jigcell.sbml2.tests
Class SBMLModelTests

java.lang.Object
  junit.framework.Assert
      junit.framework.TestCase
          jigcell.sbml2.tests.SBMLModelTests

All Implemented Interfaces:

junit.framework.Test

Direct Known Subclasses:

AlgebraicModelTests, AssignmentModelTests, BoundaryModelTests, BranchModelTests, CompartmentModelTests, DelayModelTests, EventModelTests, FunctionModelTests, ODEModelTests, UnitModelTests

abstract class SBMLModelTests
extends junit.framework.TestCase

A collection of test methods for pieces of an SBML model.

This code is licensed under the DARPA BioCOMP Open Source License. See LICENSE for more details.

Author:

Nicholas Allen

Field Summary

protected boolean	cycle
protected Model	model
protected java.lang.String	modelName

Constructor Summary

SBMLModelTests(java.lang.String name)
Creates a new test for an SBML model.

Method Summary

private boolean	doubleEquals(double d1, double d2)
protected void	setUp()
private boolean	stringEquals(java.lang.String s1, java.lang.String s2)
protected Compartment	testCompartment(java.lang.String name, boolean constant, java.lang.String outside, double size, int dimensions, java.lang.String units)
protected FunctionDefinition	testFunctionDefinition(java.lang.String name)
private Parameter	testParameter(java.util.Iterator iterator, java.lang.String name, double value, java.lang.String unit, boolean constant)
protected Parameter	testParameter(Reaction reaction, java.lang.String name, double value)
protected Parameter	testParameter(java.lang.String name, double value)
protected Parameter	testParameter(java.lang.String name, double value, java.lang.String unit, boolean constant)
protected Reaction	testReaction(java.lang.String name, java.lang.Boolean fast, boolean reversible)
protected ModifierSpeciesReference	testReactionModifier(java.util.List modifiers, java.lang.String name)
protected SpeciesReference	testReactionModifier(java.util.List modifiers, java.lang.String name, double stoichiometry)
protected Species	testSpecies(java.lang.String name, java.lang.String compartment, double initialConcentration, boolean constant, boolean boundaryCondition)
protected void	testUnit(Unit unit, int exponent, java.lang.String kindName, double multiplier, double offset, int scale)
protected UnitDefinition	testUnitDefinition(java.lang.String name, int size)

Methods inherited from class junit.framework.TestCase

countTestCases, createResult, getName, run, run, runBare, runTest, setName, tearDown, toString

Methods inherited from class junit.framework.Assert

assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertFalse, assertFalse, assertNotNull, assertNotNull, assertNotSame, assertNotSame, assertNull, assertNull, assertSame, assertSame, assertTrue, assertTrue, fail, fail

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

cycle

protected boolean cycle

model

protected Model model

modelName

protected java.lang.String modelName

Constructor Detail

SBMLModelTests

public SBMLModelTests(java.lang.String name)

Creates a new test for an SBML model.

Parameters:

name - Test name

Method Detail

setUp

protected void setUp()
              throws java.lang.Exception

Overrides:

setUp in class junit.framework.TestCase

Throws:

java.lang.Exception

testCompartment

protected Compartment testCompartment(java.lang.String name,
                                      boolean constant,
                                      java.lang.String outside,
                                      double size,
                                      int dimensions,
                                      java.lang.String units)

testFunctionDefinition

protected FunctionDefinition testFunctionDefinition(java.lang.String name)

testParameter

protected Parameter testParameter(java.lang.String name,
                                  double value)

testParameter

protected Parameter testParameter(java.lang.String name,
                                  double value,
                                  java.lang.String unit,
                                  boolean constant)

testParameter

protected Parameter testParameter(Reaction reaction,
                                  java.lang.String name,
                                  double value)

testReaction

protected Reaction testReaction(java.lang.String name,
                                java.lang.Boolean fast,
                                boolean reversible)

testReactionModifier

protected ModifierSpeciesReference testReactionModifier(java.util.List modifiers,
                                                        java.lang.String name)

testReactionModifier

protected SpeciesReference testReactionModifier(java.util.List modifiers,
                                                java.lang.String name,
                                                double stoichiometry)

testSpecies

protected Species testSpecies(java.lang.String name,
                              java.lang.String compartment,
                              double initialConcentration,
                              boolean constant,
                              boolean boundaryCondition)

testUnit

protected void testUnit(Unit unit,
                        int exponent,
                        java.lang.String kindName,
                        double multiplier,
                        double offset,
                        int scale)

testUnitDefinition

protected UnitDefinition testUnitDefinition(java.lang.String name,
                                            int size)

doubleEquals

private boolean doubleEquals(double d1,
                             double d2)

stringEquals

private boolean stringEquals(java.lang.String s1,
                             java.lang.String s2)

testParameter

private Parameter testParameter(java.util.Iterator iterator,
                                java.lang.String name,
                                double value,
                                java.lang.String unit,
                                boolean constant)