SiLeBAT/FSK-Lab

File `MathUtilities.java` has 284 lines of code (exceeds 250 allowed). Consider refactoring.
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 * Copyright (c) 2015 Federal Institute for Risk Assessment (BfR), Germany
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
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 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 *
 * Contributors:
 *     Department Biological Safety - BfR
 *******************************************************************************/
package de.bund.bfr.knime.pmm.common.math;
 
import java.util.ArrayList;
import java.util.List;
import java.util.Random;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
 
import org.apache.commons.math3.distribution.TDistribution;
import org.lsmp.djep.djep.DJep;
import org.lsmp.djep.djep.DiffRulesI;
import org.lsmp.djep.djep.diffRules.MacroDiffRules;
import org.lsmp.djep.xjep.MacroFunction;
import org.nfunk.jep.ASTConstant;
import org.nfunk.jep.ASTFunNode;
import org.nfunk.jep.ASTVarNode;
import org.nfunk.jep.Node;
import org.nfunk.jep.ParseException;
 
`MathUtilities` has 22 methods (exceeds 20 allowed). Consider refactoring.
public class MathUtilities {
 
    public static double EPSILON = 0.00001;
 
    private static Random random = null;
 
    private MathUtilities() {
    }
 
Method `nodeToString` has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
    public static String nodeToString(Node n) throws Exception {
        if (n instanceof ASTFunNode) {
            String s = n.toString() + "(";
 
            for (int i = 0; i < n.jjtGetNumChildren(); i++) {
                if (i != 0) {
                    s += ",";
                }
 
                s += nodeToString(n.jjtGetChild(i));
            }
 
            return s + ")";
        } else if (n instanceof ASTConstant) {
            return n.toString();
        } else if (n instanceof ASTVarNode) {
            return n.toString();
        } else {
            throw new Exception("Unknown Node");
        }
    }
 
Method `removeNullValues` has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
Refactor this method to reduce its Cognitive Complexity from 17 to the 15 allowed.
    public static void removeNullValues(List<Double> targetValues, List<List<Double>> argumentValues) {
        for (int i = 0; i < targetValues.size(); i++) {
            boolean remove = false;
 
            if (targetValues.get(i) == null) {
                remove = true;
                continue;
            }
 
            if (!remove) {
                for (int j = 0; j < argumentValues.size(); j++) {
                    if (argumentValues.get(j).get(i) == null) {
                        remove = true;
                        break;
                    }
                }
            }
 
            if (remove) {
                targetValues.remove(i);
 
                for (int j = 0; j < argumentValues.size(); j++) {
                    argumentValues.get(j).remove(i);
                }
 
                i--;
            }
        }
    }
 
    public static Random getRandomGenerator() {
        if (random == null) {
            random = new Random();
        }
 
        return random;
    }
 
    public static int getRandomNegativeInt() {
        if (random == null)
            random = new Random();
        int value = random.nextInt();
        if (value > 0)
            value = -value;
        return value;
    }
 
    public static double computeSum(List<Double> values) {
        double sum = 0.0;
 
        for (double v : values) {
            sum += v;
        }
 
        return sum;
    }
 
    public static DJep createParser() {
        DJep parser = new DJep();
 
        parser.setAllowAssignment(true);
        parser.setAllowUndeclared(true);
        parser.setImplicitMul(true);
        parser.addStandardFunctions();
        parser.addStandardDiffRules();
        parser.removeVariable("x");
 
        try {
Define a constant instead of duplicating this literal "log10" 3 times.
            parser.addFunction("log10", new MacroFunction("log10", 1, "ln(x)/ln(10)", parser));
            parser.addDiffRule(new MacroDiffRules(parser, "log10", "1/(x*ln(10))"));
 
            parser.addDiffRule(new ZeroDiffRule("<"));
            parser.addDiffRule(new ZeroDiffRule(">"));
            parser.addDiffRule(new ZeroDiffRule("<="));
            parser.addDiffRule(new ZeroDiffRule(">="));
            parser.addDiffRule(new ZeroDiffRule("&&"));
            parser.addDiffRule(new ZeroDiffRule("||"));
            parser.addDiffRule(new ZeroDiffRule("=="));
            parser.addDiffRule(new ZeroDiffRule("!="));
        } catch (ParseException e) {
            e.printStackTrace();
        }
 
        return parser;
    }
 
    public static String replaceVariable(String formula, String var, String newVar) {
        if (var.equals(newVar)) {
            return formula;
        }
 
