| /dports/biology/seqan1/seqan-1.3.1/seqan/graph_align/ |
| H A D | graph_align_banded_smith_waterman_clump.h | 107 TTraceValue nextTraceValue = traceValue; in _alignBandedSmithWatermanTrace() local
108 if (traceValue == Diagonal) nextTraceValue = trace[(--row) * diagonalWidth + col]; in _alignBandedSmithWatermanTrace()
109 else if (traceValue == Vertical) nextTraceValue = trace[(--row) * diagonalWidth + (++col)]; in _alignBandedSmithWatermanTrace()
110 else if (traceValue == Horizontal) nextTraceValue = trace[row * diagonalWidth + (--col)]; in _alignBandedSmithWatermanTrace()
113 if (nextTraceValue == Diagonal) _setForbiddenCell(forbidden, row+1, col+1, diagonalWidth); in _alignBandedSmithWatermanTrace()
116 while (nextTraceValue != Stop) { in _alignBandedSmithWatermanTrace()
117 if (traceValue == nextTraceValue) { in _alignBandedSmithWatermanTrace()
123 traceValue = nextTraceValue; in _alignBandedSmithWatermanTrace()
124 if (traceValue == Diagonal) nextTraceValue = trace[(--row) * diagonalWidth + col]; in _alignBandedSmithWatermanTrace()
126 else if (traceValue == Horizontal) nextTraceValue = trace[row * diagonalWidth + (--col)]; in _alignBandedSmithWatermanTrace()
[all …]
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| H A D | graph_align_smith_waterman.h | 125 …TTraceValue nextTraceValue = (len2 & 1) ? trace[(len1 - 1)*numRows + ((len2 - 1) >> 1)] >> 4 : tra… in _alignSmithWatermanTrace() local
127 if (initialDir == Diagonal) tv = (nextTraceValue & 3); in _alignSmithWatermanTrace()
129 …if ((nextTraceValue >> 2) & 1) _alignTracePrint(align, str, id1, --len1, id2, len2, (TSize) 1, Hor… in _alignSmithWatermanTrace()
132 …if ((nextTraceValue >> 3) & 1) _alignTracePrint(align, str, id1, len1, id2, --len2, (TSize) 1, Ver… in _alignSmithWatermanTrace()
140 …nextTraceValue = (len2 & 1) ? trace[(len1 - 1)*numRows + ((len2 - 1) >> 1)] >> 4 : trace[(len1 - 1… in _alignSmithWatermanTrace()
141 if ((nextTraceValue & 3) == Stop) break; in _alignSmithWatermanTrace()
143 if (tv == Diagonal) tv = (nextTraceValue & 3); in _alignSmithWatermanTrace()
145 if ((nextTraceValue >> 2) & 1) tv = Diagonal; in _alignSmithWatermanTrace()
148 if ((nextTraceValue >> 3) & 1) tv = Diagonal; in _alignSmithWatermanTrace()
164 if ((nextTraceValue >> 2) & 1) { in _alignSmithWatermanTrace()
[all …]
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| H A D | graph_align_gotoh.h | 76 …TTraceValue nextTraceValue = (len2 & 1) ? trace[(len1 - 1)*numRows + ((len2 - 1) >> 1)] >> 4 : tra… in _alignGotohTrace() local
78 if (initialDir == Diagonal) tv = (nextTraceValue & 3); in _alignGotohTrace()
80 …if ((nextTraceValue >> 2) & 1) _alignTracePrint(align, str, id1, --len1, id2, len2, (TSize) 1, Hor… in _alignGotohTrace()
83 …if ((nextTraceValue >> 3) & 1) _alignTracePrint(align, str, id1, len1, id2, --len2, (TSize) 1, Ver… in _alignGotohTrace()
91 …nextTraceValue = (len2 & 1) ? trace[(len1 - 1)*numRows + ((len2 - 1) >> 1)] >> 4 : trace[(len1 - 1… in _alignGotohTrace()
92 if (tv == Diagonal) tv = (nextTraceValue & 3); in _alignGotohTrace()
94 if ((nextTraceValue >> 2) & 1) tv = Diagonal; in _alignGotohTrace()
97 if ((nextTraceValue >> 3) & 1) tv = Diagonal; in _alignGotohTrace()
