Java.problem
Class ReactionType

java.lang.Object
  extended by Java.problem.ReactionType

public class ReactionType
extends java.lang.Object

Description of a reaction type:

Since:
1.0

Constructor Summary
ReactionType()
           
 
Method Summary
 java.lang.String get_dfdk(int ipara)
          Get the partial derivative of the kinetic equation wrt parameter ipara
 java.lang.String get_dfdX(int ivar)
          Get the partial derivative of the kinetic equation wrt variable ivar
 java.lang.String getEquation()
          Get the kinetic equation
 int getId()
          Get id of the reaction type
 java.lang.String getLocalParameterName(int i)
          Get the name of local parameter i in the kinetic equation
 java.lang.String getLocalVariableName(int i)
          Get the name of local variable i in the kinetic equation
 java.lang.String getName()
          Get the name of the reaction type
 int getNumberOfLocalParameters()
          Get the number of local parameters in the kinetic equation
 int getNumberOfLocalVariables()
          Get the number of local variables in the kinetic equation
 java.lang.String getSBML()
          Get SBML representation of the reaction equation
 int read(java.lang.String[] commands, java.io.BufferedReader in, int line_no, int debug)
          Read reaction type from input file in form of a buffered reader
 void readDerivatives(int line_no, int debug)
          Read the derivatives from file REACTIONS.txt
 void setAsGMAterm(int gma)
          Set as a GMA term with gma variables, e.g., alpha*X1^g11*X2^g12*X3^g13 for gma=3.
 java.lang.String toString()
          Get string representation
 boolean useNumericalDerivaties()
          Monitor if analytical derivatives are defined.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

ReactionType

public ReactionType()
Method Detail

read

public int read(java.lang.String[] commands,
                java.io.BufferedReader in,
                int line_no,
                int debug)
Read reaction type from input file in form of a buffered reader

Parameters:
commands - vector of strings on first line to read
in - buffered reader
line_no - current line in the buffered reader (i.e., problem file)
debug - debug level

readDerivatives

public void readDerivatives(int line_no,
                            int debug)
Read the derivatives from file REACTIONS.txt

Parameters:
line_no - the string
debug - debug level, 0=none

setAsGMAterm

public void setAsGMAterm(int gma)
Set as a GMA term with gma variables, e.g., alpha*X1^g11*X2^g12*X3^g13 for gma=3.

Parameters:
gma - the number of variables

getLocalVariableName

public java.lang.String getLocalVariableName(int i)
Get the name of local variable i in the kinetic equation

Parameters:
i - variable index
Returns:
the name

getLocalParameterName

public java.lang.String getLocalParameterName(int i)
Get the name of local parameter i in the kinetic equation

Parameters:
i - parameter index
Returns:
the name

getNumberOfLocalVariables

public int getNumberOfLocalVariables()
Get the number of local variables in the kinetic equation

Returns:
the number

getNumberOfLocalParameters

public int getNumberOfLocalParameters()
Get the number of local parameters in the kinetic equation

Returns:
the number

get_dfdX

public java.lang.String get_dfdX(int ivar)
Get the partial derivative of the kinetic equation wrt variable ivar

Parameters:
ivar - the variable index
Returns:
the partial derivative, null if not defined

get_dfdk

public java.lang.String get_dfdk(int ipara)
Get the partial derivative of the kinetic equation wrt parameter ipara

Parameters:
ipara - parameter index
Returns:
the partial derivative, null if not defined

useNumericalDerivaties

public boolean useNumericalDerivaties()
Monitor if analytical derivatives are defined.

Returns:
true if numerical derivatives will be used, otherwise analytical derivatives will be used

getName

public java.lang.String getName()
Get the name of the reaction type

Returns:
the name

getEquation

public java.lang.String getEquation()
Get the kinetic equation

Returns:
the kinetic equation

getSBML

public java.lang.String getSBML()
Get SBML representation of the reaction equation

Returns:
the SBML representation

getId

public int getId()
Get id of the reaction type

Returns:
the id

toString

public java.lang.String toString()
Get string representation

Overrides:
toString in class java.lang.Object
Returns:
the string