hashmap

Documentation

Overview

Package hashmap is a collection of defined biological alphabets such as DNA, RNA, and Protein

Index

• type Dna
  • func NewDna() *Dna
  • func (*Dna) Complement(c string) string
• type DnaIupac
  • func NewDnaIupac() *DnaIupac
  • func (*DnaIupac) Complement(c string) string
• type Protein
  • func NewProtein() *Protein
• type ProteinGapped
  • func NewProteinGapped() *ProteinGapped
• type Rna
  • func NewRna() *Rna
  • func (*Rna) Complement(c string) string
• type RnaIupac
  • func NewRnaIupac() *RnaIupac
  • func (*RnaIupac) Complement(c string) string
• type Struct
  • func New(letters string) *Struct
  • func (a Struct) Contains(letters ...string) []bool
  • func (a Struct) Length() int
  • func (a Struct) String() string

Examples

• Dna.Complement
• DnaIupac.Complement
• New
• NewDna
• NewDnaIupac
• NewProtein
• NewProteinGapped
• NewRna
• NewRnaIupac
• Rna.Complement
• RnaIupac.Complement
• Struct.Contains
• Struct.Length

Types

type Dna

type Dna struct {
	*Struct
}

Dna is the four letter standard encoding

func NewDna

func NewDna() *Dna

NewDna generates a standard DNA alphabet

Example

package main

import (
	"fmt"

	"github.com/bio-ext/bio-go/bio/alphabet/hashmap"
)

func main() {
	a := hashmap.NewDna()
	fmt.Println(a)
}

Output:

ACGT

func (*Dna) Complement

func (*Dna) Complement(c string) string

Complement produces the standard DNA complement

Example

package main

import (
	"fmt"

	"github.com/bio-ext/bio-go/bio/alphabet/hashmap"
)

func main() {
	a := hashmap.NewDna()
	fmt.Println(a.Complement("A"))
}

Output:

T

type DnaIupac

type DnaIupac struct {
	*Struct
}

DnaIupac is the sixteen letter IUPAC encoding

func NewDnaIupac

func NewDnaIupac() *DnaIupac

NewDnaIupac generates an IUPAC DNA alphabet

Example

package main

import (
	"fmt"

	"github.com/bio-ext/bio-go/bio/alphabet/hashmap"
)

func main() {
	a := hashmap.NewDnaIupac()
	fmt.Println(a)
}

Output:

-ABCDGHKMNRSTVWY

func (*DnaIupac) Complement

func (*DnaIupac) Complement(c string) string

Complement produces the IUPAC DNA complement

Example

package main

import (
	"fmt"

	"github.com/bio-ext/bio-go/bio/alphabet/hashmap"
)

func main() {
	a := hashmap.NewDnaIupac()
	fmt.Println(a.Complement("N"))
}

Output:

N

type Protein

type Protein struct {
	*Struct
}

Protein is the twenty letter standard encoding

func NewProtein

func NewProtein() *Protein

NewProtein generates a protein alphabet

Example

package main

import (
	"fmt"

	"github.com/bio-ext/bio-go/bio/alphabet/hashmap"
)

func main() {
	a := hashmap.NewProtein()
	fmt.Println(a)
}

Output:

ACDEFGHIKLMNPQRSTVWY

type ProteinGapped

type ProteinGapped struct {
	*Struct
}

ProteinGapped is the twenty letter standard encoding plus a gap letter

func NewProteinGapped

func NewProteinGapped() *ProteinGapped

NewProteinGapped generates a gapped protein alphabet

Example

package main

import (
	"fmt"

	"github.com/bio-ext/bio-go/bio/alphabet/hashmap"
)

func main() {
	a := hashmap.NewProteinGapped()
	fmt.Println(a)
}

Output:

-ACDEFGHIKLMNPQRSTVWY

type Rna

type Rna struct {
	*Struct
}

Rna is the four letter standard encoding

func NewRna

func NewRna() *Rna

NewRna generates a standard RNA alphabet

Example

package main

import (
	"fmt"

	"github.com/bio-ext/bio-go/bio/alphabet/hashmap"
)

func main() {
	a := hashmap.NewRna()
	fmt.Println(a)
}

Output:

ACGU

func (*Rna) Complement

func (*Rna) Complement(c string) string

Complement produces the standard RNA complement

Example

package main

import (
	"fmt"

	"github.com/bio-ext/bio-go/bio/alphabet/hashmap"
)

func main() {
	a := hashmap.NewRna()
	fmt.Println(a.Complement("A"))
}

Output:

U

type RnaIupac

type RnaIupac struct {
	*Struct
}

RnaIupac is the sixteen letter IUPAC encoding

func NewRnaIupac

func NewRnaIupac() *RnaIupac

NewRnaIupac generates an IUPAC RNA alphabet

Example

package main

import (
	"fmt"

	"github.com/bio-ext/bio-go/bio/alphabet/hashmap"
)

func main() {
	a := hashmap.NewRnaIupac()
	fmt.Println(a)
}

Output:

-ABCDGHKMNRSUVWY

func (*RnaIupac) Complement

func (*RnaIupac) Complement(c string) string

Complement produces the IUPAC complement

Example

package main

import (
	"fmt"

	"github.com/bio-ext/bio-go/bio/alphabet/hashmap"
)

func main() {
	a := hashmap.NewRnaIupac()
	fmt.Println(a.Complement("N"))
}

Output:

N

type Struct

type Struct struct {
	// contains filtered or unexported fields
}

Struct is a collection of letters

func New

func New(letters string) *Struct

New is a Struct generator

Example

package main

import (
	"fmt"

	"github.com/bio-ext/bio-go/bio/alphabet/hashmap"
)

func main() {
	a := hashmap.New("QWERTY")
	fmt.Println(a)
}

Output:

EQRTWY

func (Struct) Contains

func (a Struct) Contains(letters ...string) []bool

Contains confirms whether a potential letters are in the Alphabet

Example

package main

import (
	"fmt"

	"github.com/bio-ext/bio-go/bio/alphabet/hashmap"
)

func main() {
	a := hashmap.New("QWERTY")
	fmt.Println(a.Contains([]string{"Q", "WERTY", "A"}...))
}

Output:

[true false false]

func (Struct) Length

func (a Struct) Length() int

Length is numbers of letters in the Alphabet

Example

package main

import (
	"fmt"

	"github.com/bio-ext/bio-go/bio/alphabet/hashmap"
)

func main() {
	a := hashmap.New("QWERTY")
	fmt.Println(a.Length())
}

Output:

6

func (Struct) String

func (a Struct) String() string

String generates a stringified copy of the Alphabet