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Added source Matlab code for reference

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Waldir Leoncio 2019-12-16 16:47:21 +01:00
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commit b5d99903d2
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matlab/graph/@phyTree/GET.m Normal file
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function varargout = get(tr,varargin)
%GET Get information about a phylogenetic tree object.
% [VALUE1,VALUE2, ...] = GET(TREE,'NAME1','NAME2', ...) returns the
% contents of the specified fields for the PHYTREE object TREE.
%
% The valid choices for 'NAME' are:
% 'POINTERS' : branch to leaf/branch connectivity list
% 'DISTANCES' : edge length for every leaf/branch
% 'NUMLEAVES' : number of leaves
% 'NUMBRANCHES' : number of branches
% 'NUMNODES' : number of nodes (numleaves + numbranches)
% 'LEAFNAMES' : names of the leaves
% 'BRANCHNAMES' : names of the branches
% 'NODENAMES' : names of all the nodes
%
% GET(TREE) displays all property names and their current values for
% the PHYTREE object TREE.
%
% V = GET(TREE) returns a structure where each field name is the name of
% a property of TREE and each field contains the value of that property.
%
% Examples:
% tr = phytreeread('pf00002.tree')
% protein_names = get(tr,'LeafNames')
%
% See also PHYTREE, PHYTREEREAD, PHYTREE/SELECT, PHYTREE/GETBYNAME.
% Copyright 2003-2005 The MathWorks, Inc.
% $Revision: 1.1.6.7 $ $Author: batserve $ $Date: 2005/06/09 21:55:54 $
if numel(tr)~=1
error('Bioinfo:phytree:get:NoMultielementArrays',...
'Phylogenetic tree must be an 1-by-1 object.');
end
numBranches = size(tr.tree,1);
numLeaves = numBranches + 1;
numLabels = numBranches + numLeaves;
% get input without arguments displays a summary
if nargin == 1
s.NumLeaves = numLeaves;
s.NumBranches = numBranches;
s.NumNodes = numLabels;
s.Pointers = tr.tree;
s.Distances = tr.dist;
s.LeafNames = tr.names(1:numLeaves);
s.BranchNames = tr.names(numLeaves+1:numLabels);
s.NodeNames = tr.names;
if nargout == 0
disp(s)
else
varargout{1} = s;
end
return;
end
okargs = {'pointers','distances','numleaves','numbranches',...
'numnodes','leafnames','branchnames','nodenames'};
for ind = 2 : nargin
pname = varargin{ind-1};
k = find(strncmpi(pname,okargs,numel(pname)));
if isempty(k)
error('Bioinfo:phytree:get:UnknownParameterName',...
'Unknown parameter name: %s.',pname);
elseif length(k)>1
error('Bioinfo:phytree:get:AmbiguousParameterName',...
'Ambiguous parameter name: %s.',pname);
else
switch(k)
case 1 % pointers
varargout{ind-1} = tr.tree; %#ok
case 2 % distances
varargout{ind-1} = tr.dist;
case 3 % numleaves
varargout{ind-1} = numLeaves;
case 4 % numbranches
varargout{ind-1} = numBranches;
case 5 % numNodes
varargout{ind-1} = numLabels;
case 6 % leafnames
varargout{ind-1} = tr.names(1:numLeaves);
case 7 % branchnames
varargout{ind-1} = tr.names(numLeaves+1:numLabels);
case 8 % nodenames
varargout{ind-1} = tr.names;
end
end
end