113 if ((nextTraceValue >> 2) & 1) { in _alignGotohTrace()
127 if ((nextTraceValue >> 3) & 1) { in _alignGotohTrace()
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/ |
| H A D | local_alignment_banded_waterman_eggert_impl.h | 416 TTraceValue nextTraceValue = Horizontal; in _alignBandedSmithWatermanTrace() local
419 while (nextTraceValue != Stop) { in _alignBandedSmithWatermanTrace()
420 traceValue = nextTraceValue; in _alignBandedSmithWatermanTrace()
422 nextTraceValue = Stop; in _alignBandedSmithWatermanTrace()
428 nextTraceValue = Diagonal; in _alignBandedSmithWatermanTrace()
437 nextTraceValue = Vertical; in _alignBandedSmithWatermanTrace()
446 nextTraceValue = Horizontal; in _alignBandedSmithWatermanTrace()
452 if (traceValue == nextTraceValue) { in _alignBandedSmithWatermanTrace()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
| H A D | local_alignment_banded_waterman_eggert_impl.h | 416 TTraceValue nextTraceValue = Horizontal; in _alignBandedSmithWatermanTrace() local
419 while (nextTraceValue != Stop) { in _alignBandedSmithWatermanTrace()
420 traceValue = nextTraceValue; in _alignBandedSmithWatermanTrace()
422 nextTraceValue = Stop; in _alignBandedSmithWatermanTrace()
428 nextTraceValue = Diagonal; in _alignBandedSmithWatermanTrace()
437 nextTraceValue = Vertical; in _alignBandedSmithWatermanTrace()
446 nextTraceValue = Horizontal; in _alignBandedSmithWatermanTrace()
452 if (traceValue == nextTraceValue) { in _alignBandedSmithWatermanTrace()
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/ |
| H A D | local_alignment_banded_waterman_eggert_impl.h | 416 TTraceValue nextTraceValue = Horizontal; in _alignBandedSmithWatermanTrace() local
419 while (nextTraceValue != Stop) { in _alignBandedSmithWatermanTrace()
420 traceValue = nextTraceValue; in _alignBandedSmithWatermanTrace()
422 nextTraceValue = Stop; in _alignBandedSmithWatermanTrace()
428 nextTraceValue = Diagonal; in _alignBandedSmithWatermanTrace()
437 nextTraceValue = Vertical; in _alignBandedSmithWatermanTrace()
446 nextTraceValue = Horizontal; in _alignBandedSmithWatermanTrace()
452 if (traceValue == nextTraceValue) { in _alignBandedSmithWatermanTrace()
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| /dports/biology/seqan1/seqan-1.3.1/seqan/align/ |
| H A D | align_local_dynprog_banded.h | 127 TTraceValue nextTraceValue = Horizontal; in _alignBandedSmithWatermanTrace() local
130 while (nextTraceValue != Stop) { in _alignBandedSmithWatermanTrace()
131 traceValue = nextTraceValue; in _alignBandedSmithWatermanTrace()
133 nextTraceValue = Stop; in _alignBandedSmithWatermanTrace()
136 nextTraceValue = Diagonal; in _alignBandedSmithWatermanTrace()
142 nextTraceValue = Vertical; in _alignBandedSmithWatermanTrace()
149 nextTraceValue = Horizontal; in _alignBandedSmithWatermanTrace()
155 if (traceValue == nextTraceValue) { in _alignBandedSmithWatermanTrace()
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/graph_msa/ |
| H A D | graph_align_tcoffee_library.h | 157 …TTraceValue nextTraceValue = (len2 & 1) ? trace[(len1 - 1)*numRows + ((len2 - 1) >> 1)] >> 4 : tra… in _alignSmithWatermanTrace() local
