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// Copyright ©2020 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 fai
import (
"errors"
"io"
)
// File is a sequence file with an FAI index.
type File struct {
Index
r io.ReaderAt
}
// NewFile returns the sequence file for the given reader and associates it with
// the specified index.
func NewFile(r io.ReaderAt, idx Index) *File {
return &File{r: r, Index: idx}
}
// Seq returns a handle to the complete sequence identified by the given name.
func (f *File) Seq(name string) (*Seq, error) {
rec, ok := f.Index[name]
if !ok {
return nil, errors.New("fai: no sequence")
}
return &Seq{r: f.r, Record: rec, end: rec.Length}, nil
}
// Seq returns a handle to the sequence identified by the given name from the
// start position until the end position.
func (f *File) SeqRange(name string, start, end int) (*Seq, error) {
if start < 0 || end < 0 || end < start {
return nil, errors.New("fai: index out of range")
}
rec, ok := f.Index[name]
if !ok {
return nil, errors.New("fai: no sequence")
}
if rec.Length < start || rec.Length < end {
return nil, errors.New("fai: index out of range")
}
return &Seq{r: f.r, Record: rec, cur: start, start: start, end: end}, nil
}
// Seq is a handle to a sequence segment obtained from a File.
type Seq struct {
Record
r io.ReaderAt
cur int
start, end int
}
// Reset resets the position of the cursor into the sequence segment to the original start.
func (s *Seq) Reset() {
s.cur = s.start
}
// Read reads sequence data from the Seq into b.
func (s *Seq) Read(b []byte) (int, error) {
if len(b) == 0 {
return 0, nil
}
var n int
end := int(s.Record.position(s.end))
for s.cur < s.end {
cur := s.Record.position(s.cur)
eol := min(s.Record.endOfLineOffset(s.cur), end-int(cur))
_n, err := s.r.ReadAt(b[:min(eol, len(b))], cur)
s.cur += _n
n += _n
b = b[_n:]
if err != nil || len(b) == 0 {
return n, err
}
}
return n, io.EOF
}
func min(a, b int) int {
if a < b {
return a
}
return b
}
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