support

package

v0.1.10-beta Latest Latest Go to latest Published: Feb 17, 2017 License: GPL-2.0 Imports: 10 Imported by: 0

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Valid go.mod file
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Repository

github.com/benjamincjackson/gotree

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Documentation ¶

Index ¶

func Classical(reftreefile, boottreefile string, cpus int) (*tree.Tree, error)
func ComputeSupport(reftreefile, boottreefile string, logfile *os.File, empirical bool, cpus int, ...) (*tree.Tree, error)
func ComputeSupportFile(reftreefile, boottreefile *bufio.Reader, logfile *os.File, empirical bool, ...) (*tree.Tree, error)
func MastLike(reftreefile, boottreefile string, logfile *os.File, empirical bool, cpus int) (*tree.Tree, error)
func MastLikeFile(reftreefile, boottreefile *bufio.Reader, logfile *os.File, empirical bool, ...) (*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 MastSupporter
type Supporter

Constants ¶

This section is empty.

Variables ¶

This section is empty.

Functions ¶

func Classical ¶

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

func ComputeSupport ¶

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

func ComputeSupportFile ¶ added in v0.1.10

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

func MastLike ¶

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

func MastLikeFile ¶ added in v0.1.10

func MastLikeFile(reftreefile, boottreefile *bufio.Reader, logfile *os.File, empirical bool, cpus int) (*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 MastSupporter ¶ added in v0.1.4

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

func (*MastSupporter) Cancel ¶ added in v0.1.10

func (supporter *MastSupporter) Cancel()

func (*MastSupporter) Canceled ¶ added in v0.1.10

func (supporter *MastSupporter) Canceled() bool

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,
	bootTreeChannel <-chan tree.Trees, valChan chan<- bootval, randvalChan chan<- bootval, speciesChannel chan<- speciesmoved) error

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) NewBootTreeComputed ¶ added in v0.1.10

func (supporter *MastSupporter) NewBootTreeComputed()

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

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

func (*MastSupporter) Progress ¶ added in v0.1.10

func (supporter *MastSupporter) Progress() int

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,
		bootTreeChannel <-chan tree.Trees, valChan chan<- bootval, randvalChan 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
}

Source Files ¶

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