159 if (initialDir == Diagonal) tv = (nextTraceValue & 3); in _alignSmithWatermanTrace()
161 …if ((nextTraceValue >> 2) & 1) _alignTracePrint(align, str[0], str[1], id1, --len1, id2, len2, (TS… in _alignSmithWatermanTrace()
164 …if ((nextTraceValue >> 3) & 1) _alignTracePrint(align, str[0], str[1], id1, len1, id2, --len2, (TS… in _alignSmithWatermanTrace()
172 …nextTraceValue = (len2 & 1) ? trace[(len1 - 1)*numRows + ((len2 - 1) >> 1)] >> 4 : trace[(len1 - 1… in _alignSmithWatermanTrace()
173 if ((nextTraceValue & 3) == Stop) break; in _alignSmithWatermanTrace()
175 if (tv == Diagonal) tv = (nextTraceValue & 3); in _alignSmithWatermanTrace()
177 if ((nextTraceValue >> 2) & 1) tv = Diagonal; in _alignSmithWatermanTrace()
180 if ((nextTraceValue >> 3) & 1) tv = Diagonal; in _alignSmithWatermanTrace()
196 if ((nextTraceValue >> 2) & 1) { in _alignSmithWatermanTrace()
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/graph_msa/ |
| H A D | graph_align_tcoffee_library.h | 178 …TTraceValue nextTraceValue = (len2 & 1) ? trace[(len1 - 1)*numRows + ((len2 - 1) >> 1)] >> 4 : tra… in _alignSmithWatermanTrace() local
180 if (initialDir == Diagonal) tv = (nextTraceValue & 3); in _alignSmithWatermanTrace()
182 …if ((nextTraceValue >> 2) & 1) _alignTracePrint(align, str[0], str[1], id1, --len1, id2, len2, (TS… in _alignSmithWatermanTrace()
185 …if ((nextTraceValue >> 3) & 1) _alignTracePrint(align, str[0], str[1], id1, len1, id2, --len2, (TS… in _alignSmithWatermanTrace()
193 …nextTraceValue = (len2 & 1) ? trace[(len1 - 1)*numRows + ((len2 - 1) >> 1)] >> 4 : trace[(len1 - 1… in _alignSmithWatermanTrace()
194 if ((nextTraceValue & 3) == Stop) break; in _alignSmithWatermanTrace()
196 if (tv == Diagonal) tv = (nextTraceValue & 3); in _alignSmithWatermanTrace()
198 if ((nextTraceValue >> 2) & 1) tv = Diagonal; in _alignSmithWatermanTrace()
201 if ((nextTraceValue >> 3) & 1) tv = Diagonal; in _alignSmithWatermanTrace()
217 if ((nextTraceValue >> 2) & 1) { in _alignSmithWatermanTrace()
[all …]
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/graph_msa/ |
| H A D | graph_align_tcoffee_library.h | 178 …TTraceValue nextTraceValue = (len2 & 1) ? trace[(len1 - 1)*numRows + ((len2 - 1) >> 1)] >> 4 : tra… in _alignSmithWatermanTrace() local
180 if (initialDir == Diagonal) tv = (nextTraceValue & 3); in _alignSmithWatermanTrace()
182 …if ((nextTraceValue >> 2) & 1) _alignTracePrint(align, str[0], str[1], id1, --len1, id2, len2, (TS… in _alignSmithWatermanTrace()
185 …if ((nextTraceValue >> 3) & 1) _alignTracePrint(align, str[0], str[1], id1, len1, id2, --len2, (TS… in _alignSmithWatermanTrace()
193 …nextTraceValue = (len2 & 1) ? trace[(len1 - 1)*numRows + ((len2 - 1) >> 1)] >> 4 : trace[(len1 - 1… in _alignSmithWatermanTrace()
194 if ((nextTraceValue & 3) == Stop) break; in _alignSmithWatermanTrace()
196 if (tv == Diagonal) tv = (nextTraceValue & 3); in _alignSmithWatermanTrace()
198 if ((nextTraceValue >> 2) & 1) tv = Diagonal; in _alignSmithWatermanTrace()
201 if ((nextTraceValue >> 3) & 1) tv = Diagonal; in _alignSmithWatermanTrace()
217 if ((nextTraceValue >> 2) & 1) { in _alignSmithWatermanTrace()
[all …]
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