phylip

Documentation

Index

• Constants
• func WriteAlignment(al align.Alignment, strict, oneline, noblock bool) string
• type Parser
  • func NewParser(r io.Reader, strict bool) *Parser
  • func (p *Parser) IgnoreIdentical(ignore int)
  • func (p *Parser) Parse() (align.Alignment, error)
  • func (p *Parser) ParseMultiple(aligns *align.AlignChannel)
• type Scanner
  • func NewScanner(r io.Reader) *Scanner
  • func (s *Scanner) Read(n int) string
  • func (s *Scanner) Scan() (tok Token, lit string)
• type Token

Constants

const (
	FASTA_LINE_LEN   = 80 // max line length for fasta output
	FASTA_INITIAL_NB = 2  // max line length for fasta output
)

const (
	PHYLIP_LINE  = 60
	PHYLIP_BLOCK = 10
)

Functions

func WriteAlignment

func WriteAlignment(al align.Alignment, strict, oneline, noblock bool) string

Types

type Parser

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

Parser represents a parser.

func NewParser

func NewParser(r io.Reader, strict bool) *Parser

NewParser returns a new instance of Parser.

func (*Parser) IgnoreIdentical

func (p *Parser) IgnoreIdentical(ignore int)

If sets to true, then will ignore duplicate sequences that have the same name and the same sequence Otherwise, it just renames them just as the sequences that have same name and different sequences

func (*Parser) Parse

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

Parse parses a phylip alignment

func (*Parser) ParseMultiple

func (p *Parser) ParseMultiple(aligns *align.AlignChannel)

Parses mutliple phylip alignments and give them to the channel At the end (or in case of error), it closes the channel. It is better to call this functioni from a go routine since it can block the buffered channel.

type Scanner

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

Scanner represents a lexical scanner.

func NewScanner

func NewScanner(r io.Reader) *Scanner

NewScanner returns a new instance of Scanner.

func (*Scanner) Read

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

reads the next n runes from the bufferred reader.

func (*Scanner) Scan

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

Scan returns the next token and literal value.

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
	EOF              // End of File
	WS               // Whitespace
	NUMERIC          // Number of taxa and length of sequences
)