1 #ifndef GENESIS_SEQUENCE_COUNTS_H_ 2 #define GENESIS_SEQUENCE_COUNTS_H_ 245 std::string characters_;
255 #endif // include guard CountsIntType added_sequences_count() const
Return the number of processed Sequences, i.e., how many Sequences were added in total.
void clear()
Clear the object, that is, delete everything.
Store counts of the occurence for certain characters at the sites of Sequences.
CountsIntType count_of(char character, size_t site_index) const
Return the count of a specific character at a given site.
SiteCounts()=default
Default constructor.
void add_sequences(SequenceSet const &sequences, bool use_abundances=true)
Process a SequenceSet and add its counts to the existing ones for all contained Sequences.
void add_sequence(Sequence const &sequence, bool use_abundance=true)
Process a single Sequence and add its counts to the existing ones.
Container namespace for all symbols of genesis in order to keep them separate when used as a library...
SiteCounts & operator=(SiteCounts const &)=default
Default copy assignment.
size_t length() const
Return the number of sites used for counting.
void clear_counts()
Reset all counts to 0.
~SiteCounts()=default
Default destructor.
Store a set of Sequences.
uint32_t CountsIntType
Type of uint used for internally counting the freuqencies of Sequence sites.
CountsIntType count_at(size_t character_index, size_t site_index) const
Return the count for a character and a site, given their indices.
std::string characters() const
Return the character set that is used for counting.