dna

Documentation

Index

• Constants
• type DNAModel
• type F81Model
  • func NewF81Model() *F81Model
  • func (m *F81Model) Analytical() bool
  • func (m *F81Model) Eigens() (val []float64, leftvectors, rightvectors *mat.Dense, err error)
  • func (m *F81Model) InitModel(piA, piC, piG, piT float64) (err error)
  • func (m *F81Model) NState() int
  • func (m *F81Model) Pij(i, j int, l float64) float64
• type F84Model
  • func NewF84Model() *F84Model
  • func (m *F84Model) Analytical() bool
  • func (m *F84Model) Eigens() (val []float64, leftvectors, rightvectors *mat.Dense, err error)
  • func (m *F84Model) InitModel(kappa, piA, piC, piG, piT float64)
  • func (m *F84Model) NState() int
  • func (m *F84Model) Pij(i, j int, l float64) float64
• type GTRModel
  • func NewGTRModel() *GTRModel
  • func (m *GTRModel) Analytical() bool
  • func (m *GTRModel) Eigens() (val []float64, leftvectors, rightvectors *mat.Dense, err error)
  • func (m *GTRModel) InitModel(d, f, b, e, a, c, piA, piC, piG, piT float64) (err error)
  • func (m *GTRModel) NState() int
  • func (m *GTRModel) Pij(i, j int, l float64) float64
• type JCModel
  • func NewJCModel() *JCModel
  • func (m *JCModel) Analytical() bool
  • func (m *JCModel) Eigens() (val []float64, leftvectors, rightvectors *mat.Dense, err error)
  • func (m *JCModel) InitModel() (err error)
  • func (m *JCModel) NState() int
  • func (m *JCModel) Pij(i, j int, l float64) float64
• type K2PModel
  • func NewK2PModel() *K2PModel
  • func (m *K2PModel) Analytical() bool
  • func (m *K2PModel) Eigens() (val []float64, leftvectors, rightvectors *mat.Dense, err error)
  • func (m *K2PModel) InitModel(kappa float64)
  • func (m *K2PModel) NState() int
  • func (m *K2PModel) Pij(i, j int, l float64) float64
• type TN93Model
  • func NewTN93Model() *TN93Model
  • func (m *TN93Model) Analytical() bool
  • func (m *TN93Model) Eigens() (val []float64, leftvectors, rightvectors *mat.Dense, err error)
  • func (m *TN93Model) InitModel(kappa1, kappa2, piA, piC, piG, piT float64) (err error)
  • func (m *TN93Model) NState() int
  • func (m *TN93Model) Pij(i, j int, l float64) float64

Constants

const (
	DBL_MIN = 2.2250738585072014e-308
)

Types

type DNAModel

type DNAModel interface {
	Eigens() (val []float64, leftvectors, rightvectors *mat.Dense, err error)
	Analytical() bool                // returns true if analytical pij computation is possible and implemented
	Pij(i, j int, l float64) float64 // Returns -1 if not possible to compute it anatically without eigens (or not yet implemented)
}

type F81Model

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

func NewF81Model

func NewF81Model() *F81Model

func (*F81Model) Analytical

func (m *F81Model) Analytical() bool

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)

func (*F81Model) NState

func (m *F81Model) NState() int

func (*F81Model) Pij

func (m *F81Model) Pij(i, j int, l float64) float64

type F84Model

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

func NewF84Model

func NewF84Model() *F84Model

func (*F84Model) Analytical

func (m *F84Model) Analytical() bool

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)

func (*F84Model) NState

func (m *F84Model) NState() int

func (*F84Model) Pij

func (m *F84Model) Pij(i, j int, l float64) float64

type GTRModel

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

func NewGTRModel

func NewGTRModel() *GTRModel

func (*GTRModel) Analytical

func (m *GTRModel) Analytical() bool

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 * |

\          /

func (*GTRModel) NState

func (m *GTRModel) NState() int

func (*GTRModel) Pij

func (m *GTRModel) Pij(i, j int, l float64) float64

type JCModel

type JCModel struct {
}

func NewJCModel

func NewJCModel() *JCModel

func (*JCModel) Analytical

func (m *JCModel) Analytical() bool

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)

func (*JCModel) NState

func (m *JCModel) NState() int

func (*JCModel) Pij

func (m *JCModel) Pij(i, j int, l float64) float64

type K2PModel

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

func NewK2PModel

func NewK2PModel() *K2PModel

func (*K2PModel) Analytical

func (m *K2PModel) Analytical() bool

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

func (*K2PModel) NState

func (m *K2PModel) NState() int

func (*K2PModel) Pij

func (m *K2PModel) Pij(i, j int, l float64) float64

type TN93Model

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

func NewTN93Model

func NewTN93Model() *TN93Model

func (*TN93Model) Analytical

func (m *TN93Model) Analytical() bool

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)

func (*TN93Model) NState

func (m *TN93Model) NState() int

func (*TN93Model) Pij

func (m *TN93Model) Pij(i, j int, l float64) float64