tree

Mar 10, 2021

Changes in this version

type Tree

+ func (t *Tree) AddQuotes(internals, tips bool, namemap map[string]string) error

+ func (t *Tree) RemoveQuotes(internals, tips bool, namemap map[string]string) error

Mar 9, 2020

Changes in this version

+ const NIL_TIPID

type Edge

+ func (e *Edge) HashCode() uint64

+ func (e *Edge) HashEquals(h hashmap.Hasher) bool

+ func (e *Edge) IncrementSupport(support float64)

+ func (e *Edge) Inverse()

type EdgeIndex

+ func (em *EdgeIndex) Edges(minCount, maxCount int) []*KeyValue

+ type NNIRearranger struct

+ func (nnir *NNIRearranger) Rearrange(t *Tree, f func(r Rearrangement) bool)

type Node

+ func (n *Node) IsConnected(next *Node) bool

+ func (n *Node) TipIndex() int

+ type Rearrangement interface

+ Apply func() error

+ Undo func() error

+ type Rearranger interface

+ Rearrange func(t *Tree, f func(r Rearrangement) bool)

type Tree

+ func (t *Tree) CheckTreePostOrder() (err error)

+ func (t *Tree) ComputeEdgeHashes(cur, prev *Node, e *Edge)

+ func (t *Tree) ReinitInternalIndexes()

+ func (t *Tree) TipNode(name string) (tip *Node, err error)

Sep 30, 2019

Changes in this version

type NodeIndex

+ AddNode func(n *Node)

type Tree

+ func (t *Tree) CheckTree() bool

+ func (t *Tree) InsertIdenticalTip(n *Node, newTipName string) (newtipnode *Node, err error)

+ func (t *Tree) InsertIdenticalTips(identicalgroups [][]string) (err error)

Apr 29, 2019

Changes in this version

+ type TipBag struct

+ func NewTipBag() *TipBag

+ func (tb *TipBag) AddTip(t *Node) error

+ func (tb *TipBag) Clear()

+ func (tb *TipBag) Size() int

+ func (tb *TipBag) Tips() []*Node

type Tree

+ func (t *Tree) CutEdgesMaxLength(maxlen float64) (bags []*TipBag, err error)

+ func (t *Tree) PostOrder(f func(cur *Node, prev *Node, e *Edge) (keep bool))

+ func (t *Tree) PreOrder(f func(cur *Node, prev *Node, e *Edge) (keep bool))

Aug 2, 2018

Changes in this version

type Tree

+ func AllTopologies(nbTips int, rooted bool, tipNames ...string) (trees []*Tree, err error)

+ func (t *Tree) RenameAuto(internals, tips bool, length int, curid *int, namemap map[string]string) error

+ func (t *Tree) RenameRegexp(internals, tips bool, regex, replace string, namemap map[string]string) error

+ func (t *Tree) RoundLengths(precision int)

+ func (t *Tree) RoundSupports(precision int)

Mar 27, 2018

Changes in this version

type Node

+ func (n *Node) RotateNeighbors()

type Tree

+ func (t *Tree) RotateInternalNodes()

+ func (t *Tree) SortNeighborsByTips()

Mar 6, 2018

Changes in this version

+ func NewAllNodeIndex(t *Tree) *nodeIndex

type Tree

+ func (t *Tree) Delete()

Jan 30, 2018

Changes in this version

type Edge

+ func (e *Edge) AddComment(comment string)

+ func (e *Edge) ClearComments()

+ func (e *Edge) Comments() []string

+ func (e *Edge) CommentsString() string

type Tree

+ func (t *Tree) ClearEdgeComments()

+ func (t *Tree) ClearNodeComments()

Jan 8, 2018

Changes in this version

type Tree

+ func (t *Tree) ScaleLengths(factor float64)

+ func (t *Tree) ScaleSupports(factor float64)

Nov 6, 2017

Changes in this version

type Tree

+ func (t *Tree) DeepestNode() (maxnode *Node)

Sep 1, 2017

Changes in this version

+ const MaxInt

type Edge

+ func (e *Edge) NumTipsLeft() (int, error)

+ func (e *Edge) NumTipsRight() (int, error)

type Node

+ func (n *Node) ClearComments()

+ func (n *Node) CommentsString() string

type Tree

+ func RandomCaterpillarBinaryTree(nbtips int, rooted bool) (*Tree, error)

+ func (t *Tree) ClearComments()

+ func (t *Tree) CollessIndex() (colless int)

+ func (t *Tree) DeepestEdge() (maxedge *Edge)

+ func (t *Tree) MeanBranchLength() float64

+ func (t *Tree) Merge(t2 *Tree) error

+ func (t *Tree) NbCherries() (nbcherries int)

+ func (t *Tree) Nexus() string

+ func (t *Tree) ReorderEdges(n *Node, prev *Node, reversed *[]*Edge) error

+ func (t *Tree) SackinIndex() (sackin int)

Jul 3, 2017

Changes in this version

type Node

+ func (n *Node) Comments() []string

type Tree

+ func (t *Tree) ReinitIndexes()

