename TPosition, typename TSize>
128 struct Position<SeedDiagonal<TPosition, TSize> const> : Position<SeedDiagonal<TPosition, TSize> >
146 template <typename TPosition, typename TSize>
147 struct Size<SeedDiagonal<TPosition, TSize> >
149 typedef TSize Type;
152 template <typename TPosition, typename TSize>
153 struct Size<SeedDiagonal<TPosition, TSize> const> : Size<SeedDiagonal<TPosition, TSize> >
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/
H A Dseeds_seed_diagonal.h86 template <typename TPosition, typename TSize>
92 TSize length;
121 template <typename TPosition, typename TSize>
127 template <typename TPosition, typename TSize>
128 struct Position<SeedDiagonal<TPosition, TSize> const> : Position<SeedDiagonal<TPosition, TSize> >
146 template <typename TPosition, typename TSize>
147 struct Size<SeedDiagonal<TPosition, TSize> >
149 typedef TSize Type;
152 template <typename TPosition, typename TSize>
153 struct Size<SeedDiagonal<TPosition, TSize> const> : Size<SeedDiagonal<TPosition, TSize> >
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/graph_msa/
H A Dgraph_align_tcoffee_library.h138 TSize, in _isClumping() argument
139 TSize, in _isClumping()
140 TSize) in _isClumping()
188 TSize segLen = 0; in _alignSmithWatermanTrace()
450 for(TSize count = 0; count < (TSize) numAlignments; ++count) { in _localAlignment()
679 typedef std::pair<TSize, TSize> TPosSeqPair; in appendSegmentMatches()
683 for(TSize i=0; i<(TSize) ktup;++i) qIndexSize *= alphabet_size; in appendSegmentMatches()
686 for(TSize i = 0;i < (TSize) length(tupSet[k]);++i) { in appendSegmentMatches()
690 for(TSize q=0;q< (TSize) qIndexSize;++q) { in appendSegmentMatches()
1004 …_setDistanceValue(matches, pairSet, dist, (TSize) * itPair, (TSize) *(itPair + 1), (TSize) nseq, (… in appendSegmentMatches()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/graph_msa/
H A Dgraph_align_tcoffee_library.h138 TSize, in _isClumping() argument
139 TSize, in _isClumping()
140 TSize) in _isClumping()
188 TSize segLen = 0; in _alignSmithWatermanTrace()
450 for(TSize count = 0; count < (TSize) numAlignments; ++count) { in _localAlignment()
679 typedef std::pair<TSize, TSize> TPosSeqPair; in appendSegmentMatches()
683 for(TSize i=0; i<(TSize) ktup;++i) qIndexSize *= alphabet_size; in appendSegmentMatches()
686 for(TSize i = 0;i < (TSize) length(tupSet[k]);++i) { in appendSegmentMatches()
690 for(TSize q=0;q< (TSize) qIndexSize;++q) { in appendSegmentMatches()
1004 …_setDistanceValue(matches, pairSet, dist, (TSize) * itPair, (TSize) *(itPair + 1), (TSize) nseq, (… in appendSegmentMatches()
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