Added source Matlab code for reference

matlab/graph/phyTreeRead.m

@@ -0,0 +1,197 @@
+function tr  = phyTreeRead(filename)
+%PHYTREEREAD reads a NEWICK tree formatted file.
+%
+%  TREE = PHYTREEREAD(FILENAME) reads a NEWICK tree formatted file
+%  FILENAME, returning the data in the file as a PHYTREE object. FILENAME
+%  can also be a URL or MATLAB character array that contains the text of a
+%  NEWICK format file. 
+%
+%  The NEWICK tree format is found at: 
+%        http://evolution.genetics.washington.edu/phylip/newicktree.html
+%  
+%  Note: This implementation only allows binary trees, non-binary trees
+%  will be translated into a binary tree with extra branches of length 0.
+%
+%   Example:
+%
+%      tr = phytreeread('pf00002.tree')
+%
+%   See also GETHMMTREE, PHYTREE, PHYTREETOOL, PHYTREEWRITE.
+
+% Copyright 2003-2004 The MathWorks, Inc.
+% $Revision: 1.1.6.10 $ $Author: batserve $ $Date: 2004/04/14 23:57:16 $
+
+
+if nargin==0
+     [filename, pathname] = uigetfile({'*.tree';'*.dnd'},'Select Phylogenetic Tree File');
+     if ~filename
+        disp('Canceled, file not read.');
+        tr=[];
+        return;
+    end
+    filename = [pathname, filename];
+end
+    
+% check input is char
+% in a future version we may accept also cells
+if ~ischar(filename)
+    error('Bioinfo:InvalidInput','Input must be a character array')
+end
+
+if size(filename,1)>1  % is padded string ?
+    strin = cellstr(filename);
+    strin = [strin{:}];
+elseif (strfind(filename(1:min(10,end)), '://')) % is an url ?
+    if (~usejava('jvm'))
+        error('Bioinfo:NoJava','Reading from a URL requires Java.')
+    end
+    try
+        strin = urlread(filename);
+    catch
+        error('Bioinfo:CannotReadURL','Cannot read URL "%s".', filename);
+    end
+    strin = strread(strin,'%c','delimiter','\n')';
+elseif  (exist(filename,'file') || ...
+         exist(fullfile(cd,filename),'file') )    %  is a valid filename ?
+    strin = textread(filename,'%c','delimiter','\n')';
+else  % must be single a string with '\n'
+    strin = strread(filename,'%c','delimiter','\n')';
+end
+
+% characterizing the string
+numBranches = sum(strin==',');
+numLeaves   = numBranches + 1;
+numLabels   = numBranches + numLeaves;
+
+if (numBranches == 0)
+    error('Bioinfo:NoCommaInInputString', ...
+          ['There is not any comma in the data,\ninput string may not '...
+           'be in Newick style or is not a valid filename.'])
+end
+
+% find the string features: open and close parentheses and leaves
+leafPositions = regexp(strin,'[(,][^(,)]')+1;
+parenthesisPositions = regexp(strin,'[()]');
+strFeatures = strin(sort([leafPositions parenthesisPositions]));
+
+% some consistency checking on the parenthesis
+temp = cumsum((strFeatures=='(') - (strFeatures==')'));
+if any(temp(1:end-1)<1) || (temp(end)~=0)
+    error('Bioinfo:InconsistentParentheses','The parentheses structure is inconsistent,\ninput string may not be in Newick style or is not a valid filename.')
