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

resources/MatlabInterface/@JEInterface/optimize.m

@@ -0,0 +1,54 @@
+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;