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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 seq
import (
"github.com/biogo/biogo/alphabet"
"github.com/biogo/biogo/feat"
)
// Strand stores linear sequence strand information.
type Strand int8
const (
Minus Strand = iota - 1
None
Plus
)
func (s Strand) String() string {
switch s {
case Plus:
return "+"
case None:
return "."
case Minus:
return "-"
}
return "undefined"
}
// An Annotation is a basic linear sequence annotation type.
type Annotation struct {
ID string
Desc string
Loc feat.Feature
Strand Strand
Conform feat.Conformation
Alpha alphabet.Alphabet
Offset int
}
// Name returns the ID string of the sequence.
func (a *Annotation) Name() string { return a.ID }
// SetName sets the ID string of the sequence.
func (a *Annotation) SetName(id string) error { a.ID = id; return nil }
// Description returns the Desc string of the sequence.
func (a *Annotation) Description() string { return a.Desc }
// SetDescription sets the Desc string of the sequence.
func (a *Annotation) SetDescription(d string) error { a.Desc = d; return nil }
// Conformation returns the sequence conformation.
func (a *Annotation) Conformation() feat.Conformation { return a.Conform }
// SetConformation sets the sequence conformation.
func (a *Annotation) SetConformation(c feat.Conformation) error { a.Conform = c; return nil }
// Orientation returns the sequence's strand as a feat.Orientation.
func (a *Annotation) Orientation() feat.Orientation { return feat.Orientation(a.Strand) }
// SetOrientation sets the sequence'a strand from a feat.Orientation.
func (a *Annotation) SetOrientation(o feat.Orientation) error { a.Strand = Strand(o); return nil }
// Location returns the Loc field of the sequence.
func (a *Annotation) Location() feat.Feature { return a.Loc }
// SetLocation sets the Loc field of the sequence.
func (a *Annotation) SetLocation(f feat.Feature) error { a.Loc = f; return nil }
// Alphabet return the alphabet.Alphabet used by the sequence.
func (a *Annotation) Alphabet() alphabet.Alphabet { return a.Alpha }
// SetAlphabet the sets the alphabet.Alphabet used by the sequence.
func (a *Annotation) SetAlphabet(n alphabet.Alphabet) error { a.Alpha = n; return nil }
// SetOffset sets the global offset of the sequence to o.
func (a *Annotation) SetOffset(o int) error { a.Offset = o; return nil }
// Moltype returns the molecule type of the sequence.
func (a *Annotation) Moltype() feat.Moltype { return a.Alpha.Moltype() }
// CloneAnnotation returns a pointer to a copy of the receiver.
func (a *Annotation) CloneAnnotation() *Annotation { ca := *a; return &ca }
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