phylip

package
v0.2.4 Latest Latest
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This package is not in the latest version of its module.

 Go to latest Published: Nov 27, 2017 License: GPL-2.0 Imports: 9 Imported by: 0

Documentation

Index

Constants

View Source 
const (
	FASTA_LINE_LEN   = 80 // max line length for fasta output
	FASTA_INITIAL_NB = 2  // max line length for fasta output
)
View Source 
const (
	PHYLIP_LINE  = 60
	PHYLIP_BLOCK = 10
)

Variables

This section is empty.

Functions

func WriteAlignment 

func WriteAlignment(al align.Alignment, strict 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) Parse 

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

Parse parses a phylip alignment

func (*Parser) ParseMultiple added in v0.1.1 

func (p *Parser) ParseMultiple(aligns chan<- align.Alignment) error

Parses mutliple phylip alignments and give them to the channel At the end (or in case of error), it closes the 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 added in v0.2.2 

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
)

Source Files

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