+ func (t *Tree) RemoveSingleNodes()

May 29, 2017

Changes in this version

type Edge

+ func (e *Edge) LengthString() string

+ func (e *Edge) Name(rooted bool) (nodename string)

+ func (e *Edge) SupportString() string

type Tree

+ func BipartitionTree(leftTips []string, rightTips []string) (*Tree, error)

+ func (t *Tree) LeastCommonAncestorRecur(current *Node, prev *Node, tipIndex map[string]*Node) (*Node, []*Edge, int, int, bool, error)

+ func (t *Tree) LeastCommonAncestorRooted(nodeindex *nodeIndex, tips ...string) (*Node, []*Edge, bool, error)

Apr 24, 2017

Changes in this version

+ func Compare(refTree *Tree, compTrees <-chan Trees, tips, comparetreeidentical bool, ...) (<-chan BipartitionStats, error)

+ type BipartitionStats struct

+ Common int

+ Err error

+ Id int

+ Sametree bool

+ Tree1 int

+ Tree2 int

type Tree

+ func (t *Tree) SelectNodes(re string) ([]*Node, error)

+ func (t *Tree) SubTree(n *Node) *Tree

type Trees

+ Err error

Mar 10, 2017

Changes in this version

type Tree

+ func (t *Tree) InternalEdges() []*Edge

+ func (t *Tree) SortedTips() []string

Feb 13, 2017

Changes in this version

type Tree

+ func (t *Tree) Annotate(names map[string][]string)

+ func (t *Tree) CollapseTopoDepth(mindepthThreshold, maxdepthThreshold int)

+ func (t *Tree) Resolve()

Jan 30, 2017

Changes in this version

+ const NIL_DEPTH

+ const NIL_ID

+ const NIL_LENGTH

+ const NIL_PVALUE

+ const NIL_SUPPORT

type Edge

+ func (e *Edge) Locality(maxdist int, cutoff float64) (float64, float64, float64, bool, bool)

+ func (e *Edge) NeigborEdges(maxdist int) []*Edge

type Tree

+ func (t *Tree) ClearPvalues()

Jan 13, 2017

Changes in this version

type Tree

+ func (t *Tree) ToDistanceMatrix() [][]float64

Dec 12, 2016

Changes in this version

type Edge

+ func MaxLengthPath(cur *Node, prev *Node) ([]*Edge, float64)

type Tree

+ func RandomBalancedBinaryTree(depth int, rooted bool) (*Tree, error)

+ func (t *Tree) RerootMidPoint()

Dec 8, 2016

Changes in this version

type Tree

+ func RandomCaterpilarBinaryTree(nbtips int, rooted bool) (*Tree, error)

+ func RandomUniformBinaryTree(nbtips int, rooted bool) (*Tree, error)

+ func RandomYuleBinaryTree(nbtips int, rooted bool) (*Tree, error)

+ func (t *Tree) ClearLengths()

+ func (t *Tree) ClearSupports()

+ func (t *Tree) Clone() *Tree

+ func (t *Tree) CollapseLowSupport(support float64)

+ func (t *Tree) CopyEdge(e *Edge, copy *Edge)

+ func (t *Tree) CopyNode(n *Node) *Node

+ func (t *Tree) RerootOutGroup(tips ...string) error

+ func (t *Tree) SumBrLength() float64

Nov 29, 2016

Changes in this version

+ const QUARTET_CONFLICT

+ const QUARTET_DIFF

+ const QUARTET_EQUALS

type Edge

+ func (e *Edge) PValue() float64

+ func (e *Edge) SetPValue(pval float64)

+ type EdgeKey struct

+ func (k *EdgeKey) HashCode() int64

+ func (k *EdgeKey) HashEquals(h hashmap.Hasher) bool

type Node

+ func (n *Node) Id() int

+ func (n *Node) SetId(id int)

+ type Quartet struct

+ T1 uint

+ T2 uint

+ T3 uint

+ T4 uint

+ func (q *Quartet) Compare(q2 *Quartet) int

+ func (q *Quartet) HashCode() int64

+ func (q *Quartet) HashEquals(h hashmap.Hasher) bool

+ type QuartetSet struct

+ func NewQuartetSet() *QuartetSet

type Tree

+ func EdgeTree(t *Tree, e *Edge, alltips []string) *Tree

+ func (t *Tree) IndexQuartets(specific bool) *hashmap.HashMap

+ func (t *Tree) Quartets(specific bool, it func(q *Quartet))

Nov 9, 2016

Changes in this version

type Edge

+ func (e *Edge) ToStatsString() string

Oct 31, 2016

Changes in this version

type EdgeIndex

+ func (em *EdgeIndex) BitSets(minCount, maxCount int) []*KeyValue

+ type EdgeIndexInfo struct

+ Count int

+ Len float64

type Tree

+ func Consensus(trees <-chan Trees, cutoff float64) *Tree

+ func StarTree(nbtips int) (*Tree, error)

+ func StarTreeFromName(names ...string) (*Tree, error)

