genome

Documentation

Overview

Package genome defines types useful for representing cytogenetic features.

Index

• type Band
  • func (b *Band) Description() string
  • func (b *Band) End() int
  • func (b *Band) Len() int
  • func (b *Band) Location() feat.Feature
  • func (b *Band) Name() string
  • func (b *Band) Start() int
• type Chromosome
  • func (c *Chromosome) Description() string
  • func (c *Chromosome) End() int
  • func (c *Chromosome) Len() int
  • func (c *Chromosome) Location() feat.Feature
  • func (c *Chromosome) Name() string
  • func (c *Chromosome) Start() int
• type Fragment
  • func (f *Fragment) Description() string
  • func (f *Fragment) End() int
  • func (f *Fragment) Len() int
  • func (f *Fragment) Location() feat.Feature
  • func (f *Fragment) Name() string
  • func (f *Fragment) Start() int

Types

type Band

type Band struct {
	Band     string
	Desc     string
	Chr      feat.Feature
	StartPos int
	EndPos   int
	Giemsa   string
}

Band represents a chromosome band.

func (*Band) Description

func (b *Band) Description() string

func (*Band) End

func (b *Band) End() int

func (*Band) Len

func (b *Band) Len() int

func (*Band) Location

func (b *Band) Location() feat.Feature

func (*Band) Name

func (b *Band) Name() string

func (*Band) Start

func (b *Band) Start() int

type Chromosome

type Chromosome struct {
	Chr      string
	Desc     string
	Length   int
	Features []feat.Feature
}

Chromosome represent a chromosome and associated features. Elements in the Features field should return the Chromosome when their Location() method is called.

func (*Chromosome) Description

func (c *Chromosome) Description() string

func (*Chromosome) End

func (c *Chromosome) End() int

func (*Chromosome) Len

func (c *Chromosome) Len() int

func (*Chromosome) Location

func (c *Chromosome) Location() feat.Feature

func (*Chromosome) Name

func (c *Chromosome) Name() string

func (*Chromosome) Start

func (c *Chromosome) Start() int

type Fragment

type Fragment struct {
	Frag      string
	Desc      string
	Chr       feat.Feature
	ChrStart  int
	ChrEnd    int
	FragStart int
	FragEnd   int
	Type      byte
	Strand    seq.Strand
}

Fragment represents an assembly fragment.

func (*Fragment) Description

func (f *Fragment) Description() string

func (*Fragment) End

func (f *Fragment) End() int

func (*Fragment) Len

func (f *Fragment) Len() int

func (*Fragment) Location

func (f *Fragment) Location() feat.Feature

func (*Fragment) Name

func (f *Fragment) Name() string

func (*Fragment) Start

func (f *Fragment) Start() int