90 lines
3.1 KiB
Mathematica
90 lines
3.1 KiB
Mathematica
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function varargout = get(tr,varargin)
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%GET Get information about a phylogenetic tree object.
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% [VALUE1,VALUE2, ...] = GET(TREE,'NAME1','NAME2', ...) returns the
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% contents of the specified fields for the PHYTREE object TREE.
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%
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% The valid choices for 'NAME' are:
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% 'POINTERS' : branch to leaf/branch connectivity list
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% 'DISTANCES' : edge length for every leaf/branch
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% 'NUMLEAVES' : number of leaves
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% 'NUMBRANCHES' : number of branches
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% 'NUMNODES' : number of nodes (numleaves + numbranches)
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% 'LEAFNAMES' : names of the leaves
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% 'BRANCHNAMES' : names of the branches
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% 'NODENAMES' : names of all the nodes
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%
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% GET(TREE) displays all property names and their current values for
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% the PHYTREE object TREE.
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%
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% V = GET(TREE) returns a structure where each field name is the name of
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% a property of TREE and each field contains the value of that property.
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%
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% Examples:
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% tr = phytreeread('pf00002.tree')
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% protein_names = get(tr,'LeafNames')
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%
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% See also PHYTREE, PHYTREEREAD, PHYTREE/SELECT, PHYTREE/GETBYNAME.
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% Copyright 2003-2005 The MathWorks, Inc.
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% $Revision: 1.1.6.7 $ $Author: batserve $ $Date: 2005/06/09 21:55:54 $
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if numel(tr)~=1
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error('Bioinfo:phytree:get: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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% get input without arguments displays a summary
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if nargin == 1
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s.NumLeaves = numLeaves;
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s.NumBranches = numBranches;
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s.NumNodes = numLabels;
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s.Pointers = tr.tree;
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s.Distances = tr.dist;
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s.LeafNames = tr.names(1:numLeaves);
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s.BranchNames = tr.names(numLeaves+1:numLabels);
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s.NodeNames = tr.names;
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if nargout == 0
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disp(s)
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else
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varargout{1} = s;
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end
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return;
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end
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okargs = {'pointers','distances','numleaves','numbranches',...
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'numnodes','leafnames','branchnames','nodenames'};
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for ind = 2 : nargin
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pname = varargin{ind-1};
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k = find(strncmpi(pname,okargs,numel(pname)));
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if isempty(k)
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error('Bioinfo:phytree:get:UnknownParameterName',...
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'Unknown parameter name: %s.',pname);
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elseif length(k)>1
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error('Bioinfo:phytree:get:AmbiguousParameterName',...
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'Ambiguous parameter name: %s.',pname);
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else
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switch(k)
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case 1 % pointers
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varargout{ind-1} = tr.tree; %#ok
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case 2 % distances
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varargout{ind-1} = tr.dist;
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case 3 % numleaves
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varargout{ind-1} = numLeaves;
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case 4 % numbranches
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varargout{ind-1} = numBranches;
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case 5 % numNodes
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varargout{ind-1} = numLabels;
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case 6 % leafnames
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varargout{ind-1} = tr.names(1:numLeaves);
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case 7 % branchnames
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varargout{ind-1} = tr.names(numLeaves+1:numLabels);
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case 8 % nodenames
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varargout{ind-1} = tr.names;
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end
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end
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end
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