org.sbml.jsbml.ext.arrays.util

Class ArraysMath

java.lang.Object

org.sbml.jsbml.ext.arrays.util.ArraysMath

public class ArraysMath
extends Object

Since:

1.0

Version:

$Rev$

Author:

Leandro Watanabe

Last modified:

Jun 26, 2014

Constructor Summary

Constructors

Constructor and Description
ArraysMath()

Method Summary

Modifier and Type	Method and Description
static boolean	checkVectorAssignment(org.sbml.jsbml.Model model, org.sbml.jsbml.MathContainer mathContainer)
static boolean	checkVectorMath(org.sbml.jsbml.Model model, org.sbml.jsbml.MathContainer mathContainer)
static boolean	evaluateBounds(Map<String,Double> dimensionSizes, org.sbml.jsbml.ASTNode math, double size) This method is used to check if the math does not evaluate to a negative number or to a value greater or equal to a given size value.
static boolean	evaluateIndexBounds(org.sbml.jsbml.Model model, Index index) This method is used to check if the index math does not go out of bounds.
static boolean	evaluateIndexBounds(org.sbml.jsbml.Model model, org.sbml.jsbml.SBase reference, int arrayDim, org.sbml.jsbml.ASTNode math, Map<String,Double> dimSizes) This method checks if adding an Index object to a parent SBase object for referencing another SBase object does not cause out-of-bounds issues.
static boolean	evaluateIndexBounds(org.sbml.jsbml.Model model, org.sbml.jsbml.SBase parent, String refAttribute, org.sbml.jsbml.ASTNode math, int arrayDim) This method checks if adding an Index object to a parent SBase object for referencing another SBase object does not cause out-of-bounds issues.
static boolean	evaluateSelectorBounds(org.sbml.jsbml.Model model, org.sbml.jsbml.MathContainer mathContainer) This is used to check if the arguments of a selector function does not go out of bounds.
static Map<String,Double>	getDimensionSizes(org.sbml.jsbml.Model model, ArraysSBasePlugin arraysSBasePlugin) This method maps a dimension id to the size of the dimension object.
static Map<String,Double>	getLowerBound(Map<String,Double> dimSizes) This method is used to get the lower bound index from a collection of Dimension objects.
static int	getSize(org.sbml.jsbml.Model model, Dimension dimension) Gets the size of a Dimension object.
static Map<String,Double>	getUpperBound(Map<String,Double> dimSizes) This method is used to get the upper bound index from a collection of Dimension objects.
static Map<Integer,Integer>	getVectorDimensionSizes(org.sbml.jsbml.Model model, org.sbml.jsbml.ASTNode math) This is used to obtain a map containing a pair of array depth level and its size.
static boolean	isStaticallyComputable(org.sbml.jsbml.Model model, org.sbml.jsbml.ASTNode math, String... constantIds) This method is used to determine whether a MathContainer object is statically computable given a list of ids that can appear in the math.
static boolean	isStaticallyComputable(org.sbml.jsbml.Model model, Index index) This method is used to determine whether a MathContainer object is statically computable.
static boolean	isStaticallyComputable(org.sbml.jsbml.Model model, org.sbml.jsbml.MathContainer mathContainer) This method is used to determine whether a MathContainer object is statically computable.
static boolean	isStaticallyComputable(org.sbml.jsbml.Model model, org.sbml.jsbml.MathContainer mathContainer, String... constantIds) This method is used to determine whether a MathContainer object is statically computable given a list of ids that can appear in the math.
static boolean	isVectorBalanced(org.sbml.jsbml.Model model, org.sbml.jsbml.MathContainer mathContainer)
static boolean	isVectorOperation(org.sbml.jsbml.ASTNode math)

Methods inherited from class java.lang.Object

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

Constructor Detail

ArraysMath

public ArraysMath()

Method Detail

evaluateBounds

public static boolean evaluateBounds(Map<String,Double> dimensionSizes,
                                     org.sbml.jsbml.ASTNode math,
                                     double size)

This method is used to check if the math does not evaluate to a negative number or to a value greater or equal to a given size value.

Parameters:

dimensionSizes -

math -

size -

Returns:

evaluateIndexBounds

public static boolean evaluateIndexBounds(org.sbml.jsbml.Model model,
                                          Index index)

This method is used to check if the index math does not go out of bounds.

