66 lines
2.1 KiB
Mathematica
66 lines
2.1 KiB
Mathematica
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function [ptrs,dist,names] = getcanonical(tr)
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%GETCANONICAL Calculates the canonical form of a phylogenetic tree.
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%
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% PTRS = GETCANONICAL(TREE) Returns the pointers of the canonical form of
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% a phylogenetic tree. In a canonical tree the leaves are ordered
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% alphabetically and the branches are ordered first by their width and
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% then alphabetically by their first element. A canonical tree is
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% isomorphic to all the trees with the same skeleton independently of the
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% order of their leaves and branches.
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%
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% [PTRS,DIST,NAMES] = GETCANONICAL(TREE) Returns also the re-ordered
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% distances and node names.
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%
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% Example:
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% % create two trees with same skeleton but slightly different distances
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% b = [1 2; 3 4; 5 6; 7 8;9 10];
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% tr_1 = phytree(b,[.1 .2 .3 .3 .4 ]');
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% tr_2 = phytree(b,[.2 .1 .2 .3 .4 ]');
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% plot(tr_1)
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% plot(tr_2)
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%
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% % compare if the two trees are isomorphic
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% isequal(getcanonical(tr_1),getcanonical(tr_2))
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%
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% See also PHYTREE, PHYTREEREAD, PHYTREE/GETBYNAME, PHYTREE/SELECT,
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% PHYTREE/SUBTREE.
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% Copyright 2003-2006 The MathWorks, Inc.
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% $Revision: 1.1.8.2 $ $Author: batserve $ $Date: 2006/06/16 20:06:42 $
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if numel(tr)~=1
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error('Bioinfo:phytree:getcanonical:NoMultielementArrays',...
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'Phylogenetic tree must be an 1-by-1 object.');
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end
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numBranches = size(tr.tree,1);
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numLeaves = numBranches + 1;
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numLabels = numBranches + numLeaves;
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[dummy,h] = sort(tr.names(1:numLeaves)); %#ok
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h(h)=1:numLeaves;
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% compute the branch width and the first element for each one
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branchWidth = ones(numLabels,1);
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firstElement = [h;inf(numBranches,1)];
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for ind = 1:numBranches
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branchWidth(numLeaves+ind) = sum(branchWidth(tr.tree(ind,:)));
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firstElement(numLeaves+ind) = min(firstElement(tr.tree(ind,:)));
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end
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% find out how to re-order
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[dummy,ord]=sortrows([branchWidth firstElement]); %#ok
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iord(ord) = 1:numLabels;
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% re-order pointers
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ptrs = sort(iord(tr.tree(ord(numLeaves+1:numLabels)-numLeaves,:)),2);
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if nargout > 1
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dist = tr.dist(ord);
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end
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if nargout > 2
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names = tr.names(ord);
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end
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