support

package

v0.1.14-a Latest Latest Go to latest Published: Mar 31, 2017 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 ¶

func Booster(reftreefile, boottreefile string, logfile *os.File, silent bool, ...) (*tree.Tree, error)
func BoosterFile(reftreefile, boottreefile *bufio.Reader, logfile *os.File, silent bool, ...) (*tree.Tree, error)
func Classical(reftreefile, boottreefile string, cpus int) (*tree.Tree, error)
func ComputeSupport(reftreefile, boottreefile string, logfile *os.File, cpus int, ...) (*tree.Tree, error)
func ComputeSupportFile(reftreefile, boottreefile *bufio.Reader, logfile *os.File, cpus int, ...) (*tree.Tree, error)
func Update_all_i_c_post_order_boot_tree(refTree *tree.Tree, ntips uint, edges *[]*tree.Edge, bootTree *tree.Tree, ...) error
func Update_all_i_c_post_order_ref_tree(refTree *tree.Tree, edges *[]*tree.Edge, bootTree *tree.Tree, ...)
type BoosterSupporter
- func NewBoosterSupporter(silent bool, computeMovedSpecies bool, movedSpeciesCutoff float64) *BoosterSupporter
type Supporter

Constants ¶

This section is empty.

Variables ¶

This section is empty.

Functions ¶

func Booster ¶ added in v0.1.11

func Booster(reftreefile, boottreefile string, logfile *os.File, silent bool, computeMovedSpecies bool, movedSpeciedCutoff float64, cpus int) (*tree.Tree, error)

func BoosterFile ¶ added in v0.1.11

func BoosterFile(reftreefile, boottreefile *bufio.Reader, logfile *os.File, silent bool, computeMovedSpecies bool, movedSpeciedCutoff float64, cpus int) (*tree.Tree, error)

func Classical ¶

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

func ComputeSupport ¶

func ComputeSupport(reftreefile, boottreefile string, logfile *os.File, cpus int, supporter Supporter) (*tree.Tree, error)

func ComputeSupportFile ¶ added in v0.1.10

func ComputeSupportFile(reftreefile, boottreefile *bufio.Reader, logfile *os.File, cpus int, supporter Supporter) (*tree.Tree, 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

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) 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 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
}

Source Files ¶

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