Added source Matlab code for reference

matlab/graph/@phyTree/getByName.m

@@ -0,0 +1,103 @@
+function sel = getbyname(tr,query,varargin)
+%GETBYNAME Selects branches and leaves by name.
+%
+%   S = GETBYNAME(T,EXPRESSION) returns a logical vector S of size 
+%   [NUMNODES x 1] indicating the node names of the phylogenetic tree T
+%   that match the regular expression EXPRESSION regardless of case. 
+%
+%   Symbols than can be used in a matching regular expression are explained
+%   in help REGEXP.
+%
+%   When EXPRESSION is a cell array of strings, GETBYNAME returns a matrix
+%   where every column corresponds to every query in EXPRESSION.
+%
+%   S = GETBYNAME(T,STRING,'EXACT',true) looks for exact matches only
+%   (ignoring case). When STRING is a cell array of strings, GETBYNAME
+%   returns a vector with indices.
+%
+%   Example:
+%
+%      % Load a phylogenetic tree created from a protein family:
+%      tr = phytreeread('pf00002.tree');
+%       
+%      % Select all the 'mouse' and 'human' proteins:
+%      sel = getbyname(tr,{'mouse','human'});
+%      view(tr,any(sel,2));
+%       
+%   See also PHYTREE, PHYTREE/PRUNE, PHYTREE/SELECT, PHYTREE/GET.
+
+% Copyright 2003-2005 The MathWorks, Inc.
+% $Revision: 1.1.6.5 $ $Author: batserve $ $Date: 2005/06/09 21:55:55 $
+
+if numel(tr)~=1
+     error('Bioinfo:phytree:getbyname:NoMultielementArrays',...
+           'Phylogenetic tree must be an 1-by-1 object.');
+end
+
+doExactMatch = false;
+
+if  nargin > 2
+    okargs = {'exact',''};
+    for j=1:2:nargin-2
+        pname = varargin{j};
+        k = strmatch(lower(pname), okargs); %#ok
+        if isempty(k)
+            error('Bioinfo:phytree:getbyname:UnknownParameterName',...
+                'Unknown parameter name: %s.',pname);
+        elseif length(k)>1
+            error('Bioinfo:phytree:getbyname:AmbiguousParameterName',...
+                'Ambiguous parameter name: %s.',pname);
+        else
+            switch(k)
+                case 1
+                   if nargin == 3
+                       doExactMatch = true;
+                   else
+                       doExactMatch = opttf(varargin{j+1});
+                       if isempty(doExactMatch)
+                           error('Bioinfo:phytree:getbyname:InputOptionNotLogical',...
+                                '%s must be a logical value, true or false.',...
+                                 upper(char(okargs(k))));
+                       end
+                   end
+            end %switch
+        end %if
+    end %for
+end %if
+
+
+numLabels = numel(tr.names);
+if iscell(query)
+    if doExactMatch
+        sel = zeros(numLabels,1);
+    else
+        sel = false(numLabels,numel(query));
+    end
+    for ind = 1:numel(query)
+        if doExactMatch
+            sel(strcmpi(query{ind},tr.names)) = ind;
+        else
+            try
+                regexpiOutput = regexpi(tr(:).names,query{ind});
+            catch
+                error('Bioinfo:phytree:getbyname:IncorrectRegularExpression',...
+                    ['The query expression produced the following error in ' ...
+                    'REGEXPI: \n%s'],lasterr);
+            end
+            sel(:,ind) = ~cellfun('isempty',regexpiOutput);
+        end
+    end
+else % must be a single string of chars
+    if doExactMatch
+        sel = strcmpi(query,tr.names);
+    else
+        try
+            regexpiOutput = regexpi(tr(:).names,query);
+        catch
+            error('Bioinfo:phytree:getbyname:IncorrectRegularExpression',...
+                ['The query expression produced the following error in ' ...
+                'REGEXPI: \n%s'],lasterr);
+        end
+        sel = ~cellfun('isempty',regexpiOutput);
+    end
+end