+ func StarTreeFromTree(t *Tree) (*Tree, error)

+ func (t *Tree) AddBipartition(n *Node, edges []*Edge, length, support float64) *Edge

+ func (t *Tree) LeastCommonAncestorUnrooted(nodeindex *nodeIndex, tips ...string) (*Node, []*Edge, bool)

+ func (t *Tree) LeastCommonAncestorUnrootedRecur(current *Node, prev *Node, tipIndex map[string]*Node) (*Node, []*Edge, int, int, bool)

+ type Trees struct

+ Id int

+ Tree *Tree

Oct 5, 2016

Changes in this version

+ func CommonEdges(edges1 []*Edge, edges2 []*Edge, tipEdges bool) (tree1 int, common int, err error)

+ func NewNodeIndex(t *Tree) *nodeIndex

+ type Bucket []*KeyValue

+ type Edge struct

+ func (e *Edge) Bitset() *bitset.BitSet

+ func (e *Edge) DumpBitSet() string

+ func (e *Edge) FindEdge(edges []*Edge) (*Edge, error)

+ func (e *Edge) Id() int

+ func (e *Edge) Left() *Node

+ func (e *Edge) Length() float64

+ func (e *Edge) NumTips() uint

+ func (e *Edge) Right() *Node

+ func (e *Edge) SameBipartition(e2 *Edge) bool

+ func (e *Edge) SetId(id int)

+ func (e *Edge) SetLength(length float64)

+ func (e *Edge) SetSupport(support float64)

+ func (e *Edge) Support() float64

+ func (e *Edge) TipPresent(id uint) bool

+ func (e *Edge) TopoDepth() (int, error)

+ type EdgeIndex struct

+ func NewEdgeIndex(size int64, loadfactor float64) *EdgeIndex

+ func (em *EdgeIndex) AddEdgeCount(e *Edge)

+ func (em *EdgeIndex) PutEdgeValue(e *Edge, value int)

+ func (em *EdgeIndex) Value(e *Edge) (int, bool)

+ type KeyValue struct

+ type Node struct

+ func (n *Node) AddComment(comment string)

+ func (n *Node) Depth() (int, error)

+ func (n *Node) EdgeIndex(e *Edge) (int, error)

+ func (n *Node) Edges() []*Edge

+ func (n *Node) Name() string

+ func (n *Node) Neigh() []*Node

+ func (n *Node) Newick(parent *Node, newick *bytes.Buffer)

+ func (n *Node) Nneigh() int

+ func (n *Node) NodeIndex(next *Node) (int, error)

+ func (n *Node) Parent() (*Node, error)

+ func (n *Node) ParentEdge() (*Edge, error)

+ func (n *Node) SetDepth(depth int)

+ func (n *Node) SetName(name string)

+ func (n *Node) Tip() bool

+ type NodeIndex interface

+ GetNode func(name string) (*Node, bool)

+ type Tree struct

+ func NewTree() *Tree

+ func RandomBinaryTree(nbtips int) (*Tree, error)

+ func (t *Tree) AllTipNames() []string

+ func (t *Tree) ClearBitSets() error

+ func (t *Tree) CollapseShortBranches(length float64)

+ func (t *Tree) CommonEdges(t2 *Tree, tipEdges bool) (tree1 int, common int, err error)

+ func (t *Tree) CompareTipIndexes(t2 *Tree) error

+ func (t *Tree) ComputeDepths()

+ func (t *Tree) ConnectNodes(parent *Node, child *Node) *Edge

+ func (t *Tree) Edges() []*Edge

+ func (t *Tree) ExistsTip(name string) (bool, error)

+ func (t *Tree) GraftTipOnEdge(n *Node, e *Edge) (*Edge, *Edge, *Node, error)

+ func (t *Tree) MeanBrLength() float64

+ func (t *Tree) MeanSupport() float64

+ func (t *Tree) MedianSupport() float64

+ func (t *Tree) NbTips() (int, error)

+ func (t *Tree) NewEdge() *Edge

+ func (t *Tree) NewNode() *Node

+ func (t *Tree) Newick() string

+ func (t *Tree) Nodes() []*Node

+ func (t *Tree) RemoveEdges(edges ...*Edge)

+ func (t *Tree) RemoveTips(names ...string) error

+ func (t *Tree) Rename(namemap map[string]string) error

+ func (t *Tree) Reroot(n *Node) error

+ func (t *Tree) RerootFirst() error

+ func (t *Tree) Root() *Node

+ func (t *Tree) Rooted() bool

+ func (t *Tree) SetRoot(r *Node)

+ func (t *Tree) ShuffleTips()

+ func (t *Tree) String() string

+ func (t *Tree) SumBranchLengths() float64

+ func (t *Tree) TipEdges() []*Edge

+ func (t *Tree) TipIndex(name string) (uint, error)

+ func (t *Tree) Tips() []*Node

+ func (t *Tree) UnRoot()

+ func (t *Tree) UpdateBitSet() error

+ func (t *Tree) UpdateTipIndex()