support

package
v0.2.1 Latest Latest
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 Go to latest Published: May 29, 2017 License: GPL-2.0 Imports: 9 Imported by: 0

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Index

Constants

This section is empty.

Variables

This section is empty.

Functions

func Booster added in v0.1.11 

func Booster(reftree *tree.Tree, boottrees <-chan tree.Trees, logfile *os.File, silent bool, computeMovedSpecies bool, movedSpeciedCutoff float64, cpus int) error

func Classical 

func Classical(reftree *tree.Tree, boottrees <-chan tree.Trees, cpus int) error

Computes bootstrap supports of reftree branches, given trees in boottrees channel

func ComputeSupport 

func ComputeSupport(reftree *tree.Tree, boottrees <-chan tree.Trees, logfile *os.File, cpus int, supporter Supporter) error

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, min_dist_edge *[]int) error

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 BoosterSupporter added in v0.1.11 

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

func NewBoosterSupporter added in v0.1.13 

func NewBoosterSupporter(silent bool, computeMovedSpecies bool, movedSpeciesCutoff float64) *BoosterSupporter

func (*BoosterSupporter) Cancel added in v0.1.11 

func (supporter *BoosterSupporter) Cancel()

func (*BoosterSupporter) Canceled added in v0.1.11 

func (supporter *BoosterSupporter) Canceled() bool

func (*BoosterSupporter) ComputeValue added in v0.1.11 

func (supporter *BoosterSupporter) ComputeValue(refTree *tree.Tree, cpu int, edges []*tree.Edge,
	bootTreeChannel <-chan tree.Trees, valChan chan<- bootval, speciesChannel chan<- speciesmoved) error

Thread that takes bootstrap trees from the channel, computes the transfer dist for each edges of the ref tree and send it to the result channel At the end, returns the number of treated trees

func (*BoosterSupporter) ExpectedRandValues added in v0.1.11 

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

func (*BoosterSupporter) Init added in v0.1.11 

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

func (*BoosterSupporter) NewBootTreeComputed added in v0.1.11 

func (supporter *BoosterSupporter) NewBootTreeComputed()

func (*BoosterSupporter) NormalizeByExpected added in v0.2.0 

func (supporter *BoosterSupporter) NormalizeByExpected() bool

func (*BoosterSupporter) PrintMovingTaxa added in v0.1.13 

func (supporter *BoosterSupporter) PrintMovingTaxa() bool

func (*BoosterSupporter) Progress added in v0.1.11 

func (supporter *BoosterSupporter) Progress() int

type ClassicalSupporter added in v0.2.0 

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

func NewClassicalSupporter added in v0.2.0 

func NewClassicalSupporter(silent bool) *ClassicalSupporter

func (*ClassicalSupporter) Cancel added in v0.2.0 

func (supporter *ClassicalSupporter) Cancel()

func (*ClassicalSupporter) Canceled added in v0.2.0 

func (supporter *ClassicalSupporter) Canceled() bool

func (*ClassicalSupporter) ComputeValue added in v0.2.0 

func (supporter *ClassicalSupporter) ComputeValue(refTree *tree.Tree, cpu int, edges []*tree.Edge,
	bootTreeChannel <-chan tree.Trees, valChan chan<- bootval, speciesChannel chan<- speciesmoved) error

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

func (*ClassicalSupporter) ExpectedRandValues added in v0.2.0 

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

func (*ClassicalSupporter) Init added in v0.2.0 

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

func (*ClassicalSupporter) NewBootTreeComputed added in v0.2.0 

func (supporter *ClassicalSupporter) NewBootTreeComputed()

func (*ClassicalSupporter) NormalizeByExpected added in v0.2.0 

func (supporter *ClassicalSupporter) NormalizeByExpected() bool

func (*ClassicalSupporter) PrintMovingTaxa added in v0.2.0 

func (supporter *ClassicalSupporter) PrintMovingTaxa() bool

func (*ClassicalSupporter) Progress added in v0.2.0 

func (supporter *ClassicalSupporter) Progress() int

type Supporter 

type Supporter interface {
	Init(maxdepth int, nbtips int)
	ExpectedRandValues(depth int) float64
	ComputeValue(refTree *tree.Tree, cpu int, edges []*tree.Edge,
		bootTreeChannel <-chan tree.Trees, valChan chan<- bootval, speciesChannel chan<- speciesmoved) error
	// Returns the number of bootstrap trees that have been computed
	Progress() int
	// Increments the number of trees processed
	NewBootTreeComputed()
	// Tells the supported to stop accepting new bootstrap trees from the bootTreeChannel
	// It will just finish the current computations
	Cancel()
	// Tells if hasbeen canceled or not
	Canceled() bool
	// Print moving taxa
	PrintMovingTaxa() bool

	// If true, the support is 1-avg_value/ExpectedRandValues()
	// If false, the support is avg
	NormalizeByExpected() bool
}

Source Files

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