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// Copyright ©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 genome defines types useful for representing cytogenetic features.
package genome
import (
"github.com/biogo/biogo/feat"
"github.com/biogo/biogo/seq"
)
// Chromosome represent a chromosome and associated features. Elements in the
// Features field should return the Chromosome when their Location() method is
// called.
type Chromosome struct {
Chr string
Desc string
Length int
Features []feat.Feature
}
func (c *Chromosome) Start() int { return 0 }
func (c *Chromosome) End() int { return c.Length }
func (c *Chromosome) Len() int { return c.Length }
func (c *Chromosome) Name() string { return c.Chr }
func (c *Chromosome) Description() string { return c.Desc }
func (c *Chromosome) Location() feat.Feature { return nil }
// Band represents a chromosome band.
type Band struct {
Band string
Desc string
Chr feat.Feature
StartPos int
EndPos int
Giemsa string
}
func (b *Band) Start() int { return b.StartPos }
func (b *Band) End() int { return b.EndPos }
func (b *Band) Len() int { return b.End() - b.Start() }
func (b *Band) Name() string { return b.Band }
func (b *Band) Description() string { return b.Desc }
func (b *Band) Location() feat.Feature { return b.Chr }
// Fragment represents an assembly fragment.
type Fragment struct {
Frag string
Desc string
Chr feat.Feature
ChrStart int
ChrEnd int
FragStart int
FragEnd int
Type byte
Strand seq.Strand
}
func (f *Fragment) Start() int { return f.ChrStart }
func (f *Fragment) End() int { return f.ChrEnd }
func (f *Fragment) Len() int { return f.End() - f.Start() }
func (f *Fragment) Name() string { return f.Frag }
func (f *Fragment) Description() string { return f.Desc }
func (f *Fragment) Location() feat.Feature { return f.Chr }
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