[INFRA] Move seqan3::search from search/algorithm/ to search/.
#1696
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@@ Coverage Diff @@
## master #1696 +/- ##
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- Coverage 97.67% 97.65% -0.03%
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Files 237 237
Lines 9045 9050 +5
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+ Hits 8835 8838 +3
- Misses 210 212 +2
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simonsasse
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include/seqan3/search/all.hpp
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| @@ -35,9 +35,56 @@ | |||
| * SeqAn currently supports very fast FM indices. For more details visit the \ref submodule_fm_index | |||
| * "FM Index submodule". | |||
| * | |||
| * ## Search Algorithms | |||
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| * ## Search Algorithms | |
| * ## Search algorithm |
include/seqan3/search/all.hpp
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| * The Search module offers a simple unified interface that allows searching FM indices and choosing the best | ||
| * algorithm based on the index at hand. | ||
| * | ||
| * ## FM Indices |
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| * ## FM Indices | |
| * ## FM indices |
include/seqan3/search/all.hpp
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| * | ||
| * A search scheme is a collection of searches, where each search `s` specifies the order in which the blocks are | ||
| * searched (`s.pi`), the lower error bounds (`s.l`) and the upper error bounds (`s.u`). If the number of blocks that | ||
| * the query sequences are split into are known at compile time, the data structure `search` is recommended, otherwise |
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| * the query sequences are split into are known at compile time, the data structure `search` is recommended, otherwise | |
| * the query sequences are split into are known at compile time, the data structure seqan3::detail::search is recommended, otherwise |
include/seqan3/search/all.hpp
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| * represented as `std::vector` of seqan3::detail::search_dyn. | ||
| * | ||
| * All optimum search schemes are disjoint, i.e. no error configuration is covered by more than one search. Thus there | ||
| * is no need for a filtration phase after searching to remove duplicate hits. Allowing insertions and deletions will |
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| * is no need for a filtration phase after searching to remove duplicate hits. Allowing insertions and deletions will | |
| * is no need for a filtration phase after searching to remove duplicate hits when searching with hamming distance. Allowing insertions and deletions will, however, |
include/seqan3/search/all.hpp
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| * the query sequences are split into are known at compile time, the data structure `search` is recommended, otherwise | ||
| * one has to use seqan3::detail::search_dyn. The first one implements its member variables as an an `std::array` of | ||
| * integers, the latter as an `std::vector` of integers. | ||
| * Similarily search schemes are defined. They are either implemented as an `std::array` of searches if the number of |
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| * Similarily search schemes are defined. They are either implemented as an `std::array` of searches if the number of | |
| * Search schemes are defined similiar. They are either implemented as an `std::array` of searches if the number of |
|
Also please add a API changelog entry. |
Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>
rrahn
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Apr 1, 2020
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Resolves #1695