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Some cleanup and starting test file.

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This commit is contained in:
leandrohw 2018-03-25 21:50:32 -07:00
parent 8553a3dcef
commit e493cfc7bb
20 changed files with 402 additions and 223 deletions
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13
learn/src/main/java/edu/utah/ece/async/ibiosim/learn/parameterestimator/ParameterEstimator.java
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@ -44,18 +44,6 @@ import edu.utah.ece.async.ibiosim.learn.parameterestimator.methods.sres.SRES;
*/
public class ParameterEstimator
{
static double relativeError = 1e-6;
static double absoluteError = 1e-9;
static int numSteps;
static double maxTimeStep = Double.POSITIVE_INFINITY;
static double minTimeStep = 0.0;
static long randomSeed = 0;
static int runs = 1;
static double stoichAmpValue = 1.0;
static boolean genStats = false;
static String selectedSimulator = "";
static ArrayList<String> interestingSpecies = new ArrayList<String>();
static String quantityType = "amount";
/**
* This function is used to execute parameter estimation from a given SBML file. The input model serves
@ -83,7 +71,6 @@ public class ParameterEstimator
double[] lowerbounds = new double[numberofparameters];
double[] upperbounds = new double[numberofparameters];
HierarchicalSimulation sim = new HierarchicalODERKSimulator(properties, false);
sim.initialize(randomSeed, 0);
for (int i = 0; i < numberofparameters; i++)
{