dna

package
v0.3.1-alpha2 Latest Latest
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 Go to latest Published: May 6, 2019 License: GPL-2.0 Imports: 3 Imported by: 0

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Index

Constants

View Source 
const (
	DBL_MIN = 2.2250738585072014e-308
)

Variables

This section is empty.

Functions

This section is empty.

Types

type DNAModel 

type DNAModel interface {
	Eigens() (val []float64, leftvectors, rightvectors *mat.Dense, err error)
	// contains filtered or unexported methods
}

type F81Model 

type F81Model struct {
	// contains filtered or unexported fields
}

func NewF81Model 

func NewF81Model() *F81Model

func (*F81Model) Eigens 

func (m *F81Model) Eigens() (val []float64, leftvectors, rightvectors *mat.Dense, err error)

func (*F81Model) InitModel 

func (m *F81Model) InitModel(piA, piC, piG, piT float64) (err error)

type F84Model 

type F84Model struct {
	// contains filtered or unexported fields
}

func NewF84Model 

func NewF84Model() *F84Model

func (*F84Model) Eigens 

func (m *F84Model) Eigens() (val []float64, leftvectors, rightvectors *mat.Dense, err error)

See http://biopp.univ-montp2.fr/Documents/ClassDocumentation/bpp-phyl/html/F84_8cpp_source.html

func (*F84Model) InitModel 

func (m *F84Model) InitModel(kappa, piA, piC, piG, piT float64)

type GTRModel 

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

func NewGTRModel 

func NewGTRModel() *GTRModel

func (*GTRModel) Eigens 

func (m *GTRModel) Eigens() (val []float64, leftvectors, rightvectors *mat.Dense, err error)

func (*GTRModel) InitModel 

func (m *GTRModel) InitModel(d, f, b, e, a, c, piA, piC, piG, piT float64) (err error)
/          \

| * d f b | | d * e a | | f e * c | | b a c * | 

\          /

type JCModel 

type JCModel struct {
}

func NewJCModel 

func NewJCModel() *JCModel

func (*JCModel) Eigens 

func (m *JCModel) Eigens() (val []float64, leftvectors, rightvectors *mat.Dense, err error)

Left vectors and right vectors are given in column-major format

func (*JCModel) InitModel 

func (m *JCModel) InitModel() (err error)

type K2PModel 

type K2PModel struct {
	// contains filtered or unexported fields
}

func NewK2PModel 

func NewK2PModel() *K2PModel

func (*K2PModel) Eigens 

func (m *K2PModel) Eigens() (val []float64, leftvectors, rightvectors *mat.Dense, err error)

func (*K2PModel) InitModel 

func (m *K2PModel) InitModel(kappa float64)

For Eigen values/vectors computation

type Pij 

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

Probability matrix

func NewPij 

func NewPij(m DNAModel, l float64) (pij *Pij, err error)

func (*Pij) Pij 

func (pij *Pij) Pij(i, j int) float64

func (*Pij) SetLength 

func (pij *Pij) SetLength(l float64) (err error)

type TN93Model 

type TN93Model struct {
	// contains filtered or unexported fields
}

func NewTN93Model 

func NewTN93Model() *TN93Model

func (*TN93Model) Eigens 

func (m *TN93Model) Eigens() (val []float64, leftvectors, rightvectors *mat.Dense, err error)

func (*TN93Model) InitModel 

func (m *TN93Model) InitModel(kappa1, kappa2, piA, piC, piG, piT float64) (err error)

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