merge sbg with github

changeGeneAssociation.m

@@ -53,7 +53,10 @@
     for i = 1:length(genes)
         if (translateNamesFlag)
             % Translate gene names to systematic names
-            [isInList,translID] = ismember(genes{i},geneNameList);
+            genes{i}
+            geneNameList
+            systNameList
+            [isInList,translID] = ismember(genes{i},geneNameList)            
             if isInList
                 newGene = systNameList{translID};
                 grRule = regexprep(grRule,[genes{i} '$'],newGene);

checkCobraModelUnique.m

@@ -46,9 +46,9 @@
         fprintf('%s\n',thisMetName);
         if (renameFlag)
             fprintf('Renaming non-unique metabolites\n');
-            rxnIDs = findRxnIDs(model,thisMetName);
-            for j = 1:length(rxnIDs)
-                model.rxns{rxnIDs(j)} = [thisMetName '_' num2str(j)];
+            metIDs = findMetIDs(model,thisMetName);
+            for j = 1:length(metIDs)
+                model.mets{metIDs(j)} = [thisMetName '_' num2str(j)];
                 fprintf('%s\n',model.mets{rxnIDs(j)});
             end
         end

checkDuplicateRxn.m

@@ -1,4 +1,4 @@
-function [model,removed] = checkDuplicateRxn(model,method)
+function [model,removed, rxnRelationship] = checkDuplicateRxn(model,method)
 %checkDuplicateRxn Checks model for duplicate reactions and removes them
 %
 % [model,removed] = checkDuplicateRxn(model,method)
@@ -13,10 +13,12 @@
 % removed   reaction numbers that were removed
 %
 % Aarash Bordbar 02/11/08
+% Uri David Akavia 20-Feb-2014
 
+model = removeMetabolites(model, model.mets(all(model.S == 0,2)));
 [nMets,nRxns] = size(model.S);
- removed = '';
-cnt = 1;
+removed = cell(0); 
+cnt = 0;
 switch method
     case 1
         h = waitbar(0, 'Checking by Abbreviation ...');
@@ -38,27 +40,39 @@
         end
         close(h);
     case 2
-        h = waitbar(0, 'Checking by reaction ...');
-        for i = 1:nMets
-            possibleMatches = find(model.S(i,:));
-            for j = 1:length(possibleMatches)
-                for k = 1:length(possibleMatches)
-                    if model.S(:,possibleMatches(j)) == model.S(:,possibleMatches(k)) & strcmp(model.rxns(possibleMatches(j)),model.rxns(possibleMatches(k))) == 0
-                        model = removeRxns(model,model.rxns(possibleMatches(k)));
-                        removed{cnt,1} = model.rxns(possibleMatches(k));
-                        cnt = cnt+1;
-                    elseif model.S(:,possibleMatches(j)) == model.S(:,possibleMatches(k)) & strcmp(model.rxns(possibleMatches(j)),model.rxns(possibleMatches(k))) == 1
-                        model2 = model;
-                        model2.rxns{possibleMatches(j)} = '';
-                        model2 = removeRxns(model2,model.rxns(possibleMatches(j)));
-                        model2.rxns{possibleMatches(j)} = model.rxns{possibleMatches(j)};
-                        model = model2;
-                        removed{cnt,1} = model.rxns{possibleMatches(j)};
-                        cnt = cnt+1;
-                    end
-                end
-            end
-            waitbar(i/nMets,h);
-        end
-        close(h);
+		h = waitbar(0, 'Checking by reaction ...');
+		[~, ia, ic] = unique(model.S', 'rows');
+		reactionsToRemove = cell(0);
+		rxnsKept = cell(0);
+		duplicateReactions = cell(0);
+		if (length(ia) ~= length(ic))
+			for rxnInd=1:max(ic)
+				% If the current reaction appears more than once
+				if (sum(rxnInd == ic) > 1)
+					identicalRxns = find(ic == rxnInd);
+					rxnWithDuplicates = model.rxns(identicalRxns(1));
+					rxnsToRemove = model.rxns(identicalRxns(2:end))';
+					% Same abbreviation
+					if (strcmp(rxnWithDuplicates, rxnsToRemove))
+						model2 = model;
+						model2.rxns(identicalRxns(1)) = '';
+						model2 = removeRxns(model2, rxnsToRemove);
+						model2.rxns(identicalRxns(1)) = rxnWithDuplicates;
+						removed = [removed; rxnsToRemove'];
+						cnt = cnt+1;
+					else
+						reactionsToRemove = [reactionsToRemove, rxnsToRemove];
+					end
+					rxnsKept = [rxnsKept; rxnWithDuplicates];
+					duplicateReactions = [duplicateReactions; {rxnsToRemove}];
+				end
+				waitbar(rxnInd/max(ic), h);
+			end
+			removed = [removed; reactionsToRemove'];
+			model = removeRxns(model, reactionsToRemove);
+			cnt = cnt + length(reactionsToRemove);
+			rxnRelationship.keptRxns = rxnsKept;
+			rxnRelationship.duplicates = duplicateReactions;
+		end
+		close(h);
 end

