support

package
v0.2.7 Latest Latest
Warning

This package is not in the latest version of its module.

 Go to latest Published: Jan 30, 2018 License: GPL-2.0 Imports: 11 Imported by: 0

Documentation

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, computeMovedSpecies, computeTransferPerBranches, computeHighTransferPerBranches bool, movedSpeciedCutoff float64, normalizedByExpected bool, 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 NormalizeTransferDistancesByDepth added in v0.2.4 

func NormalizeTransferDistancesByDepth(t *tree.Tree)

This function takes all branch support values (that are considered as average transfer distances over bootstrap trees), normalizes them by the depth and convert them to similarity, i.e: 

1-avg_dist/(depth-1)

func ReformatAvgDistance added in v0.2.4 

func ReformatAvgDistance(t *tree.Tree)

This function writes on the child node name the string: "branch_id|avg_dist|depth" and removes support information from each branch

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, computeMovedSpecies, computeTransferPerBranches, computeHighTransferPerBranches bool, movedSpeciesCutoff float64, normalizeByExpected bool) *BoosterSupporter

computeTransferPerBranches and computeHighTransferPerBranches are mutually expclusive computeTransferPerBranches has priority over computeHighTransferPerBranches

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,
	taxPerBranchChannel chan<- []*list.List) 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) PrintHighTaxPerBranches added in v0.2.4 

func (supporter *BoosterSupporter) PrintHighTaxPerBranches() bool

func (*BoosterSupporter) PrintMovingTaxa added in v0.1.13 

func (supporter *BoosterSupporter) PrintMovingTaxa() bool

func (*BoosterSupporter) PrintTaxPerBranches added in v0.2.4 

func (supporter *BoosterSupporter) PrintTaxPerBranches() 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,
	taxPerBranchChannel chan<- []*list.List) 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) PrintHighTaxPerBranches added in v0.2.4 

func (supporter *ClassicalSupporter) PrintHighTaxPerBranches() bool

func (*ClassicalSupporter) PrintMovingTaxa added in v0.2.0 

func (supporter *ClassicalSupporter) PrintMovingTaxa() bool

func (*ClassicalSupporter) PrintTaxPerBranches added in v0.2.4 

func (supporter *ClassicalSupporter) PrintTaxPerBranches() 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,
		taxPerBranchChannel chan<- []*list.List) 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
	PrintTaxPerBranches() bool
	PrintHighTaxPerBranches() bool

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

Source Files

View all Source files

Jump to

Keyboard shortcuts

? : This menu
/ : Search site
f or F : Jump to
y or Y : Canonical URL
go.dev uses cookies from Google to deliver and enhance the quality of its services and to analyze traffic. Learn more.