clustal

type Parser ¶

type Parser struct {
	// contains filtered or unexported fields
}

Parser represents a parser. If ignore is align.IGNORE_NONE: Does not ignore anything If ignore is align.IGNORE_NAME: Ignore sequences having the same name (keep the first one whatever their sequence) If ignore is align.IGNORE_SEQUENCE: Ignore sequences having the same name and the same sequence Otherwise, sets IGNORE_NONE

func NewParser(r io.Reader) *Parser

func (p *Parser) Alphabet(alphabet int) *Parser

func (p *Parser) IgnoreIdentical(ignore int) *Parser

func (p *Parser) Parse() (al align.Alignment, err error)

type Scanner ¶

type Scanner struct {
	// contains filtered or unexported fields
}

Scanner represents a lexical scanner.

func NewScanner(r io.Reader) *Scanner

func (s *Scanner) Read(n int) string

func (s *Scanner) Scan() (tok Token, lit string)

type Token ¶

type Token int64

const (
	ILLEGAL    Token = iota
	INTEGER          // Number of sequences or length
	IDENTIFIER       // Identifier of sequence or part of sequence
	ENDOFLINE        // End of line token
	CLUSTAL          // Start of the file: "^CLUSTAL"
	EOF              // End of File
	WS               // Whitespace
	NUMERIC          // Number of taxa and length of sequences
)