1 #ifndef GENESIS_SEQUENCE_FORMATS_PHYLIP_READER_H_ 2 #define GENESIS_SEQUENCE_FORMATS_PHYLIP_READER_H_ 102 size_t num_sequences = 0;
107 size_t len_sequences = 0;
192 SequenceSet read( std::shared_ptr<utils::BaseInputSource> source )
const;
205 void read( std::shared_ptr<utils::BaseInputSource> source,
SequenceSet& target )
const;
221 Header parse_phylip_header(
232 std::string parse_phylip_label(
243 std::string parse_phylip_sequence_line(
250 void parse_phylip_sequential(
258 void parse_phylip_interleaved(
317 size_t label_length()
const;
355 bool remove_digits()
const;
381 std::string valid_chars()
const;
397 Mode mode_ = Mode::kSequential;
398 size_t label_length_ = 0;
400 SiteCasing site_casing_ = SiteCasing::kToUpper;
401 bool remove_digits_ =
false;
402 bool use_validation_ =
false;
410 #endif // include guard Read Phylip sequence data.
Container namespace for all symbols of genesis in order to keep them separate when used as a library...
Mode
Enum to distinguish between the different file variants of Phylip. See mode( Mode value ) for more de...
Store a set of Sequences.
SiteCasing
Enumeration of casing methods to apply to each site of a Sequence.