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de.bund.bfr.knime.pmm.common/src/de/bund/bfr/knime/pmm/common/math/MathUtilities.java

Summary

Maintainability
D
1 day
Test Coverage

File MathUtilities.java has 284 lines of code (exceeds 250 allowed). Consider refactoring.
Open

/*******************************************************************************
 * 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

MathUtilities has 22 methods (exceeds 20 allowed). Consider refactoring.
Open

public class MathUtilities {

    public static double EPSILON = 0.00001;

    private static Random random = null;

Method removeNullValues has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
Open

    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) {

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method nodeToString has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    public static String nodeToString(Node n) throws Exception {
        if (n instanceof ASTFunNode) {
            String s = n.toString() + "(";

            for (int i = 0; i < n.jjtGetNumChildren(); i++) {

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method isFunctionDefinedFor has 7 arguments (exceeds 4 allowed). Consider refactoring.
Open

    public static boolean isFunctionDefinedFor(String formula, List<String> parameters, List<Double> parameterValues,
            String variable, double minValue, double maxValue, int steps) {

Method getAllButBoundaryCondition has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

    public static String getAllButBoundaryCondition(String formula) {
        String cond = getBoundaryCondition(formula);

        if (cond != null) {
            String f = formula.replace("*(((((" + cond + ")))))", "");

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Method evaluateFunction has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

    public static List<Double> evaluateFunction(String formula, List<String> parameters, List<Double> parameterValues,
            List<String> variables, List<List<Double>> variableValues) {

Method differentiate has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

        public Node differentiate(ASTFunNode node, String var, Node[] children, Node[] dchildren, DJep djep)

Method evaluateFunction has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    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();

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Refactor this method to reduce its Cognitive Complexity from 17 to the 15 allowed.
Open

    public static void removeNullValues(List<Double> targetValues, List<List<Double>> argumentValues) {

Cognitive Complexity is a measure of how hard the control flow of a method is to understand. Methods with high Cognitive Complexity will be difficult to maintain.

See

Define a constant instead of duplicating this literal "log10" 3 times.
Open

            parser.addFunction("log10", new MacroFunction("log10", 1, "ln(x)/ln(10)", parser));

Duplicated string literals make the process of refactoring error-prone, since you must be sure to update all occurrences.

On the other hand, constants can be referenced from many places, but only need to be updated in a single place.

Noncompliant Code Example

With the default threshold of 3:

public void run() {
  prepare("action1");                              // Noncompliant - "action1" is duplicated 3 times
  execute("action1");
  release("action1");
}

@SuppressWarning("all")                            // Compliant - annotations are excluded
private void method1() { /* ... */ }
@SuppressWarning("all")
private void method2() { /* ... */ }

public String method3(String a) {
  System.out.println("'" + a + "'");               // Compliant - literal "'" has less than 5 characters and is excluded
  return "";                                       // Compliant - literal "" has less than 5 characters and is excluded
}

Compliant Solution

private static final String ACTION_1 = "action1";  // Compliant

public void run() {
  prepare(ACTION_1);                               // Compliant
  execute(ACTION_1);
  release(ACTION_1);
}

Exceptions

To prevent generating some false-positives, literals having less than 5 characters are excluded.

Make sure "targetTotalSumOfSquares" can't be zero before doing this division.
Open

        double rSquared = 1 - sse / targetTotalSumOfSquares;

If the denominator to a division or modulo operation is zero it would result in a fatal error.

When working with double or float, no fatal error will be raised, but it will lead to unusual result and should be avoided anyway.

This rule supports primitive int, long, double, float as well as BigDecimal and BigInteger.

Noncompliant Code Example

void test_divide() {
  int z = 0;
  if (unknown()) {
    // ..
    z = 3;
  } else {
    // ..
  }
  z = 1 / z; // Noncompliant, possible division by zero
}

Compliant Solution

void test_divide() {
  int z = 0;
  if (unknown()) {
    // ..
    z = 3;
  } else {
    // ..
    z = 1;
  }
  z = 1 / z;
}

See

  • MITRE, CWE-369 - Divide by zero
  • CERT, NUM02-J. - Ensure that division and remainder operations do not result in divide-by-zero errors
  • CERT, INT33-C. - Ensure that division and remainder operations do not result in divide-by-zero errors

Identical blocks of code found in 2 locations. Consider refactoring.
Open

                for (int j = 0; j < variables.size(); j++) {
                    parser.setVarValue(variables.get(j), variableValues.get(j).get(i));
                }
de.bund.bfr.knime.pmm.common/src/de/bund/bfr/knime/pmm/common/math/ParameterOptimizer.java on lines 206..209

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 44.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 3 locations. Consider refactoring.
Open

        for (int i = 0; i < parameters.size(); i++) {
            parser.addConstant(parameters.get(i), parameterValues.get(i));
        }
de.bund.bfr.knime.pmm.common/src/de/bund/bfr/knime/pmm/common/chart/Plotable.java on lines 940..942
de.bund.bfr.knime.pmm.common/src/de/bund/bfr/knime/pmm/common/math/MathUtilities.java on lines 215..217

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 40.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

Similar blocks of code found in 3 locations. Consider refactoring.
Open

        for (int i = 0; i < parameters.size(); i++) {
            parser.addConstant(parameters.get(i), parameterValues.get(i));
        }
de.bund.bfr.knime.pmm.common/src/de/bund/bfr/knime/pmm/common/chart/Plotable.java on lines 940..942
de.bund.bfr.knime.pmm.common/src/de/bund/bfr/knime/pmm/common/math/MathUtilities.java on lines 187..189

Duplicated Code

Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

Tuning

This issue has a mass of 40.

We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

Refactorings

Further Reading

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