104 lines
3.6 KiB
Mathematica
104 lines
3.6 KiB
Mathematica
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function sel = getbyname(tr,query,varargin)
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%GETBYNAME Selects branches and leaves by name.
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%
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% S = GETBYNAME(T,EXPRESSION) returns a logical vector S of size
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% [NUMNODES x 1] indicating the node names of the phylogenetic tree T
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% that match the regular expression EXPRESSION regardless of case.
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%
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% Symbols than can be used in a matching regular expression are explained
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% in help REGEXP.
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%
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% When EXPRESSION is a cell array of strings, GETBYNAME returns a matrix
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% where every column corresponds to every query in EXPRESSION.
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%
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% S = GETBYNAME(T,STRING,'EXACT',true) looks for exact matches only
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% (ignoring case). When STRING is a cell array of strings, GETBYNAME
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% returns a vector with indices.
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%
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% Example:
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%
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% % Load a phylogenetic tree created from a protein family:
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% tr = phytreeread('pf00002.tree');
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%
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% % Select all the 'mouse' and 'human' proteins:
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% sel = getbyname(tr,{'mouse','human'});
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% view(tr,any(sel,2));
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%
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% See also PHYTREE, PHYTREE/PRUNE, PHYTREE/SELECT, PHYTREE/GET.
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% Copyright 2003-2005 The MathWorks, Inc.
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% $Revision: 1.1.6.5 $ $Author: batserve $ $Date: 2005/06/09 21:55:55 $
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if numel(tr)~=1
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error('Bioinfo:phytree:getbyname:NoMultielementArrays',...
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'Phylogenetic tree must be an 1-by-1 object.');
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end
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doExactMatch = false;
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if nargin > 2
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okargs = {'exact',''};
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for j=1:2:nargin-2
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pname = varargin{j};
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k = strmatch(lower(pname), okargs); %#ok
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if isempty(k)
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error('Bioinfo:phytree:getbyname: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:getbyname: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
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if nargin == 3
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doExactMatch = true;
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else
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doExactMatch = opttf(varargin{j+1});
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if isempty(doExactMatch)
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error('Bioinfo:phytree:getbyname:InputOptionNotLogical',...
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'%s must be a logical value, true or false.',...
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upper(char(okargs(k))));
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end
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end
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end %switch
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end %if
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end %for
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end %if
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numLabels = numel(tr.names);
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if iscell(query)
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if doExactMatch
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sel = zeros(numLabels,1);
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else
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sel = false(numLabels,numel(query));
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end
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for ind = 1:numel(query)
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if doExactMatch
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sel(strcmpi(query{ind},tr.names)) = ind;
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else
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try
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regexpiOutput = regexpi(tr(:).names,query{ind});
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catch
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error('Bioinfo:phytree:getbyname:IncorrectRegularExpression',...
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['The query expression produced the following error in ' ...
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'REGEXPI: \n%s'],lasterr);
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end
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sel(:,ind) = ~cellfun('isempty',regexpiOutput);
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end
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end
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else % must be a single string of chars
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if doExactMatch
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sel = strcmpi(query,tr.names);
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else
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try
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regexpiOutput = regexpi(tr(:).names,query);
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catch
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error('Bioinfo:phytree:getbyname:IncorrectRegularExpression',...
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['The query expression produced the following error in ' ...
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'REGEXPI: \n%s'],lasterr);
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end
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sel = ~cellfun('isempty',regexpiOutput);
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end
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end
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