getbyname (phytree)

Branches and leaves from phytree object

Syntax

S = getbyname(Tree, Expression)
S = getbyname(Tree, Key)
S = getbyname(Tree, Key, 'Exact', ExactValue)

Arguments

Tree

phytree object created by phytree function (object constructor) or phytreeread function.

Expression

Regular expression (MATLAB) or cell array of regular expressions to search for in Tree.

Key

Character vector or cell array of character vectors to search for in Tree.

ExactValueControls whether the full exact node name must match the character vector(s), ignoring case. Choices are true or false (default). When true, S is a numeric column vector indicating which node names match a query exactly, in full.

Description

S = getbyname(Tree, Expression) searches the nodes names in Tree, a phytree object, for the regular expression(s) specified by Expression. It returns S, a logical matrix of size NumNodes-by-M, where M is either 1 or the length of Expression. Each row in S corresponds to a node, and each column corresponds to a query in Expression. The logical matrix S indicates the node names that match Expression, ignoring case.

S = getbyname(Tree, Key) searches the nodes names in Tree, a phytree object, for the character vector(s) specified by Key. It returns S, a logical matrix of size NumNodes-by-M, where M is either 1 or the length of Key. Each row in S corresponds to a node, and each column corresponds to a query in Key. The logical matrix S indicates the node names that match Key, ignoring case.

S = getbyname(Tree, Key, 'Exact', ExactValue) specifies whether the full exact node name must match the character vector(s), ignoring case. Choices are true or false (default). When true, S is a numeric column vector indicating which node names match a query exactly, in full.

Examples

  1. Read a phylogenetic tree file created from a protein family into a phytree object.

    tr = phytreeread('pf00002.tree');
  2. Determine all the mouse and human proteins by searching for nodes that include the character vectors 'mouse' and 'human' in their names.

    sel = getbyname(tr,{'mouse','human'});
    view(tr,any(sel,2));

Introduced before R2006a