external/libSBML-5.11.4-matlab/README.md

@@ -0,0 +1,34 @@
+## **libSBML-5.11.4 MATLAB interface**
+
+**LibSBML** is a free, open-source programming library to help you read, write, manipulate, translate, and validate [SBML](http://sbml.org) files and data streams. 
+
+This archive contains standalone binaries for the libSBML MATLAB interface.  It the interface files are ready to run; they require no compilation or additional steps beyond informing MATLAB about the path to the folder where you unpacked the archive.  Instructions for doing this are given below.
+
+
+### Installation instructions
+
+1. Extract the archive somewhere on your local computer.
+
+2. Start your copy of MATLAB and add the folder to your MATLAB path using [addPath](http://www.mathworks.com/help/matlab/ref/addpath.html). 
+
+3. Verify that everything works.  You can do this easily by changing into that folder within your running MATLAB environment, then issuing the command `TranslateSBML('test.xml')` in MATLAB.  If everything went as planned, the output of that command will be a MATLAB structure representing the toy test model.
+
+4. Save the changes to your MATLAB path for future use.  To do this, you can use the [savepath](http://www.mathworks.com/help/matlab/ref/savepath.html) command in MATLAB.
+
+
+### Help and support
+
+For more information about the libSBML MATLAB interface, please see the [libSBML MATLAB API Documentation][1].
+
+Please report any problems you encounter using libSBML either to the
+developers directly (using the email address <libsbml-team@caltech.edu>) or using the [issue tracker][2].
+
+Thank you for your interest in libSBML!
+
+The LibSBML Team.
+
+
+[![SBML Logo](http://sbml.org/images/8/82/Official-sbml-supported-70.jpg)](http://sbml.org)
+
+[1]: http://sbml.org/Software/libSBML/docs/matlab-api/libsbml-matlab-reading-files.html
+[2]: https://sourceforge.net/tracker/?group_id=71971&atid=942737

external/sbml/libsbml-5.10.2/src/bindings/matlab/buildSBML.m → external/libSBML-5.11.4-matlab/buildSBML.m

@@ -272,7 +272,7 @@ function buildSBML(varargin)
   % same time this new build scheme was introduced.
 