        String newFormular = " " + formula + " ";
 
        for (int i = 1; i < newFormular.length() - var.length(); i++) {
            boolean matches = newFormular.substring(i, i + var.length()).equals(var);
            boolean start = !isVariableCharacter(newFormular.charAt(i - 1));
            boolean end = !isVariableCharacter(newFormular.charAt(i + var.length()));
 
            if (matches && start && end) {
                String prefix = newFormular.substring(0, i);
                String postfix = newFormular.substring(i + var.length());
 
                newFormular = prefix + newVar + postfix;
                i = prefix.length() + newVar.length();
            }
        }
 
        return newFormular.replace(" ", "");
    }
 
Method `isFunctionDefinedFor` has 7 arguments (exceeds 4 allowed). Consider refactoring.
    public static boolean isFunctionDefinedFor(String formula, List<String> parameters, List<Double> parameterValues,
            String variable, double minValue, double maxValue, int steps) {
        DJep parser = createParser();
        Node function = null;
 
        parser.addVariable(variable, 0.0);
 
Similar blocks of code found in 3 locations. Consider refactoring.
        for (int i = 0; i < parameters.size(); i++) {
            parser.addConstant(parameters.get(i), parameterValues.get(i));
        }
 
        try {
            function = parser.parse(formula.substring(formula.indexOf("=") + 1));
 
            for (int i = 0; i < steps; i++) {
                double value = minValue + (double) i / (double) (steps - 1) * (maxValue - minValue);
 
                parser.setVarValue(variable, value);
 
                if (!(parser.evaluate(function) instanceof Double)) {
                    return false;
                }
            }
        } catch (ParseException e) {
            e.printStackTrace();
        }
 
        return true;
    }
 
Method `evaluateFunction` has 5 arguments (exceeds 4 allowed). Consider refactoring.
Method `evaluateFunction` has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
    public static List<Double> evaluateFunction(String formula, List<String> parameters, List<Double> parameterValues,
            List<String> variables, List<List<Double>> variableValues) {
        List<Double> values = new ArrayList<>();
        DJep parser = createParser();
 
Similar blocks of code found in 3 locations. Consider refactoring.
        for (int i = 0; i < parameters.size(); i++) {
            parser.addConstant(parameters.get(i), parameterValues.get(i));
        }
 
        for (int i = 0; i < variables.size(); i++) {
            parser.addVariable(variables.get(i), 0.0);
        }
 
        try {
            Node function = parser.parse(formula.substring(formula.indexOf("=") + 1));
 
            for (int i = 0; i < variableValues.get(0).size(); i++) {
Identical blocks of code found in 2 locations. Consider refactoring.
                for (int j = 0; j < variables.size(); j++) {
                    parser.setVarValue(variables.get(j), variableValues.get(j).get(i));
                }
 
                values.add((Double) parser.evaluate(function));
            }
        } catch (ParseException e) {
            e.printStackTrace();
        }
 
        return values;
    }
 
    private static class ZeroDiffRule implements DiffRulesI {
 
        private String name;
 
        public ZeroDiffRule(String name) {
            this.name = name;
        }
 
        @Override
Method `differentiate` has 5 arguments (exceeds 4 allowed). Consider refactoring.
        public Node differentiate(ASTFunNode node, String var, Node[] children, Node[] dchildren, DJep djep)
                throws ParseException {
            return djep.getNodeFactory().buildConstantNode(0.0);
        }
 
