support

Documentation

Index

• func FBP(reftree *tree.Tree, boottrees <-chan tree.Trees, cpus int, sup *Supporter) error
• func MinTransferDist(refedge *tree.Edge, reftree, boottree *tree.Tree, ntips int, ...) (dist int, minedge *tree.Edge, speciestoadd, speciestoremove []*tree.Node)
• func NormalizeTransferDistancesByDepth(edges []*tree.Edge, nboot int)
• func ReformatAvgDistance(t *tree.Tree, nboot int)
• func TBE(reftree *tree.Tree, boottrees <-chan tree.Trees, cpu int, outrawtree bool, ...) (rawtree *tree.Tree, err error)
• func UpdateTaxaMoveArrays(ref, boot *tree.Edge, dist, p int, moved_species []int, ...)
• type Supporter
  • func NewSupporter() *Supporter
  • func (sup *Supporter) Cancel()
  • func (sup *Supporter) Canceled() bool
  • func (sup *Supporter) IncrementProgress()
  • func (sup *Supporter) Progress() int

Functions

func FBP

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

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

func MinTransferDist

func MinTransferDist(refedge *tree.Edge, reftree, boottree *tree.Tree, ntips int, bootedges []*tree.Edge, absent bool) (dist int, minedge *tree.Edge, speciestoadd, speciestoremove []*tree.Node)

This function computes the min transfer distance between the refedge and the bootstrap tree. If "absent" is true, then we know that the ref branch is not present in the bootstrap tree (it is faster to compute then), and we stop if dist == 1 Else: we do not know, we do the full postorder traversal, and speciestoadd && speciestoremove are filled

func NormalizeTransferDistancesByDepth

func NormalizeTransferDistancesByDepth(edges []*tree.Edge, nboot int)

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

func ReformatAvgDistance(t *tree.Tree, nboot int)

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

func TBE

func TBE(reftree *tree.Tree, boottrees <-chan tree.Trees, cpu int,
	outrawtree bool, computeavgtaxa, computeperbranchtaxa bool, distcutoff float64,
	logfile *os.File, sup *Supporter) (rawtree *tree.Tree, err error)

computes the transfer dist for each edges of the ref tree outrawtree: if tree with average transfer distance (non normalized) must be computed if false: then output rawtree is null

func UpdateTaxaMoveArrays

func UpdateTaxaMoveArrays(ref, boot *tree.Edge, dist, p int,
	moved_species []int, moved_species_per_branch [][]int, nb_branches_close *int,
	speciestoadd, speciestoremove []*tree.Node, distcutoff float64, mindepth int,
	computeavgtaxa, computeperbranchtaxa bool, mux *sync.Mutex)

Looking at number of times each taxon moves around low distance branches moved_species: array of size number of nodes in the tree species_to_add & species_to_remove: Array of species (tree nodes) that move distcutoff: if the bootstrap branch is too distant from the ref branch in terms of normalized transfer dist, then does not count

Types

type Supporter

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

func NewSupporter

func NewSupporter() *Supporter

Returns the progress of the analysis

func (*Supporter) Cancel

func (sup *Supporter) Cancel()

Tells the supported to stop the analysis It will just finish the current computations

func (*Supporter) Canceled

func (sup *Supporter) Canceled() bool

Tells if hasbeen canceled or not

func (*Supporter) IncrementProgress

func (sup *Supporter) IncrementProgress()

Increments the progress of the analysis

func (*Supporter) Progress

func (sup *Supporter) Progress() int

Returns the progress of the analysis