clustal

package

v0.3.2 Latest Latest Go to latest Published: Jan 14, 2020 License: GPL-2.0 Imports: 10 Imported by: 0

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Valid go.mod file
Redistributable license
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Repository

github.com/fredericlemoine/goalign

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Documentation ¶

Index ¶

Constants
func WriteAlignment(al align.Alignment) string
type Parser
- func NewParser(r io.Reader) *Parser
- func (p *Parser) IgnoreIdentical(ignore bool)
- func (p *Parser) Parse() (align.Alignment, error)
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 ¶

View Source

const (
	CLUSTAL_LINE = 50
)

Variables ¶

This section is empty.

Functions ¶

func WriteAlignment ¶

func WriteAlignment(al align.Alignment) string

Types ¶

type Parser ¶

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

Parser represents a parser.

func NewParser ¶

func NewParser(r io.Reader) *Parser

NewParser returns a new instance of Parser.

func (*Parser) IgnoreIdentical ¶ added in v0.3.1

func (p *Parser) IgnoreIdentical(ignore bool)

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 clustal alignment

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
	CLUSTAL          // Start of the file: "^CLUSTAL"
	EOF              // End of File
	WS               // Whitespace
	NUMERIC          // Number of taxa and length of sequences
)

Source Files ¶

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