OpenMS
2.5.0
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#include <OpenMS/ANALYSIS/ID/AhoCorasickAmbiguous.h>
Public Types | |
typedef uint32_t | TSize |
typedef Value< TNeedle >::Type | TKeyword |
typedef Value< TKeyword >::Type | TAlphabet |
typedef Graph< Automaton< TAlphabet > > | TGraph |
typedef VertexDescriptor< TGraph >::Type | TVert |
typedef __uint8 | KeyWordLengthType |
Public Member Functions | |
Pattern () | |
void | init (TNeedle const &ndl, KeyWordLengthType max_AAA=3, KeyWordLengthType max_mm=0) |
Pattern Ctor with vector of needles, i.e. keywords/peptides. More... | |
~Pattern () | |
Public Attributes | |
const TVert | nilVal |
NULL pointer for trie; e.g. returned when no successor is found. More... | |
Holder< TNeedle > | data_host |
holds needles, i.e. Peptides More... | |
TGraph | data_graph |
regular trie data More... | |
String< String< TSize > > | data_map_outputNodes |
regular trie data – plus: this gets augmented with all suffix traversals which are output nodes More... | |
String< KeyWordLengthType > | data_node_depth |
depths of each graph node More... | |
KeyWordLengthType | max_ambAA |
ambiguity; default: 3 More... | |
KeyWordLengthType | max_mmAA |
mismatches; default: 0 More... | |
String< TVert > | parentMap |
allows to find parent of each node More... | |
Private Member Functions | |
Pattern (Pattern const &other) | |
Pattern const & | operator= (Pattern const &other) |
typedef __uint8 KeyWordLengthType |
typedef uint32_t TSize |
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private |
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inline |
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inline |
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inline |
Pattern Ctor with vector of needles, i.e. keywords/peptides.
The vector ndl
must not be empty!
References seqan::isAmbiguous(), and seqan::setHost().
TGraph data_graph |
regular trie data
Referenced by seqan::_consumeChar(), seqan::_createAcTrie(), seqan::_masterConsumeChar(), and seqan::setHost().
Holder<TNeedle> data_host |
holds needles, i.e. Peptides
Referenced by seqan::setHost().
String<String<TSize> > data_map_outputNodes |
regular trie data – plus: this gets augmented with all suffix traversals which are output nodes
Referenced by seqan::_createAcTrie(), seqan::addHits(), and seqan::setHost().
String<KeyWordLengthType> data_node_depth |
depths of each graph node
Referenced by seqan::_consumeChar(), seqan::_createAcTrie(), seqan::_masterConsumeChar(), seqan::addHits(), and seqan::find().
KeyWordLengthType max_ambAA |
ambiguity; default: 3
Referenced by seqan::_masterConsumeChar(), and seqan::_spawnConsumeChar().
KeyWordLengthType max_mmAA |
mismatches; default: 0
Referenced by seqan::_masterConsumeChar(), and seqan::_spawnConsumeChar().
const TVert nilVal |
NULL pointer for trie; e.g. returned when no successor is found.
Referenced by seqan::_consumeChar().
String<TVert> parentMap |
allows to find parent of each node
Referenced by seqan::_createAcTrie().