Parameters:

model -

index -

Returns:

evaluateIndexBounds

public static boolean evaluateIndexBounds(org.sbml.jsbml.Model model,
                                          org.sbml.jsbml.SBase reference,
                                          int arrayDim,
                                          org.sbml.jsbml.ASTNode math,
                                          Map<String,Double> dimSizes)

This method checks if adding an Index object to a parent SBase object for referencing another SBase object does not cause out-of-bounds issues.

Parameters:

model -

reference -

arrayDim -

math -

dimSizes -

Returns:

evaluateIndexBounds

public static boolean evaluateIndexBounds(org.sbml.jsbml.Model model,
                                          org.sbml.jsbml.SBase parent,
                                          String refAttribute,
                                          org.sbml.jsbml.ASTNode math,
                                          int arrayDim)

This method checks if adding an Index object to a parent SBase object for referencing another SBase object does not cause out-of-bounds issues.

Parameters:

model -

parent -

refAttribute -

math -

arrayDim -

Returns:

evaluateSelectorBounds

public static boolean evaluateSelectorBounds(org.sbml.jsbml.Model model,
                                             org.sbml.jsbml.MathContainer mathContainer)

This is used to check if the arguments of a selector function does not go out of bounds.

Parameters:

model -

mathContainer -

Returns:

getSize

public static int getSize(org.sbml.jsbml.Model model,
                          Dimension dimension)

Gets the size of a Dimension object.

Parameters:

model -

dimension -

Returns:

getDimensionSizes

public static Map<String,Double> getDimensionSizes(org.sbml.jsbml.Model model,
                                                   ArraysSBasePlugin arraysSBasePlugin)

This method maps a dimension id to the size of the dimension object.

Parameters:

model -

arraysSBasePlugin -

Returns:

getLowerBound

public static Map<String,Double> getLowerBound(Map<String,Double> dimSizes)

This method is used to get the lower bound index from a collection of Dimension objects.

Parameters:

dimSizes -

Returns:

getUpperBound

public static Map<String,Double> getUpperBound(Map<String,Double> dimSizes)

This method is used to get the upper bound index from a collection of Dimension objects.

Parameters:

dimSizes -

Returns:

isStaticallyComputable

public static boolean isStaticallyComputable(org.sbml.jsbml.Model model,
                                             Index index)

This method is used to determine whether a MathContainer object is statically computable.

Parameters:

model -

index -

Returns:

isStaticallyComputable

public static boolean isStaticallyComputable(org.sbml.jsbml.Model model,
                                             org.sbml.jsbml.MathContainer mathContainer)

This method is used to determine whether a MathContainer object is statically computable.

Parameters:

model -

mathContainer -

Returns:

isStaticallyComputable

public static boolean isStaticallyComputable(org.sbml.jsbml.Model model,
                                             org.sbml.jsbml.MathContainer mathContainer,
                                             String... constantIds)

This method is used to determine whether a MathContainer object is statically computable given a list of ids that can appear in the math.

Parameters:

model -

mathContainer -

constantIds -

Returns:

isStaticallyComputable

public static boolean isStaticallyComputable(org.sbml.jsbml.Model model,
                                             org.sbml.jsbml.ASTNode math,
                                             String... constantIds)

This method is used to determine whether a MathContainer object is statically computable given a list of ids that can appear in the math.

Parameters:

model -

math -

constantIds -

Returns:

isVectorOperation

public static boolean isVectorOperation(org.sbml.jsbml.ASTNode math)

Parameters:

math -

Returns:

checkVectorMath

public static boolean checkVectorMath(org.sbml.jsbml.Model model,
                                      org.sbml.jsbml.MathContainer mathContainer)

Parameters:

model -

mathContainer -

Returns:

checkVectorAssignment

public static boolean checkVectorAssignment(org.sbml.jsbml.Model model,
                                            org.sbml.jsbml.MathContainer mathContainer)

Parameters:

model -

mathContainer -

Returns:

getVectorDimensionSizes

public static Map<Integer,Integer> getVectorDimensionSizes(org.sbml.jsbml.Model model,
                                                           org.sbml.jsbml.ASTNode math)

This is used to obtain a map containing a pair of array depth level and its size.

Parameters:

model -

math -

Returns:

isVectorBalanced

public static boolean isVectorBalanced(org.sbml.jsbml.Model model,
                                       org.sbml.jsbml.MathContainer mathContainer)

Parameters:

model -

mathContainer -

Returns: