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| LCSEPM (const Sequence &seqA_, const Sequence &seqB_, const PatternPairMap &myPatterns, PatternPairMap &myLCSEPM) |
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virtual | ~LCSEPM () |
| Destructor.
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void | MapToPS (const std::string &sequenceA, const std::string &sequenceB, PatternPairMap &myMap, const std::string &file1, const std::string &file2) |
| output chained EPMs to PS files More...
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void | calculateLCSEPM (bool quiet) |
| calculates the best chain of EPMs, the LCS-EPM
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std::pair< SequenceAnnotation, SequenceAnnotation > | anchor_annotation () |
| get anchor annotation
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void | output_locarna (const std::string &sequenceA, const std::string &sequenceB, const std::string &outfile) |
| outputs anchor constraints to be used as input for locarna
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void | output_clustal (const std::string &outfile_name) |
| writes chain as clustal alignment
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computes the best chain of EPMs, the LCS-EPM