Adding current version of JEInterface (Matlab Interface) to resource folder

resources/MatlabInterface/@JEInterface/JEInterface.m

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+function int = JEInterface(interfaceName, fhandle, range, varargin)
+% JavaEva Interface for Matlab
+%       JEInterface(interfaceName, fhandle, range [, optset, defaultargs])
+% arguments: 
+%   interfaceName: a JEInterface instance needs to know its own
+%       name as a String to allow callbacks from Java.
+%   fhandle: a function handle defining the optimization target.
+%   range: a 2 x dim array defining the solution subspace with lower and
+%      upper bounds.
+%   optset: (optional) an optimset struct defining optimization parameters,
+%       especially tolerance and maximum function calls. Defaults to the
+%       JavaEvA default values.
+%   defaultArgs: (optional) additional constant argument to the target
+%       function, empty by default.
+
+int.args = [];
+int.opts = optimset('MaxFunEvals', javaeva.OptimizerFactory.getDefaultFitCalls, 'TolX', 1e-4, 'TolFun', 1e-4);
+int.finished = 1;
+int.result = [];
+int.callback='';
+int.f = '';
+int.dim = 0;
+int.range = [];
+int.mp = [];
+int.msg = '';
+int.funCalls = 0;
+
+if (isa(interfaceName, 'char'));
+    int.callback = interfaceName;
+else 
+    error('Wrong first argument type, expected char');
+end
+if (isa(fhandle, 'function_handle'))
+    int.f = fhandle;
+else
+    error('Wrong second argument type, expected function_handle');
+end
+if (isa(range, 'double') && (size(range,1) == 2))
+    int.dim=length(range);
+    int.range=transpose(range);
+else
+    error('Wrong third argument type, expected double array of 2 x dim');
+end
+
+int = class(int,'JEInterface');
+
+switch nargin
+    case {3}
+    case {4,5}
+        if (isa(varargin{1}, 'struct'))
+            int.opts = varargin{1};
+            if (isempty(int.opts.TolX)) ; int.opts.TolX = 1e-4; end
+            if (isempty(int.opts.TolFun)) ; int.opts.TolFun = 1e-4; end
+        else
+            error('Wrong fifth argument type, expected optimset struct');
+        end
+        if (nargin > 4)        
+            int.args = varargin{2};
+        end
+    otherwise
+        error('Wrong number of arguments!')
+end
+
+% finally create the java object
+int.mp = javaeva.server.go.problems.MatlabProblem(int.callback, int.dim, int.range);
+
+        
+
+

resources/MatlabInterface/@JEInterface/evaluateJE.m

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+function v = evaluate(int)
+% Interface function for JavaEvA 2.
+% Will be called by the MatlabProblem to obtain the target function value
+% for a sample individual.
+
+x = int.mp.getCurrentDoubleArray;
+if (isempty(int.args))
+    int.mp.setResult(feval(int.f, x));
+else
+    int.mp.setResult(feval(int.f, x, int.args));
+end

resources/MatlabInterface/@JEInterface/getMessage.m

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+function str = getMessage(int)
+% Get information string received from JavaEvA.
+
+str = int.msg;

resources/MatlabInterface/@JEInterface/getOpt.m

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+function val = getOpt(int, optName)
+% Set a single optimset value within the JI instance.
+% Arguments: 
+%           int: the JEInterface instance
+%           optName: name of the option to change, e.g. 'MaxFunEvals'
+%           optVal: new value
+
+val = optimget(int.opts, optName);

resources/MatlabInterface/@JEInterface/getOptions.m

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+function opts = getOptions(int)
+% Return the current optimset structure used by the interface
+
+opts = int.opts;

resources/MatlabInterface/@JEInterface/getResult.m

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+function v = getResult(int)
+% Returns the optimization solution if the run has been finished, or an
+% intermediate solution if the run has not finished yet or an empty array
+% if there is no intermediate solution yet.
+
+if (isFinished(int)) 
+    v = int.result;
+else
+    v = int.mp.getIntermediateResult();
+end

