Added source Matlab code for reference

matlab/graph/@phyTree/getMatrix.m

@@ -0,0 +1,62 @@
+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