   our_name   = sprintf('%s.m', mfilename);
-  other_name = 'OutputSBML.c';
+  other_name = 'OutputSBML.cpp';
   if ~exist(fullfile(pwd, our_name), 'file') ...
         || ~exist(fullfile(pwd, other_name), 'file')
     error_incorrect_dir('matlab');
@@ -692,43 +692,43 @@ function compile_mex(include_dir, library_dir, matlab_octave)
     if isWindows()
       fhandle = @mex;
       disp('  - Building TranslateSBML ...');
-      feval(fhandle, 'TranslateSBML.c', inc_arg, inc_arg2, library_dir, '-DWIN32');
+      feval(fhandle, 'TranslateSBML.cpp', inc_arg, inc_arg2, library_dir, '-DWIN32');
       disp('  - Building OutputSBML ...');
-      feval(fhandle, 'OutputSBML.c', inc_arg, inc_arg2, library_dir, '-DWIN32');
+      feval(fhandle, 'OutputSBML.cpp', inc_arg, inc_arg2, library_dir, '-DWIN32');
     else
       fhandle = @mex;
       disp('  - Building TranslateSBML ...');
       if ~isempty(altoptions)
-        feval(fhandle, 'TranslateSBML.c', '-f', altoptions, inc_arg, inc_arg2, lib_arg, added_args);
+        feval(fhandle, 'TranslateSBML.cpp', '-f', altoptions, inc_arg, inc_arg2, lib_arg, added_args);
       else
-        feval(fhandle, 'TranslateSBML.c', inc_arg, inc_arg2, lib_arg, added_args);
+        feval(fhandle, 'TranslateSBML.cpp', inc_arg, inc_arg2, lib_arg, added_args);
       end;
       disp('  - Building OutputSBML ...');
       if ~isempty(altoptions)
-        feval(fhandle, 'OutputSBML.c', '-f', altoptions, inc_arg, inc_arg2, lib_arg, added_args);
+        feval(fhandle, 'OutputSBML.cpp', '-f', altoptions, inc_arg, inc_arg2, lib_arg, added_args);
       else
-        feval(fhandle, 'OutputSBML.c', inc_arg, inc_arg2, lib_arg, added_args);
+        feval(fhandle, 'OutputSBML.cpp', inc_arg, inc_arg2, lib_arg, added_args);
       end;
     end;
   else
     if isWindows()
       fhandle = @mkoctfile;
       disp('  - Building TranslateSBML ...');
-      feval(fhandle, '--mex', 'TranslateSBML.c', '-DUSE_OCTAVE', inc_arg, inc_arg2, ...
+      feval(fhandle, '--mex', 'TranslateSBML.cpp', '-DUSE_OCTAVE', inc_arg, inc_arg2, ...
             '-lbz2', '-lz', library_dir);
       disp('  - Building OutputSBML ...');
-      feval(fhandle, '--mex', 'OutputSBML.c', '-DUSE_OCTAVE', inc_arg, inc_arg2, ...
+      feval(fhandle, '--mex', 'OutputSBML.cpp', '-DUSE_OCTAVE', inc_arg, inc_arg2, ...
             '-lbz2', '-lz', library_dir);
     else
       fhandle = @mkoctfile;
       disp('  - Building TranslateSBML ...');
-      feval(fhandle, '--mex', 'TranslateSBML.c', '-DUSE_OCTAVE', inc_arg, inc_arg2, ...
+      feval(fhandle, '--mex', 'TranslateSBML.cpp', '-DUSE_OCTAVE', inc_arg, inc_arg2, ...
             '-lbz2', '-lz', lib_arg, added_args);
       disp('  - Building OutputSBML ...');
-      feval(fhandle, '--mex', 'OutputSBML.c', '-DUSE_OCTAVE', inc_arg, inc_arg2, ...
+      feval(fhandle, '--mex', 'OutputSBML.cpp', '-DUSE_OCTAVE', inc_arg, inc_arg2, ...
             '-lbz2', '-lz', lib_arg, added_args);
     end;
-%   mkoctfile --mex TranslateSBML.c -DUSE_OCTAVE inc_arg inc_arg2 -lbz2 -lz lib_arg;
+%   mkoctfile --mex TranslateSBML.cpp -DUSE_OCTAVE inc_arg inc_arg2 -lbz2 -lz lib_arg;
   end;
 
   transFile = strcat('TranslateSBML.', mexext());
@@ -774,12 +774,12 @@ function copy_matlab_dir(orig_dir, working_dir)
 
   % Copy files from src/bindings/matlab.
 
