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alignio.go
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alignio.go
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// Copyright ©2011-2013 The bíogo Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.
// Package alignio for reading and writing multiple sequence alignment files
package alignio
import (
"github.com/biogo/biogo/io/seqio"
"github.com/biogo/biogo/seq/multi"
"io"
)
// Reader implements multiple sequence reading from a seqio.Reader.
type Reader struct {
r seqio.Reader
m *multi.Multi
}
// NewReader return a new Reader that will read sequences from r into m.
func NewReader(r seqio.Reader, m *multi.Multi) *Reader {
return &Reader{r, m}
}
// Read the contents of the embedded seqio.Reader into a seq.Sequence.
// Returns the Alignment, or nil and an error if an error occurs.
func (r *Reader) Read() (*multi.Multi, error) {
for {
s, err := r.r.Read()
if err != nil {
if err == io.EOF {
break
} else {
return nil, err
}
}
r.m.Add(s)
}
m, t := r.m, *r.m
t.Seq = nil
r.m = &t
return m, nil
}
// Writer implements multiple sequence writing to a seqio.Writer.
type Writer struct {
w seqio.Writer
}
// Return a new Writer.
func NewWriter(w seqio.Writer) *Writer {
return &Writer{w}
}
// Write a multi.Multi to the embedded seqio.Writer.
// Returns the number of bytes written and any error.
func (w *Writer) Write(m *multi.Multi) (n int, err error) {
var _n int
for _, s := range m.Seq {
_n, err = w.w.Write(s)
n += _n
if err != nil {
break
}
}
return
}