Last change
on this file was
13639,
checked in by westram, 9 years ago
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- full update from child 'pars' into 'trunk'
- adds:
|
-
Property svn:eol-style set to
native
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Property svn:keywords set to
Author Date Id Revision
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File size:
2.0 KB
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Line | |
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1 | // =============================================================== // |
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2 | // // |
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3 | // File : AP_seq_dna.hxx // |
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4 | // Purpose : // |
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5 | // // |
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6 | // Institute of Microbiology (Technical University Munich) // |
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7 | // http://www.arb-home.de/ // |
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8 | // // |
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9 | // =============================================================== // |
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10 | |
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11 | #ifndef AP_SEQ_DNA_HXX |
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12 | #define AP_SEQ_DNA_HXX |
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13 | |
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14 | #ifndef AP_SEQUENCE_HXX |
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15 | #include <AP_sequence.hxx> |
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16 | #endif |
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17 | #ifndef DOWNCAST_H |
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18 | #include <downcast.h> |
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19 | #endif |
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20 | |
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21 | class AP_sequence_parsimony : public AP_sequence { // derived from a Noncopyable |
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22 | void build_table(); |
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23 | AP_FLOAT count_weighted_bases() const OVERRIDE; |
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24 | |
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25 | void set(const char *sequence) OVERRIDE; |
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26 | void unset() OVERRIDE; |
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27 | |
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28 | char *seq_pars; // AP_BASES |
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29 | |
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30 | public: |
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31 | static char *table; |
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32 | |
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33 | AP_sequence_parsimony(const AliView *aliview); |
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34 | ~AP_sequence_parsimony() OVERRIDE; |
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35 | |
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36 | const char *get_sequence() const { |
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37 | lazy_load_sequence(); |
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38 | ap_assert(seq_pars); |
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39 | return seq_pars; |
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40 | } |
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41 | const unsigned char *get_usequence() const { return (const unsigned char*)get_sequence(); } |
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42 | |
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43 | AP_sequence *dup() const OVERRIDE; // used to get the real new element |
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44 | AP_FLOAT combine(const AP_sequence *lefts, const AP_sequence *rights, char *mutation_per_site) OVERRIDE; |
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45 | void partial_match(const AP_sequence* part, long *overlap, long *penalty) const OVERRIDE; |
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46 | uint32_t checksum() const OVERRIDE; |
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47 | |
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48 | bool equals(const AP_sequence_parsimony *other) const; |
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49 | bool equals(const AP_sequence *other) const OVERRIDE { return equals(DOWNCAST(const AP_sequence_parsimony*, other)); } |
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50 | }; |
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51 | |
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52 | |
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53 | #else |
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54 | #error AP_seq_dna.hxx included twice |
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55 | #endif // AP_SEQ_DNA_HXX |
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