        @Override
        public String getName() {
            return name;
        }
 
    }
 
    public static Double getMSE(Double rmse) {
        if (rmse == null) {
            return null;
        }
 
        return rmse * rmse;
    }
 
    public static Double getRMSE(double sse, double numParam, double numSample) {
        if (numParam >= numSample) {
            return null;
        }
 
        return Math.sqrt(sse / (numSample - numParam));
    }
 
    public static Double getRMSE(double sse, double numSample) {
        return Math.sqrt(sse / numSample);
    }
 
    public static Double getRSquared(double sse, List<Double> targetValues) {
        double targetMean = MathUtilities.computeSum(targetValues) / targetValues.size();
        double targetTotalSumOfSquares = 0.0;
 
        for (int i = 0; i < targetValues.size(); i++) {
            targetTotalSumOfSquares += Math.pow(targetValues.get(i) - targetMean, 2.0);
        }
 
Make sure "targetTotalSumOfSquares" can't be zero before doing this division.
        double rSquared = 1 - sse / targetTotalSumOfSquares;
 
        // rSquare < 0 möglich, siehe hier:
        // http://mars.wiwi.hu-berlin.de/mediawiki/sk/index.php/Bestimmtheitsmass
        return Math.max(rSquared, 0.0);
    }
 
    public static Double akaikeCriterion(final int numParam, final int numSample, final double sse) {
        if (numSample <= numParam + 2) {
            return null;
        }
 
        return numSample * Math.log(sse / numSample) + 2 * (numParam + 1)
                + 2 * (numParam + 1) * (numParam + 2) / (numSample - numParam - 2);
    }
 
    public static double getPValue(double tValue, int degreesOfFreedom) {
        TDistribution dist = new TDistribution(degreesOfFreedom);
 
        return 1.0 - dist.probability(-Math.abs(tValue), Math.abs(tValue));
    }
 
    public static boolean isVariableCharacter(char ch) {
        return Character.isLetterOrDigit(ch) || ch == '_' || ch == '$';
    }
 
    public static int generateID(int seed) {
        Random rand = new Random(seed);
        int id = rand.nextInt();
 
        if (id > 0) {
            id = -id;
        }
 
        return id;
    }
 
    public static String getBoundaryCondition(String formula) {
        Pattern p = Pattern.compile("\\*\\(\\(\\(\\(\\(.+\\)\\)\\)\\)\\)$");
        Matcher m = p.matcher(formula);
 
        while (m.find()) {
            String s = m.group();
 
            s = s.substring(6, s.length() - 5);
 
            if (countOccurences(s, '(') == countOccurences(s, ')')) {
                return s;
            }
        }
 
        return null;
    }
 
Method `getAllButBoundaryCondition` has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
    public static String getAllButBoundaryCondition(String formula) {
        String cond = getBoundaryCondition(formula);
 
        if (cond != null) {
            String f = formula.replace("*(((((" + cond + ")))))", "");
 
            int i = f.indexOf("=");
 
            if (f.charAt(i + 1) == '(' && f.endsWith(")")) {
                String withoutBrackets = f.substring(i + 2, f.length() - 1);
 
                try {
                    createParser().parse(withoutBrackets);
                    f = f.substring(0, i + 1) + withoutBrackets;
                } catch (ParseException e) {
                    // Do not remove brackets when expression without brackets
                    // cannot be parsed
                }
            }
 
            return f;
        } else {
            return formula;
        }
    }
 
    public static String getFormula(String formula, String boundaryCondition) {
        if (boundaryCondition != null && !boundaryCondition.isEmpty()) {
            int i = formula.indexOf("=");
 
            return formula.substring(0, i + 1) + "(" + formula.substring(i + 1) + ")*(((((" + boundaryCondition
                    + ")))))";
        } else {
            return formula;
        }
    }
 
    public static boolean isValid(Object value) {
        return value instanceof Double && !((Double) value).isNaN() && !((Double) value).isInfinite();
    }
 
    private static int countOccurences(String s, char c) {
        int n = 0;
 
        for (int i = 0; i < s.length(); i++) {
            if (s.charAt(i) == c) {
                n++;
            }
        }
 
        return n;
    }
 
}