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java.lang.ObjectJava.problem.ReactionType
public class ReactionType
Description of a reaction type:
Constructor Summary | |
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ReactionType()
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Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public ReactionType()
Method Detail |
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public int read(java.lang.String[] commands, java.io.BufferedReader in, int line_no, int debug)
commands
- vector of strings on first line to readin
- buffered readerline_no
- current line in the buffered reader (i.e., problem file)debug
- debug levelpublic void readDerivatives(int line_no, int debug)
line_no
- the stringdebug
- debug level, 0=nonepublic void setAsGMAterm(int gma)
gma
- the number of variablespublic java.lang.String getLocalVariableName(int i)
i
- variable index
public java.lang.String getLocalParameterName(int i)
i
- parameter index
public int getNumberOfLocalVariables()
public int getNumberOfLocalParameters()
public java.lang.String get_dfdX(int ivar)
ivar
- the variable index
public java.lang.String get_dfdk(int ipara)
ipara
- parameter index
public boolean useNumericalDerivaties()
public java.lang.String getName()
public java.lang.String getEquation()
public java.lang.String getSBML()
public int getId()
public java.lang.String toString()
toString
in class java.lang.Object
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