support

package

v0.1.6 Latest Latest Go to latest Published: Dec 12, 2016 License: GPL-2.0 Imports: 10 Imported by: 0

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Valid go.mod file
Redistributable license
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Stable version
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Repository

github.com/benjamincjackson/gotree

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Documentation ¶

Index ¶

Constants
func Classical(reftreefile, boottreefile string, cpus int) *tree.Tree
func ComputeSupport(reftreefile, boottreefile string, empirical bool, cpus int, ...) *tree.Tree
func MastLike(reftreefile, boottreefile string, empirical bool, cpus int) *tree.Tree
func Parsimony(reftreefile, boottreefile string, empirical bool, cpus int) *tree.Tree
func Update_all_i_c_post_order_boot_tree(refTree *tree.Tree, ntips uint, edges *[]*tree.Edge, bootTree *tree.Tree, ...)
func Update_all_i_c_post_order_ref_tree(refTree *tree.Tree, edges *[]*tree.Edge, bootTree *tree.Tree, ...)
type MastSupporter
type Supporter

Constants ¶

View Source

const (
	STATENULL = -1 // Null state
	STATE0    = 0  // State 0
	STATE1    = 1  // State 1
	STATE01   = 2  // State 0/1
)

Variables ¶

This section is empty.

Functions ¶

func Classical ¶

func Classical(reftreefile, boottreefile string, cpus int) *tree.Tree

func ComputeSupport ¶

func ComputeSupport(reftreefile, boottreefile string, empirical bool, cpus int, supporter Supporter) *tree.Tree

func MastLike ¶

func MastLike(reftreefile, boottreefile string, empirical bool, cpus int) *tree.Tree

func Parsimony ¶

func Parsimony(reftreefile, boottreefile string, empirical bool, cpus int) *tree.Tree

func Update_all_i_c_post_order_boot_tree ¶ added in v0.1.4

func Update_all_i_c_post_order_boot_tree(refTree *tree.Tree, ntips uint, edges *[]*tree.Edge,
	bootTree *tree.Tree, bootEdges *[]*tree.Edge,
	i_matrix *[][]uint16, c_matrix *[][]uint16, hamming *[][]uint16, min_dist *[]uint16)

func Update_all_i_c_post_order_ref_tree ¶ added in v0.1.4

func Update_all_i_c_post_order_ref_tree(refTree *tree.Tree, edges *[]*tree.Edge, bootTree *tree.Tree, bootEdges *[]*tree.Edge, i_matrix *[][]uint16, c_matrix *[][]uint16)

Types ¶

type MastSupporter ¶ added in v0.1.4

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

func (*MastSupporter) ComputeValue ¶ added in v0.1.4

func (supporter *MastSupporter) ComputeValue(refTree *tree.Tree, empiricalTrees []*tree.Tree, cpu int, empirical bool, edges []*tree.Edge, randEdges [][]*tree.Edge,
	wg *sync.WaitGroup, bootTreeChannel <-chan tree.Trees, valChan chan<- bootval, randvalChan chan<- bootval)

Thread that takes bootstrap trees from the channel, computes the mastlike dist for each edges of the ref tree and send it to the result channel

func (*MastSupporter) ExpectedRandValues ¶ added in v0.1.4

func (supporter *MastSupporter) ExpectedRandValues(depth int) float64

func (*MastSupporter) Init ¶ added in v0.1.4

func (supporter *MastSupporter) Init(maxdepth int, nbtips int)

func (*MastSupporter) ProbaDepthValue ¶ added in v0.1.4

func (supporter *MastSupporter) ProbaDepthValue(d int, v int) float64

type Supporter ¶

type Supporter interface {
	Init(maxdepth int, nbtips int)
	ExpectedRandValues(depth int) float64
	ProbaDepthValue(d int, v int) float64
	ComputeValue(refTree *tree.Tree, empiricalTrees []*tree.Tree, cpu int, empirical bool, edges []*tree.Edge, randEdges [][]*tree.Edge,
		wg *sync.WaitGroup, bootTreeChannel <-chan tree.Trees, valChan chan<- bootval, randvalChan chan<- bootval)
}

Source Files ¶

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