Added source Matlab code for reference

matlab/graph/@phyTree/getNewickStr.m

@@ -0,0 +1,133 @@
+function str = getnewickstr(tr,varargin)
+%GETNEWICKSTR creates a NEWICK formatted string.
+%
+%   STR = GETNEWICKSTR(TREE) returns the NEWICK formatted string of the
+%   phylogenetic tree object TREE. 
+%
+%   GETNEWICKSTR(...,'DISTANCES',false) excludes the distances from the
+%   output. Default is true.
+%
+%   GETNEWICKSTR(...,'BRANCHNAMES',true) includes the branch names into the
+%   output. Default is false. 
+%
+%   The NEWICK tree format is found at: 
+%        http://evolution.genetics.washington.edu/phylip/newicktree.html
+%
+%   Example:
+%
+%      seqs = int2nt(ceil(rand(10)*4));      % some random sequences
+%      dist = seqpdist(seqs,'alpha','nt');   % pairwise distances
+%      tree = seqlinkage(dist);              % construct phylogenetic tree
+%      str  = getnewickstr(tree)             % get the NEWICK string
+%     
+%   See also PHYTREE, PHYTREEREAD, PHYTREEWRITE, PHYTREETOOL, SEQLINKAGE,
+%   PHYTREE/GET, PHYTREE/GETBYNAME, PHYTREE/GETCANONICAL. 
+
+%  Undocumented:
+%   GETSTR(...,'MULTILINE',true) introduces 'new line' characters for a
+%   multi-line output. This option is used by PHYTREEWRITE. Default is
+%   false.
+
+% Copyright 2003-2005 The MathWorks, Inc.
+% $Revision: 1.1.8.1 $ $Author: batserve $ $Date: 2005/06/09 21:55:57 $
+
+if numel(tr)~=1
+     error('Bioinfo:phytree:getstr:NoMultielementArrays',...
+           'Phylogenetic tree must be an 1-by-1 object.');
+end
+
+numBranches = size(tr.tree,1);
+numLeaves = numBranches + 1;
+numLabels = numBranches + numLeaves; 
+
+% set defaults
+writeDistances = true;
+writeBranchNames = false;
+multiLine = false;
+
+nvarargin = numel(varargin);
+if nvarargin
+    if rem(nvarargin,2)
+        error('Bioinfo:phytree:getstr:IncorrectNumberOfArguments',...
+            'Incorrect number of arguments to %s.',mfilename);
+    end
+    okargs = {'multiline','distances','branchnames'};
+    for j=1:2:nvarargin
+        pname = varargin{j};
+        pval = varargin{j+1};
+        k = find(strncmpi(pname,okargs,numel(pname)));
+        if isempty(k)
+            error('Bioinfo:phytree:getstr:UnknownParameterName',...
+                'Unknown parameter name: %s.',pname);
+        elseif length(k)>1
+            error('Bioinfo:AmbiguousParameterName',...
+                'Ambiguous parameter name: %s.',pname);
+        else
+            switch(k)
+                case 1  % multi-lines
+                    multiLine = opttf(pval);
+                    if isempty(multiLine)
+                        error('Bioinfo:phytree:getstr:multiLineOptionNotLogical',...
+                            '%s must be a logical value, true or false.',...
+                            upper(char(okargs(k))));
+                    end
+                case 2 % write distances
+                    writeDistances = opttf(pval);
+                    if isempty(writeDistances)
+                        error('Bioinfo:phytree:getstr:writeDistancesOptionNotLogical',...
+                            '%s must be a logical value, true or false.',...
+                            upper(char(okargs(k))));
+                    end
+                case 3 % write branch names
+                    writeBranchNames = opttf(pval);
+                    if isempty(writeBranchNames)
+                        error('Bioinfo:phytree:getstr:writeBranchNamesOptionNotLogical',...
+                            '%s must be a logical value, true or false.',...
+                            upper(char(okargs(k))));
+                    end                    
+            end
+        end
+    end
+end
+
+for i=1:numLabels-1;
+    if (i<=numLeaves || writeBranchNames)
+        if writeDistances 
+            namedist{i} = [tr.names{i} ':' num2str(tr.dist(i))]; %#ok
+        else
+            namedist{i} = tr.names{i};
+        end
+    elseif writeDistances && ~writeBranchNames
+        namedist{i} = [':' num2str(tr.dist(i))]; %#ok
+    else 
+        namedist{i} = '';
+    end
+end
+
+if writeBranchNames
+    namedist{numLabels} = [tr.names{numLabels} ';'];
+else
+    namedist{numLabels} = ';';
+end
+
+for i=1:numBranches
+    if tr.tree(i,1) > numLeaves
+        t1 = branchstr{tr.tree(i,1)};
+    else
+        t1 = namedist{tr.tree(i,1)};
+    end
+    if tr.tree(i,2) > numLeaves
+        t2 = branchstr{tr.tree(i,2)};
+    else
+        t2 = namedist{tr.tree(i,2)};
+    end
+    branchstr{i+numLeaves} = ...
+        [ '(\n' t1 ',\n' t2 ')\n' , namedist{i+numLeaves} ]; %#ok
+end
+
+str = sprintf(branchstr{numLabels});
+
+if ~multiLine
+    str = strrep(str,sprintf('\n'),'');
+end
+