For each external node of Tree tree: Cleans up SWISS-PROT
species names: It removes everything (including ) after a potential
"/", "_", "-", "\", ";", ".".
For each node of Tree tree: Extracts the species name
(as SWISS-PROT abbreviation) from the sequence name
(if SWISS-PROT names are used) and writes it to
the species name field if this is empty.
Calculates the distance of the Node with seq name seq_name
to the LCA of ext_nodes, which has been set either with
constructor DistanceCalculator(Tree,Vector) or method
setTreeAndExtNodes(Tree,Vector).
Calculates the distance of Node n to the root of Tree t which
has been set either with a constructor, setTree(Tree), or
setTreeAndExtNodes(Tree,Vector).
Calculates the distance of the Node with seq name seq_name
to the root of Tree t, which has been set either with a
constructor, setTree(Tree), or setTreeAndExtNodes(Tree,Vector).
Returns the order in which ortholog (o),
"super ortholog" (s) and distance (d) are
returned and sorted (priority of sort always
goes from left to right), given sort.
Reads in multiple Trees from a File multipletreefile,
containing Tree descriptions in New Hampshire (NH) or
New Hampshire X (NHX) format separated by semicolons followed
by a newline.
Sets a boolean which could represent whether placement
of an additional Node on the parent branch of this Node
makes the likelihood of the resulting tree significantly worse.
Sets the rooted Tree t and the external Nodes ext_nodes for which
the mean distance to their lowest common ancestor and its variance
and standard deviation are calculated.
Sets the rooted Tree t and the external Nodes ext_nodes for which
the mean distance to their lowest common ancestor and its variance
and standard deviation are calculated.
Returns a boolean which could represent whether placement
of an additional Node on the parent branch of this Node
makes the likelihood of the resulting tree significantly worse.