Change of line endings and test model for SBML

initCobraToolbox.m

@@ -95,16 +95,16 @@ function initCobraToolbox()
     % define the root path of The COBRA Toolbox and change to it.
     CBTDIR = fileparts(which('initCobraToolbox'));
     cd(CBTDIR);
-            
+
     % add the external install folder
     addpath(genpath([CBTDIR filesep 'external' filesep 'install']));
-    
+
     %And the rdir directory
     addpath(genpath([CBTDIR filesep 'external' filesep 'rdir']));
 
     % add the install folder
-    addpath(genpath([CBTDIR filesep 'src' filesep 'base' filesep 'install']));   
-    
+    addpath(genpath([CBTDIR filesep 'src' filesep 'base' filesep 'install']));
+
     % check if git is installed
     checkGit();
 
@@ -203,12 +203,12 @@ function initCobraToolbox()
             fprintf(' Done.\n');
         end
     end
-    
-    %create the Cleanup function    
+
+    %create the Cleanup function
     %get the current content of the init Folder
     dirContent = rdir(['**' filesep '*']);
     finishup = onCleanup(@() removeGitIgnoredNewFiles(CBTDIR,dirContent));
-    
+
     % add the folders of The COBRA Toolbox
     folders = {'tutorials', 'papers', 'binary', 'deprecated', 'src', 'test', '.tmp'};
 
@@ -229,7 +229,7 @@ function initCobraToolbox()
             addpath(genpath(tmpDir));
         end
     end
-    
+
     %Adapt the mac path depending on the mac version.
     if ismac
         adaptMacPath()
@@ -264,7 +264,7 @@ function initCobraToolbox()
     end
 
     % define xml test file
-    xmlTestModel = 'Ec_iAF1260_flux1.xml';
+    xmlTestModel = 'ecoli_core_model.xml';
     xmlTestFile = [getDistributedModelFolder(xmlTestModel) filesep xmlTestModel];
 
     % save the userpath
@@ -303,10 +303,10 @@ function initCobraToolbox()
     % define categories of solvers: LP, MILP, QP, MIQP, NLP
     OPT_PROB_TYPES = {'LP', 'MILP', 'QP', 'MIQP', 'NLP'};
     %Lets define a order of the solvers fields. Starting with the most
-    %common solvers others will be added as needed. 
+    %common solvers others will be added as needed.
     SOLVERS = struct('gurobi',struct(),...
                      'ibm_cplex',struct(),...
-                     'tomlab_cplex',struct(),...                     
+                     'tomlab_cplex',struct(),...
                      'glpk',struct(),...
                      'mosek',struct(),...
                      'matlab',struct());
@@ -371,14 +371,14 @@ function initCobraToolbox()
     % check the installation of the solver
     for i = 1:length(supportedSolversNames)
         %We will validate all solvers in init. After this, all solvers are
-        %checked, whether they actually work and the SOLVERS field is set. 
+        %checked, whether they actually work and the SOLVERS field is set.
         [solverOK,solverInstalled] = changeCobraSolver(supportedSolversNames{i},...
                                      SOLVERS.(supportedSolversNames{i}).type{1},...
                                      0, false, 2);
-        if solverOK            
-            SOLVERS.(supportedSolversNames{i}).working = true;        
+        if solverOK
+            SOLVERS.(supportedSolversNames{i}).working = true;
         end
-        SOLVERS.(supportedSolversNames{i}).installed = solverInstalled;        
+        SOLVERS.(supportedSolversNames{i}).installed = solverInstalled;
     end
 
     if ENV_VARS.printLevel
@@ -539,21 +539,21 @@ function initCobraToolbox()
     if status_setSSLVerify ~= 0
         fprintf(strrep(result_setSSLVerify, '\', '\\'));
         warning('Your global git configuration could not be restored.');
-    end    
-    
+    end
+
     %Finally set up the COBRA System path
     addCOBRABinaryPathToSystemPath();
-        
+
     % change back to the current directory
     cd(currentDir);
-    
+
     % clear all temporary variables
     % Note: global variables are kept in memory - DO NOT clear all the variables!
     if ENV_VARS.printLevel
         clearvars
     end
-        
-    
+
+
 end
 
 function checkGit()
@@ -654,4 +654,4 @@ function checkGit()
             end
         end
     end
-end
+end