CONVENIENCE

The Convenience folder contains a number of convenience functions for checking information or manipulating math expressions.

Function are:

y = CheckValidUnitKind(kind)

Takes

1. kind, a string representing a unit kind

Returns

1. y =
   • 1 if the string represents a valid unit kind
   • 0 otherwise

NOTE: This is identical to the function isValidUnitKind

newArray = LoseWhiteSpace(charArray)

Takes

1. charArray, an array of characters

Returns

1. the array with any white space removed

EXAMPLE:

     newArray = LoseWhiteSpace('     exa  mp le')

     newArray = 'example'

pairs = PairBrackets(expression)

Takes

1. expression, a string representation of a math expression

Returns

1. an array of the indices of each pair of brackets ordered from the opening bracket index

EXAMPLE:

     pairs = PairBrackets('(a+((b*c)/(a+b)))')

     pairs = 
                 1   17
                 4   16
                 5    9
                 11  15

output = Rearrange(expression, name)

Takes

1. expression, a string representation of a math expression
2. name, a string representing the name of a variable

Returns

1. the expression rearranged in terms of the variable

EXAMPLE:

     output   =   Rearrange('X + Y - Z', 'X')

     output   =   '-Y+Z'

newArray = RemoveDuplicates(array)

Takes

1. array, any array

Returns

1. the array with any duplicate entries removed

EXAMPLE:

          newArray = RemoveDuplicates([2, 3, 4, 3, 2, 5])
          newArray = [2, 3, 4, 5]

value = Substitute(expression, SBMLModel)

Takes

1. expression, a string representation of a math expression
2. SBMLModel, an SBML Model structure

Returns

1. the value of the expression when all variables within the model have been substituted

EXAMPLE:

     Consider m to be an SBMLModel containing a species with 
                id = 'g' and initialConcentration = '3' 

     value = Substitute('g*2', m)

     value = 6

newExpression = SubstituteConstants(expression, SBMLModel)

Takes

1. expression, a string representation of a math expression
2. SBMLModel, an SBML Model structure

Returns

1. the string representation of the expression when all constants within the model have been substituted

EXAMPLE:

     Consider m to be an SBMLModel containing a parameter
          with id = 'g', constant = '1' and value = 3' 

     newExpression = SubstituteConstants('2 * g * S1', SBMLModel)

     newExpression = '2 * 3 * S1'

newExpression = SubstituteFunction(expression, SBMLFunctionDefinition)

Takes

1. expression, a string representation of a math expression
2. SBMLFunctionDefinition, an SBML FunctionDefinition structure

Returns

1. newExpression
   • the string representation of the expression when any instances of the functionDefinition have been substituted
   • an empty string if the functiondefinition is not in the original expression

EXAMPLE:

     Consider fD to be an SBMLFunctionDefinition 
          with id = 'g' and math = 'lambda(x,x+0.5)' 

     formula = SubstituteFormula('g(y)', fD)

     formula = 'y+0.5'


     formula = SubstituteFormula('h(y)', fD)

     formula = ''

y = isIntegralNumber(number)

Takes

1. number, any number

Returns

1. y =
2. 1 if the number represents an integer
3. 0 otherwise

EXAMPLE:

          y = isIntegralNumber(int32(3))
          y = 1

          y = isIntegralNumber(double(3.2))
          y = 0

          y = isIntegralNumber(double(3))
          y = 1

NOTE: The inbuilt 'isinteger' function only returns true if the number has been declared as having an integer type, whereas the default type for numbers in MATLAB is double. This function will return '1' if the number represents an integer.

y = isValidUnitKind(kind)

Takes

1. kind, a string representing a unit kind

returns

1. y =
   • 1 if the string represents a valid unit kind
   • 0 otherwise

NOTE: This is identical to the function CheckValidUnitKind

index = matchFunctionName(expression, name)

Takes

1. expression, a string representation of a math expression
2. name, a string representing the name of a function

Returns

1. the index of the starting point of 'name' in the 'expression'

EXAMPLE:

     index = matchFunctionName('f*g', 'g')

     index = []


     index = matchFunctionName('add(d,g_1)', 'add')

     index = 0


     index = matchFunctionName('add(add(a,b), c)', 'add')

     index = [1, 5]

NOTE: This differs from the 'strfind' function in that it checks that the name is used as a function call.

index = matchName(expression, name)

Takes

1. expression, a string representation of a math expression
2. name, a string representing the name of a variable

Returns

1. the index of the starting point of 'name' in the 'expression'

EXAMPLE:

     index = matchName('f*g', 'g')

     index = 3


     index = matchName('f*g_1', 'g')

     index = []


     index = matchName('f*g(a,g)', 'g')

     index = 7

NOTE: This differs from the 'strfind' function in that it checks that the name is used as a variable.

value = piecewise(value1, test, value2)

Takes

1. value1, the value to return if the test is true
2. test, a boolean test that will return true or false
3. value2, the value to return if the test is false

Returns

1. value =
   • value1, if test returns true
   • value2, if test returns false

EXAMPLE:

          value = piecewise(3, 1<2, 4)
          value = 3

          value = piecewise(3, 1>2, 4)
          value = 4

NOTE: This function provides the functionality of the MathML 'piecewise' function.

y = testmember(value, array)

Takes

1. value, any number/string
2. array, an array of objects

Returns

1. y =
   • 1 if value is a member of the array
   • 0 otherwise

NOTE: this function is necessary for octave to emulate the MATLAB functionality of the 'ismember' function