Tokenize an alignment string into alignment_tokens. More...

Public Member Functions
void	set_alignment (const std::string &aln)
	Set a new alignment string to be tokenized.

const std::string &	get_alignment () const
	Get the reference to the current alignment string.

void	set_reverse (const bool rev)
	Tokenize back-to-front.

const alignment_token &	current () const
	Get the current alignment_token.

bool	has_data ()
	Check if there is a current alignment_token.

void	next ()
	Advance to the next alignment_token.

Detailed Description

Tokenize an alignment string into alignment_tokens.

Alignment string examples:

<ACGGGGT>AAATAGCG[GC][AC][G-][T-][T-]ATG[-A][L25]ACG[F60]

<ACGGGGT>AAATAGCG[GA|CC][GTT|—]ATG[-A][L25]ACG[F60]

ATTA{CT}TTA

ATTA(C-)TTA

The documentation for this class was generated from the following file:

Public Member Functions