loadEcModel

 loadEcModel
   Loads the ecModel that matches the modelAdapter. By default, it loads
   the models/ecModel.yml in the directory specified as param.path in
   the modelAdapter. Alternative files in the same folder can be loaded by
   providing the appropriate filename. If loading models from other
   locations, one can directly use readYAMLmodel.

 Input:
   filename        name of the ecModel file (Optional, default 'ecModel.yml').
                   Fill should be located in the models/ subfolder of
                   param.path as specified in the modelAdapter.
   modelAdapter    a loaded model adapter, from where the model folder is
                   read (Optional, will otherwise use the default model adapter).

 Output:
   model           an ecModel in GECKO 3 format (with ecModel.ec structure)

 Usage:
   model = loadEcModel(filename, modelAdapter)

0001 function model = loadEcModel(filename, modelAdapter)
0002 % loadEcModel
0003 %   Loads the ecModel that matches the modelAdapter. By default, it loads
0004 %   the models/ecModel.yml in the directory specified as param.path in
0005 %   the modelAdapter. Alternative files in the same folder can be loaded by
0006 %   providing the appropriate filename. If loading models from other
0007 %   locations, one can directly use readYAMLmodel.
0008 %
0009 % Input:
0010 %   filename        name of the ecModel file (Optional, default 'ecModel.yml').
0011 %                   Fill should be located in the models/ subfolder of
0012 %                   param.path as specified in the modelAdapter.
0013 %   modelAdapter    a loaded model adapter, from where the model folder is
0014 %                   read (Optional, will otherwise use the default model adapter).
0015 %
0016 % Output:
0017 %   model           an ecModel in GECKO 3 format (with ecModel.ec structure)
0018 %
0019 % Usage:
0020 %   model = loadEcModel(filename, modelAdapter)
0021 
0022 if nargin < 2 || isempty(modelAdapter)
0023     modelAdapter = ModelAdapterManager.getDefault();
0024     if isempty(modelAdapter)
0025         error('Either send in a modelAdapter or set the default model adapter in the ModelAdapterManager.')
0026     end
0027 end
0028 params = modelAdapter.getParameters();
0029 if nargin < 1 || isempty(filename)
0030     filename = 'ecModel.yml';
0031 else
0032 end
0033 
0034 if ~endsWith(filename,{'yml','yaml'})
0035     error(['ecModels should preferably be distributed in YAML file format, ', ...
0036            'as otherwise model content will be lost. If the model is in ', ...
0037            'SBML format, you can use the usual importModel function to load ', ...
0038            'this as any other genome-scale model.'])
0039 end
0040 
0041 filename = fullfile(params.path,'models',filename); 
0042 if endsWith(filename,{'yml','yaml'})
0043     model = readYAMLmodel(filename);
0044 elseif endsWith(filename,{'xml','sbml'})
0045     model = importModel(filename);
0046 end
0047 end