62 lines
2.2 KiB
Matlab
62 lines
2.2 KiB
Matlab
function [cm lab dist] = getmatrix(tr,varargin)
|
|
%GETMATRIX converts a Phytree Object into a relationship matrix.
|
|
%
|
|
% [MATRIX, ID, DISTANCES] = GETMATRIX(T) converts the phylogenetic tree
|
|
% object T into a logical sparse matrix, where 1's indicate that a branch
|
|
% node (row index) is connected to its child (column index). The child
|
|
% can be either another branch node or a leaf node. ID is a list of the
|
|
% labels that correspond to the rows and columns of MATRIX, first the
|
|
% leaf nodes from 1 to NUMLEAVES, then the branch nodes from NUMLEAVES+1
|
|
% to NUMLEAVES+NUMBRANCHES, being the root the last node. DISTANCES is
|
|
% a column vector with one entry for every nonzero entry in MATRIX
|
|
% traversed columnwise and representing the distance between the branch
|
|
% node and the child.
|
|
%
|
|
% Example:
|
|
%
|
|
% T = phytreeread('pf00002.tree')
|
|
% [MATRIX ID DIST] = getmatrix(T);
|
|
%
|
|
% See also PHYTREE, PHYTREE/GET, PHYTREE/PDIST, PHYTREE/PRUNE, PHYTREETOOL.
|
|
|
|
% Copyright 2006 The MathWorks, Inc.
|
|
% $Revision: 1.1.6.1 $ $Date: 2006/06/16 20:06:43 $
|
|
|
|
|
|
%%% check arguments
|
|
if nargin > 1
|
|
if rem(nargin,2) == 0
|
|
error('Bioinfo:phytree:getmatrix:IncorrectNumberOfArguments',...
|
|
'Incorrect number of arguments to %s.',mfilename);
|
|
end
|
|
okargs = {'no_input_arguments'};
|
|
for j=1:2:nargin-2
|
|
pname = varargin{j};
|
|
pval = varargin{j+1};
|
|
if(isstruct(pval))
|
|
error('Bioinfo:phytree:getmatrix:StructParamError',...
|
|
'parameter cannot be a struct');
|
|
end
|
|
k = find(strncmpi(pname, okargs,length(pname)));
|
|
if isempty(k)
|
|
error('Bioinfo:phytree:getmatrix:UnknownParameterName',...
|
|
'Unknown parameter name: %s.',pname);
|
|
elseif length(k)>1
|
|
error('Bioinfo:phytree:getmatrix:AmbiguousParameterName',...
|
|
'Ambiguous parameter name: %s.',pname);
|
|
else
|
|
switch(k)
|
|
end
|
|
end
|
|
end
|
|
end
|
|
|
|
numLeaves = size(tr.tree,1)+1;
|
|
numNodes = numLeaves + numLeaves -1;
|
|
cm = sparse(repmat(numLeaves+1:numNodes,1,2),tr.tree(:),true,numNodes,numNodes);
|
|
if nargout>1
|
|
lab = tr.names;
|
|
end
|
|
if nargout>2
|
|
dist = tr.dist;
|
|
end
|