I need to accede to the numerical value (written in black letters) but am not able. Exists some method to accede to this field in the bookstore (and I have not seen it)?
If you are only interested in the parameter value you can use the
getParameters() and then use getValue() method on the resulting
Parameter object.
Most likely you want to know the math too, so you will need to get the
kinetic law and then use the getMath() method.
This will return ASTNode (Abstract Syntax Tree).
There is an ASTNode class in the javadoc org.sbml.libsbml.ASTNode that
has methods to help parse the abstract syntax tree.
You will see that most of the get methods return ints; you will need to
look these up in the constant field values to see what the int returned
actually represents. http://sbml.org/software/libsbml/docs/java/constant-values.html contains
this information.
I need to accede to the numerical value (written in black letters) but
am not able. Exists some method to accede to this field in the
bookstore (and I have not seen it)?
Hi,
Most likely you want to know the math too, so you will need to get the
kinetic law and then use the getMath() method.
This will return ASTNode (Abstract Syntax Tree).
Hi!
How can I covert ASTNode in to double or float number?
I have been trying it, but I have not been able it to do.
If i use getParameters() and then getValue(), I can't accede to that value.
When a ASTNode is created, you need have a type of libsbmlConstants by using class constructor or setType() function. When you getMath() as an ASTNode, you may need access ASTNode with loop (for list) or recursively (for child) but first call getType() to check the type. Then based on the type to check isXXX() function and finally call getName() or getValue().
> When a ASTNode is created, you need have a type of libsbmlConstants
> by using class constructor or setType() function. When you getMath
> () as an ASTNode, you may need access ASTNode with loop (for list)
> or recursively (for child) but first call getType() to check the
> type. Then based on the type to check isXXX() function and finally
> call getName() or getValue().
Actually, getType() and isXXX() provide the same information. The
getType() method is useful in 'switch' statements, e.g.:
switch (node.getType())
{
case AST_PLUS : ... beak;
case AST_MINUS: ... break;
/* etc. */
}
while isXXX() is arguably a little bit more succinct and readable
than getType() == AST_XXX. Also, the isXXX() methods can encompass a
range of values returned by getType(). For example, isLogical() is
equivalent to (getType() >= AST_RELATIONAL_AND) && (getType() <=
AST_RELATIONAL_XOR).
For extracting numeric values, here are the predicates (isXXX()
methods) and their corresponding accessor methods:
isInteger () -> getInteger()
isRational() -> getNumerator() and getDenominator()
isReal () -> getReal()
getType() == AST_REAL_E -> getReal() or getMantissa() and
getExponent()
For "special" numeric values, there's also:
isInfinity ()
isNegInfinity()
isNaN ()
In these cases getReal() still returns the appropriate floating point
value.
double value = model.getReaction("Reaction_6").getKineticLaw
().getMath().getLeftChild().getReal();
But in general, you should probably put in some sanity checks (or run
the libSBML consistency checks) in case the model author has omitted
something. For example:
Reaction r = model.getReaction("Reaction_6");
if ( r.isSetKineticLaw() )
{
KineticLaw kl = getKineticLaw();
if ( kl.isSetMath() )
{
ASTNode math = kl.getMath();
double value = math.getLeftChild().getReal();
}
}
I hope this helps.
Thanks.
Ben
On Jun 27, 2006, at 11:30 AM, Juanky wrote:
> I'm develop a parser using libsbml in Java. The parser this to 90%.
> I only need a part.
> In this fragment of xml:
>
> <reaction id="Reaction_6" reversible="true">
> - <listOfReactants>
> <speciesReference id="EGFR-EGF2*" speciesType="s" />
> </listOfReactants>
> - <listOfProducts>
> <speciesReference id="EGFR-EGF2" speciesType="s" />
> </listOfProducts>
> - <kineticLaw>
> - <math xmlns="http://www-w3.org/1998/MathMathML">
> - <apply>
> <times />
> <cn>0.0271</cn>
> <ci>EGFR-EGF2*</ci>
> </apply>
> </math>
> </kineticLaw>
> </reaction>
>
> I need to accede to the numerical value (written in black letters)
> but am not able. Exists some method to accede to this field in the
> bookstore (and I have not seen it)?
27 Jun '06 05:37