resources/MatlabInterface/@JEInterface/isFinished.m

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+function b = isFinished(int)
+% Returns 1 if the optimization was finished, else 0
+
+b = int.finished;

resources/MatlabInterface/@JEInterface/optimize.m

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+function retInt = optimize(int, optType, varargin)
+% Start a JavaEvA optimization run.
+%       optimize(interface, optType, [, outputFilePrefix ] )
+% where
+%       interface: instance of JEInterface
+%       optType: integer indicating the type of the optimization strategy
+%       to use.
+%       resultFilePrefix: (optional) char prefix for an optional verbose
+%           output file
+
+if (int.finished == 0) 
+    error('please wait for the current run to finish');
+end
+if ((nargin == 2) || (nargin == 3))
+    if (nargin == 3) 
+        outputFilePrefix = varargin{1};
+    else
+        outputFilePrefix = 'none';
+    end
+
+    if (~isa(int, 'JEInterface') || ~isscalar(optType) || ~isa(outputFilePrefix, 'char'))
+        error('Invalid argument!')
+    end
+    int.finished = 0;
+    int.msg = 'running...';
+    % adapt options possibly changed by the user, concerning
+    xTol = int.opts.TolX;
+    maxEvals = int.opts.MaxFunEvals;
+    fTol = int.opts.TolFun;
+    % construct Terminators
+    import javaeva.server.go.operators.terminators.PhenotypeConvergenceTerminator;
+    import javaeva.server.go.operators.terminators.FitnessConvergenceTerminator;    
+    import javaeva.server.go.operators.terminators.CombinedTerminator;
+    import javaeva.server.go.operators.terminators.EvaluationTerminator;
+
+    % set some default values if theyre not given
+    if (isempty(int.opts.TolX)) ; xTol = 1e-4; end
+    if (isempty(int.opts.TolFun)) ; fTol = 1e-4; end
+    % fminsearch, for example, always uses TolX and TolFun with default
+    % values of 1e-4 in . Thats what we do as well
+    convTerm = CombinedTerminator(FitnessConvergenceTerminator(fTol, int32(5), 0, 1), PhenotypeConvergenceTerminator(xTol, 5, 0, 1), 1);
+
+    % if MaxFunEvals is defined additionally, combine an
+    % EvaluationTerminator in disjunction, as Matlab does.
+    if (~isempty(maxEvals))
+        javaeva.OptimizerFactory.setTerminator(convTerm);
+        javaeva.OptimizerFactory.addTerminator(EvaluationTerminator(maxEvals), 0);
+    end
+    
+    int.mp.optimize(optType, outputFilePrefix);
+else
+    error('Wrong number of arguments!')
+end
+retInt=int;

resources/MatlabInterface/@JEInterface/setOpt.m

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+function int = setOpt(int, optName, optVal)
+% Set a single optimset value within the JI instance.
+% Arguments: 
+%           int: the JEInterface instance
+%           optName: name of the option to change, e.g. 'MaxFunEvals'
+%           optVal: new value
+
+opts = optimset(int.opts, optName, optVal);
+int.opts = opts;

resources/MatlabInterface/@JEInterface/setOptions.m

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+function int = setOptions(int, options)
+% Set the optimization options for the interface.
+%   parameters:
+%       int:    an interface instance
+%       options:    an optimset instance
+
+int.opts = options;

resources/MatlabInterface/@JEInterface/setResultJE.m

@@ -0,0 +1,9 @@
+function int = setJEResult(int, result)
+% Interface function to be called by JavaEvA 2.
+
+% Write back the solution and retrieve some additional data.
+
+int.result = result;
+int.finished = 1;
+int.msg=int.mp.getInfoString;
+int.funCalls=int.mp.getFunctionCalls;

resources/MatlabInterface/@JEInterface/stopOptimize.m

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+function int = stopOptimize(int)
+% Stop a running optimization
+
+int.mp.stopOptimize