Binary unrooted topology (rooted at leaf with ID zero) More...

Collaboration diagram for topology_struct:

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Data Fields
topol_node *	nodelist

double *	blength
	vector of nodes (the first are the leaves).

int	id
	Branch lengths, with mean, min, max vectors for topology_space.

topol_node	root
	topology ID (should be updated by hand, e.g. by functions in topology_space.c)

int	nleaves
	Pointer to root node.

int	nnodes
	Number of leaves .

topol_node	undo_prune
	Number of nodes, including leaves ( for a binary rooted tree).

topol_node	undo_regraft
	How to revert most recent SPR move (prune node).

bool	undo_lca
	How to revert most recent SPR move (regraft node).

topol_node *	postorder
	revert SPR move is lca type or not

topol_node *	undone
	pointers to all internal nodes in postorder (from last to first is preorder)

int	n_undone
	pointers to outdated nodes in postorder (from last to first is preorder)

uint32_t	hashID1
	number of outdated nodes (which need likelihood calc etc) in topology_struct::undone.

uint32_t	hashID2

bool	traversal_updated
	hash values of tree, ideally a unique value for each tree (collisions happen...)

int	ref_counter
	zero if postorder[] vector needs update, one if we can use postdorder[] to traverse tree

char_vector	taxlabel
	number of references of topology (how many places are pointing to it)

int *	index
	Taxon names (just a pointer; actual values are setup by newick_tree_struct or alignment_struct)

bool	quasirandom
	sandbox vector used in spr moves / quasirandom tree shuffle just to avoid recurrent allocation

Detailed Description

Binary unrooted topology (rooted at leaf with ID zero)

The documentation for this struct was generated from the following file:

Data Fields