nexus

Documentation

Index

• func WriteAlignment(al align.Alignment) string
• type Parser
  • func NewParser(r io.Reader) *Parser
  • func (p *Parser) IgnoreIdentical(ignore int)
  • func (p *Parser) Parse() (al align.Alignment, err error)
• type Scanner
  • func NewScanner(r io.Reader) *Scanner
  • func (s *Scanner) Scan() (tok Token, lit string)
• type Token

Functions

func WriteAlignment

func WriteAlignment(al align.Alignment) string

Types

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

func NewParser(r io.Reader) *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() (al align.Alignment, err error)

Parses Nexus content from the reader

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) 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
	EOF
	WS
	IDENT        // Name of Node, or comment, or keyword
	NUMERIC      // Any numerical value
	OPENBRACK    // [ : For comment
	CLOSEBRACK   // ] : For comment
	ENDOFCOMMAND // ; End of command
	ENDOFLINE    // \r \n

	// Keywords
	NEXUS     // #NEXUS : Start of nexus file
	EQUAL     // '=' between keyword and value
	BEGIN     // Begin
	DATA      // Begin data -> Alignment
	TAXA      // Begin taxa -> Definition of taxa
	TAXLABELS // Begin taxa : list of  taxlabels
	TREES     // Begin trees -> Definition of trees
	TREE      // A specific tree in the BEGIN TREES section

	DIMENSIONS // Dimensions
	NTAX       // Dimensions : Number of taxa
	NCHAR      // Dimensions : Length of alignment

	FORMAT    // Format
	DATATYPE  // Format datatype=dna
	MISSING   // Format missing=?  missing char
	GAP       // Format gap=- gap character
	MATCHCHAR // Format matchchar=.  matching character compared to first seq

	MATRIX // Matrix
	END    // End
)