protein

Documentation

Index

• Constants
• Variables
• type ProtDistModel
  • func NewProtDistModel(model int, modelfreqs bool, usegamma bool, alpha float64, removegaps bool) (*ProtDistModel, error)
  • func (model *ProtDistModel) InitModel(a align.Alignment, weights []float64) (err error)
  • func (model *ProtDistModel) JC69Dist(a align.Alignment, weights []float64, selected []bool) (p *mat.Dense, q *mat.Dense, dist *mat.Dense)
  • func (model *ProtDistModel) MLDist(a align.Alignment, weights []float64) (p, q, dist *mat.Dense, err error)
  • func (model *ProtDistModel) Ns() int

Constants

const (
	BRENT_ITMAX = 10000
	BRENT_ZEPS  = 1.e-10
	BRENT_CGOLD = 0.3819660
	DBL_MIN     = 2.2250738585072014e-308

	BL_MIN = 1.e-08
	BL_MAX = 100.0
)

const (
	PROT_DIST_MAX = 20.00
)

Variables

var DBL_EPSILON float64 = math.Nextafter(1, 2) - 1

Types

type ProtDistModel

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

func NewProtDistModel

func NewProtDistModel(model int, modelfreqs bool, usegamma bool, alpha float64, removegaps bool) (*ProtDistModel, error)

Initialize a new protein model, given the name of the model as const int: MODEL_DAYHOFF, MODEL_JTT, MODEL_MTREV, MODEL_LG or MODEL_WAG

func (*ProtDistModel) InitModel

func (model *ProtDistModel) InitModel(a align.Alignment, weights []float64) (err error)

func (*ProtDistModel) JC69Dist

func (model *ProtDistModel) JC69Dist(a align.Alignment, weights []float64, selected []bool) (p *mat.Dense, q *mat.Dense, dist *mat.Dense)

Basic JC69 Protein Distance Matrix

func (*ProtDistModel) MLDist

func (model *ProtDistModel) MLDist(a align.Alignment, weights []float64) (p, q, dist *mat.Dense, err error)

func (*ProtDistModel) Ns

func (model *ProtDistModel) Ns() int