phylip

package
v0.4.1 Latest Latest
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 Go to latest Published: Jul 10, 2026 License: GPL-2.0 Imports: 9 Imported by: 3

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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, 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) Alphabet added in v0.3.8 

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

alphabet: can be align.BOTH (auto detect alphabet), align.NUCLEOTIDS (considers alignment as nucleotides), or align.AMINOACIDS (considers the alignment as aminoacids). If not auto, can return an error if the alignment is not compatible with the given alphabet. If another value is given, then align.BOTH is considered

func (*Parser) IgnoreIdentical added in v0.3.1 

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

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)

Parse parses a phylip alignment

func (*Parser) ParseMultiple added in v0.1.1 

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 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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