+end
+
+dist = zeros(numLabels,1);             % allocating space for distances
+tree = zeros(numBranches,2);           % allocating space for tree pointers
+names = cell(numLabels,1);             % allocating space for tree labels
+
+try
+
+% extract label information for the leaves
+leafData = regexp(strin,'[(,][^(,);\[\]]+','match');
+for j=1:numel(leafData)
+    coi = find(leafData{j}==':',1,'last');
+    if isempty(coi) % if no colon no length, the whole label is the name
+        dist(j) = 0;
+        names{j} = leafData{j}(2:end);
+    else % if there is colon, get name and length
+        dist(j) = strread(leafData{j}(coi+1:end),'%f');
+        names{j} = leafData{j}(2:coi-1);
+    end
+end 
+% uniformizing empty cells, value inside the brackets can never be empty
+% because branch names will always be empty
+[names{cellfun('isempty',names)}] = deal('');
+        
+% extract label information for the parenthesis
+parenthesisData = regexp(strin,')[^(,);\[\]]*','match');
+parenthesisDist = zeros(numel(parenthesisData),1);
+for j=1:numel(parenthesisData)
+    coi = find(parenthesisData{j}==':',1,'last');
+    if isempty(coi) % if no colon no length, the whole label is the name
+        parenthesisDist(j) = 0;
+        parenthesisData{j} = parenthesisData{j}(2:end);
+    else % if there is colon, get name and length
+        parenthesisDist(j) = strread(parenthesisData{j}(coi+1:end),'%f');
+        parenthesisData{j} = parenthesisData{j}(2:coi-1);
+    end
+end 
+% uniformizing empty cells, value inside brackes may be empty
+if any(cellfun('isempty',parenthesisData))
+    [parenthesisData{cellfun('isempty',parenthesisData)}] = deal('');
+end
+
+li = 1; bi = 1; pi = 1;          % indexes for leaf, branch and parentheses
+queue = zeros(1,2*numLeaves); qp = 0; % setting the queue (worst case size)
+
+j = 1;
+
+while j <= numel(strFeatures)
+    switch strFeatures(j)
+        case ')' % close parenthesis, pull values from the queue to create
+                 % a new branch and push the new branch # into the queue                 
+            lastOpenPar = find(queue(1:qp)==0,1,'last');     
+            numElemInPar = min(3,qp-lastOpenPar);
+            switch numElemInPar
+                case 2  % 99% of the cases, two elements in the parenthesis
+                    bp = bi + numLeaves;
+                    names{bp} = parenthesisData{pi};      % set name
+                    dist(bp) = parenthesisDist(pi);       % set length 
+                    tree(bi,:) = queue(qp-1:qp); 
+                    qp = qp - 2; % writes over the open par mark
+                    queue(qp) = bp;
+                    bi = bi + 1;
+                    pi = pi + 1;
+                case 3  % find in non-binary trees, create a phantom branch
+                    bp = bi + numLeaves;
+                    names{bp} = '';      % set name
+                    dist(bp) = 0;        % set length 
+                    tree(bi,:) = queue(qp-1:qp); 
+                    qp = qp - 1; % writes over the left element
+                    queue(qp) = bp;
+                    bi = bi + 1;
+                    j = j - 1; %repeat this closing branch to get the rest
+                case 1  % parenthesis with no meaning (holds one element)
+                    qp = qp - 1;
+                    queue(qp) = queue(qp+1);
+                    pi = pi + 1;
+                case 0  % an empty parenthesis pair
+                    error('Bioinfo:ParenthesisPairWithNoData', ...
+                          ['Found parenthesis pair with no data,\n', ...
+                           'input string may not be in Newick style or',...
+                           'is not a valid filename.'])
+            end % switch numElemInPar
+            
+        case '(' % an open parenthesis marker (0) pushed into the queue
+            qp = qp + 1;
+            queue(qp) = 0;
+            
+        otherwise % a new leaf pushed into the queue
+            qp = qp + 1;
+            queue(qp) = li;
+            li = li + 1;
+    end % switch strFeatures
+    j = j + 1;
+end % while j ...
+
+catch 
+   le = lasterror;
+   if strcmp(le.identifier,'Bioinfo:ParenthesisPairWithNoData')
+       rethrow(le)
+   else
+       error('Bioinfo:IncorrectString',...
+             ['An error occurred while trying to interpret the data,\n'...
+              'input string may not be in Newick style or is not a '...
+              'valid filename.'])
+   end
+end    
+
+% make sure all dists are greater than 0
+dist = max(0,dist);
+
+if sum(dist) == 0  % there was no distance information so force to an unitary ultrametric tree
+    tr = phyTree(tree,names);
+elseif sum(dist(1:numLeaves)) == 0 % no dist infor for leaves, so force an ultrametric tree    
+    tr = phyTree(tree,dist(numLeaves+1:end),names);
+else % put all info into output object
+    tr = phyTree(tree,dist,names);
+end