-  [success, msg, msgid] = copyfile('TranslateSBML.c', working_dir);
+  [success, msg, msgid] = copyfile('TranslateSBML.cpp', working_dir);
   if ~success
     error(sprintf('\n%s\n%s\n', msg, 'Build failed.'));
   end;
 
-  [success, msg, msgid] = copyfile('OutputSBML.c', working_dir);
+  [success, msg, msgid] = copyfile('OutputSBML.cpp', working_dir);
   if ~success
     error(sprintf('\n%s\n%s\n', msg, 'Build failed.'));
   end;
@@ -884,8 +884,8 @@ function error_incorrect_dir(expected)
 
     %copy files to libsbml
     cd(orig_dir);
-    copyfile('TranslateSBML.c', new_dir);
-    copyfile('OutputSBML.c', new_dir);
+    copyfile('TranslateSBML.cpp', new_dir);
+    copyfile('OutputSBML.cpp', new_dir);
     copyfile('*.m', new_dir);
     copyfile('*.xml', new_dir);
     cd(new_dir);

external/libSBML-5.11.4-matlab/isFbcEnabled.m

@@ -0,0 +1,76 @@
+function fbcEnabled = isFbcEnabled()
+% Checks whether the version of libSBML has been built with 
+% the FBC package extension enabled
+
+% Filename    : isFbcEnabled.m
+% Description : check fbc status
+% Author(s)   : SBML Team <sbml-team@caltech.edu>
+% Organization: EMBL-EBI, Caltech
+% Created     : 2011-02-08
+%
+% This file is part of libSBML.  Please visit http://sbml.org for more
+% information about SBML, and the latest version of libSBML.
+%
+% Copyright (C) 2013-2014 jointly by the following organizations:
+%     1. California Institute of Technology, Pasadena, CA, USA
+%     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+%     3. University of Heidelberg, Heidelberg, Germany
+%
+% Copyright (C) 2009-2011 jointly by the following organizations: 
+%     1. California Institute of Technology, Pasadena, CA, USA
+%     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+%  
+% Copyright (C) 2006-2008 by the California Institute of Technology,
+%     Pasadena, CA, USA 
+%  
+% Copyright (C) 2002-2005 jointly by the following organizations: 
+%     1. California Institute of Technology, Pasadena, CA, USA
+%     2. Japan Science and Technology Agency, Japan
+% 
+% This library is free software; you can redistribute it and/or modify
+% it under the terms of the GNU Lesser General Public License as
+% published by the Free Software Foundation.  A copy of the license
+% agreement is provided in the file named "LICENSE.txt" included with
+% this software distribution and also available online as
+% http://sbml.org/software/libsbml/license.html
+
+% assume not enabled
+fbcEnabled = 0;
+
+if (isoctave() == '0')
+  filename = fullfile(tempdir, 'fbc.xml');
+else
+  filename = fullfile(pwd, 'fbc.xml');
+end;
+writeTempFile(filename);
+
+try
+  [m, e] = TranslateSBML(filename, 1, 0);
+
+  if (length(e) == 0 && isfield(m, 'fbc_version') == 1 )
+    fbcEnabled = 1;
+  end;
+
+  delete(filename);
+
+catch
+
+  delete(filename);
+
+  return
+end;
+
+
+
+
+function writeTempFile(filename)
+
+fout = fopen(filename, 'w');
+
+fprintf(fout, '<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n');
+fprintf(fout, '<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" ');
+fprintf(fout, 'xmlns:fbc=\"http://www.sbml.org/sbml/level3/version1/fbc/version1\" ');
+fprintf(fout, 'level=\"3\" version=\"1\" fbc:required=\"false\">\n');
+fprintf(fout, '  <model/>\n</sbml>\n');
+
+fclose(fout);