| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/alignment/ |
| H A D | align_assignment1.cpp | 13 typedef Iterator<TRow>::Type TRowIterator; in main() typedef
34 TRowIterator itRow1 = begin(row1); in main()
35 TRowIterator itEndRow1 = end(row1); in main()
36 TRowIterator itRow2 = begin(row2); in main()
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| H A D | align.cpp | 122 typedef Iterator<TRow>::Type TRowIterator; in main() typedef
123 TRowIterator it = begin(row1), in main()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/pairwise_sequence_alignment/ |
| H A D | alignment_global_assignment3.cpp | 12 typedef Iterator<TRow>::Type TRowIterator; in main() typedef
35 TRowIterator it = iter(row(align, i), 0); in main()
36 TRowIterator itEnd = iter(row(align, i), aliLength); in main()
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/ |
| H A D | align_iterator_base.h | 65 typedef typename Iterator<TRow, Standard>::Type TRowIterator; typedef
67 typedef String<TRowIterator> TIterators;
161 typedef typename Iterator<TRow, Standard>::Type TRowIterator; in goNext() typedef
162 typedef String<TRowIterator> TIterators; in goNext()
201 typedef typename Iterator<TRow, Standard>::Type TRowIterator; in goPrevious() typedef
202 typedef String<TRowIterator> TIterators; in goPrevious()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
| H A D | align_iterator_base.h | 65 typedef typename Iterator<TRow, Standard>::Type TRowIterator; typedef
67 typedef String<TRowIterator> TIterators;
161 typedef typename Iterator<TRow, Standard>::Type TRowIterator; in goNext() typedef
162 typedef String<TRowIterator> TIterators; in goNext()
201 typedef typename Iterator<TRow, Standard>::Type TRowIterator; in goPrevious() typedef
202 typedef String<TRowIterator> TIterators; in goPrevious()
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| /dports/biology/seqan1/seqan-1.3.1/seqan/align/ |
| H A D | align_iterator_base.h | 51 typedef typename Iterator<TRow, Standard>::Type TRowIterator; typedef
53 typedef String<TRowIterator> TIterators;
156 typedef typename Iterator<TRow, Standard>::Type TRowIterator; in goNext() typedef
157 typedef String<TRowIterator> TIterators; in goNext()
199 typedef typename Iterator<TRow, Standard>::Type TRowIterator; in goPrevious() typedef
200 typedef String<TRowIterator> TIterators; in goPrevious()
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| H A D | align_algorithms.h | 72 typedef typename Iterator<TRow>::Type TRowIterator; in _pumpTraceToAlign() typedef
79 TRowIterator it0 = begin(row(align_, 0)); in _pumpTraceToAlign()
80 TRowIterator it1 = begin(row(align_, 1)); in _pumpTraceToAlign()
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/ |
| H A D | align_iterator_base.h | 65 typedef typename Iterator<TRow, Standard>::Type TRowIterator; typedef
67 typedef String<TRowIterator> TIterators;
172 typedef typename Iterator<TRow, Standard>::Type TRowIterator; in goNext() typedef
173 typedef String<TRowIterator> TIterators; in goNext()
215 typedef typename Iterator<TRow, Standard>::Type TRowIterator; in goPrevious() typedef
216 typedef String<TRowIterator> TIterators; in goPrevious()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align/ |
| H A D | test_alignment_algorithms_dynamic_gap.h | 53 typedef typename Iterator<TRow, Standard>::Type TRowIterator; in _validateAlignment() typedef
60 TRowIterator itH = begin(row(align, 0), Standard()); in _validateAlignment()
61 TRowIterator itV = begin(row(align, 1), Standard()); in _validateAlignment()
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| /dports/biology/seqan1/seqan-1.3.1/seqan/graph_msa/ |
| H A D | graph_align_tcoffee_base.h | 959 typedef typename Iterator<TRow>::Type TRowIterator; in convertAlignment() typedef
967 String<TRowIterator> rowIter; in convertAlignment()
1007 typedef typename Iterator<TRow, Standard>::Type TRowIterator; in convertAlignment() typedef
1014 String<TRowIterator> rowIter; in convertAlignment()
1015 String<TRowIterator> rowIterEnd; in convertAlignment()
1025 TRowIterator pos1 = value(rowIter,alignRow1); in convertAlignment()
1026 TRowIterator pos2 = value(rowIter,alignRow2); in convertAlignment()
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/graph_msa/ |
| H A D | graph_align_tcoffee_base.h | 984 typedef typename Iterator<TRow>::Type TRowIterator; in convertAlignment() typedef
992 String<TRowIterator> rowIter; in convertAlignment()
1032 typedef typename Iterator<TRow, Standard>::Type TRowIterator; in convertAlignment() typedef
1039 String<TRowIterator> rowIter; in convertAlignment()
1040 String<TRowIterator> rowIterEnd; in convertAlignment()
1050 TRowIterator pos1 = value(rowIter,alignRow1); in convertAlignment()
1051 TRowIterator pos2 = value(rowIter,alignRow2); in convertAlignment()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/graph_msa/ |
| H A D | graph_align_tcoffee_base.h | 984 typedef typename Iterator<TRow>::Type TRowIterator; in convertAlignment() typedef
992 String<TRowIterator> rowIter; in convertAlignment()
1032 typedef typename Iterator<TRow, Standard>::Type TRowIterator; in convertAlignment() typedef
1039 String<TRowIterator> rowIter; in convertAlignment()
1040 String<TRowIterator> rowIterEnd; in convertAlignment()
1050 TRowIterator pos1 = value(rowIter,alignRow1); in convertAlignment()
1051 TRowIterator pos2 = value(rowIter,alignRow2); in convertAlignment()
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/graph_msa/ |
| H A D | graph_align_tcoffee_base.h | 983 typedef typename Iterator<TRow>::Type TRowIterator; in convertAlignment() typedef
991 String<TRowIterator> rowIter; in convertAlignment()
1031 typedef typename Iterator<TRow, Standard>::Type TRowIterator; in convertAlignment() typedef
1038 String<TRowIterator> rowIter; in convertAlignment()
1039 String<TRowIterator> rowIterEnd; in convertAlignment()
1049 TRowIterator pos1 = value(rowIter,alignRow1); in convertAlignment()
1050 TRowIterator pos2 = value(rowIter,alignRow2); in convertAlignment()
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| /dports/biology/seqan1/seqan-1.3.1/seqan/seeds2/ |
| H A D | align_chain_banded.h | 616 typedef typename Iterator<TRow, Standard>::Type TRowIterator;
631 for (TRowIterator it = begin(row(alignment, 0)); it != end(row(alignment, 0)); ++it, ++i) {
638 for (TRowIterator it = begin(row(alignment, 1)); it != end(row(alignment, 1)); ++it, ++i) {
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