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parser.go
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parser.go
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package fasta
import (
"bytes"
"errors"
"io"
"regexp"
"strings"
"github.com/evolbioinfo/goalign/align"
)
// Parser represents a parser.
type Parser struct {
s *Scanner
buf struct {
tok Token // last read token
lit string // last read literal
n int // buffer size (max=1)
}
}
// NewParser returns a new instance of Parser.
func NewParser(r io.Reader) *Parser {
return &Parser{s: NewScanner(r)}
}
// scan returns the next token from the underlying scanner.
// If a token has been unscanned then read that instead.
func (p *Parser) scan() (tok Token, lit string) {
// If we have a token on the buffer, then return it.
if p.buf.n != 0 {
p.buf.n = 0
return p.buf.tok, p.buf.lit
}
// Otherwise read the next token from the scanner.
tok, lit = p.s.Scan()
// Save it to the buffer in case we unscan later.
p.buf.tok, p.buf.lit = tok, lit
return
}
// unscan pushes the previously read token back onto the buffer.
func (p *Parser) unscan() { p.buf.n = 1 }
// scanIgnoreEndOfLine scans the next EOL token.
func (p *Parser) scanIgnoreEndOfLine() (tok Token, lit string) {
tok, lit = p.scan()
if tok == ENDOFLINE {
tok, lit = p.scan()
}
return
}
// Parse parses a FASTA alignment
func (p *Parser) Parse() (al align.Alignment, err error) {
al = align.NewAlign(align.UNKNOWN)
err = p.parseGeneric(al)
return
}
// ParseUnalign parses an unaligned FASTA file
func (p *Parser) ParseUnalign() (sb align.SeqBag, err error) {
sb = align.NewSeqBag(align.UNKNOWN)
err = p.parseGeneric(sb)
return
}
func (p *Parser) parseGeneric(sb align.SeqBag) (err error) {
// The first token should be a ">"
tok, lit := p.scanIgnoreEndOfLine()
if tok != STARTIDENT {
err = errors.New("Fasta file should start with a > ")
return
}
p.unscan()
var curseq bytes.Buffer
curname := ""
firstSpaces := regexp.MustCompile("^( +)")
for tok != EOF {
tok, lit = p.scanIgnoreEndOfLine()
switch tok {
case STARTIDENT:
tok, lit = p.scan()
if tok != IDENTIFIER {
err = errors.New("> should be followed by a sequence identifier")
return
}
if curseq.Len() > 0 {
if err = sb.AddSequence(curname, curseq.String(), ""); err != nil {
return
}
curseq.Reset()
} else if curname != "" {
err = errors.New("A Fasta entry has a name but no sequence (" + curname + ")")
return
}
curname = firstSpaces.ReplaceAllString(lit, "")
case IDENTIFIER:
curseq.WriteString(strings.Replace(lit, " ", "", -1))
case EOF:
if curseq.Len() > 0 {
if err = sb.AddSequence(curname, curseq.String(), ""); err != nil {
return
}
}
}
}
sb.AutoAlphabet()
return
}