sysBiolAlg-class: Class '"sysBiolAlg"'
In sybil: Efficient Constrained Based Modelling

Description Details Objects from the Class Slots Methods Author(s) See Also Examples

The class sysBiolAlg holds an object of class optObj which is generated concerning a particular algorithm, e.g. FBA or ROOM. This class is extended by other classes and will not be used as is. The representation of class sysBiolAlg is used as superclass.

The initialize method has the following arguments:

solver: Single character string giving the solver package to use. See SYBIL_SETTINGS for possible values.
Default: SYBIL_SETTINGS("SOLVER").
method: Single character string giving the method the desired solver has to use. SYBIL_SETTINGS for possible values.
Default: SYBIL_SETTINGS("METHOD").
solverParm: A named data frame or list containing parameters for the specified solver. Parameters can be set as data frame or list: solverParm = list(parm1 = val1, parm2 = val2) with parm1 and parm2 being the names of two different parameters and val1 and val2 the corresponding values. For possible parameters and values see the documentation of the used solver package (e.g. glpkAPI).
Default: SYBIL_SETTINGS("SOLVER_CTRL_PARM").
termOut: A single boolean, numeric or character value, controling the amount of terminal output of the solver software. See also initProb (argument to) for more details.
Default: NULL.
sbalg: Single character string containing the name of the algorithm to use.
pType: Single character string containing the type of the problem object. Can be "lp": linear program, mip: mixed integer program or "qp": quadratic program.
Default: "lp".
scaling: Scaling options used to scale the constraint matrix. If set to NULL, no scaling will be performed (see scaleProb).
Default: NULL.
fi: Pointers to columns (variables) representing a flux (reaction) in the original network. The variable fldind[i] in the problem object represents reaction i in the original network.
nCols: Number of columns (variables) of the problem object.
nRows: Number of rows (constraints) of the problem object.
mat: An object of class Matrix. The constraint matrix of the problem object. The number of columns in mat must be nCols and the number of rows in mat must be nRows.
ub: A numeric vector of length nCols giving the upper bounds of the variables of the problem object.
lb: A numeric vector of length nCols giving the lower bounds of the variables of the problem object.
obj: A numeric vector of length nCols giving the objective coefficients of the variables of the problem object.
rlb: A numeric vector of length nRows giving the right hand side of the problem object. If argument rub is not NULL, rlb contains the lower bounds of the constraints of the problem object.
rtype: A character vector of length nRows giving the constraint type. See loadLPprob for details.
lpdir: Single character string containing the direction of optimization. Can be set to "min" or "max".
Default: "max".
rub: A numeric vector of length nRows giving the right hand side of the problem object. If not NULL, it contains the upper bounds of the constraints of the problem object.
Default: NULL.
ctype: A character vector of length nCols giving the variable type. If set to NULL, no specific variable type is set, which usually means, all variables are treated as continuous variables. See loadLPprob for details.
Default: NULL.
cnames: A character vector of length nCols giving the variable names. If set to NULL, no specific variable names are set.
Default: NULL.
rnames: A character vector of length nRows giving the constraint names. If set to NULL, no specific constraint names are set.
Default: NULL.
pname: A single character string containing a name for the problem object.
Default: NULL.
retAlgPar: A single boolean flag, if algorithm specific parameters should be saved in the object extending class sysBiolAlg.
Default: TRUE.
algPar: A named list containing algorithm specific parameters.
Default: NULL.

A virtual Class: No objects may be created from it.

problem:: Object of class "optObj" containing the problem object.
algorithm:: Object of class "character" containing the name of the algorithm.
nr:: Object of class "integer" containing the number of rows of the problem object.
nc:: Object of class "integer" containing the number of columns of the problem object
fldind:: Object of class "integer" pointers to columns (variables) representing a flux (reaction) in the original network. The variable fldind[i] in the problem object represents reaction i in the original network.
alg_par:: Object of class "list" containing a named list of algorithm specific parameters.

algorithm: signature(object = "sysBiolAlg"): gets the algorithm slot.
algorithm<-: signature(object = "sysBiolAlg"): sets the algorithm slot.
alg_par: signature(object = "sysBiolAlg"): gets the alg_par slot.
alg_par<-: signature(object = "sysBiolAlg"): sets the alg_par slot.
fldind: signature(object = "sysBiolAlg"): gets the fldind slot.
fldind<-: signature(object = "sysBiolAlg"): sets the fldind slot.
nc: signature(object = "sysBiolAlg"): gets the nc slot.
nc<-: signature(object = "sysBiolAlg"): sets the nc slot.
nr: signature(object = "sysBiolAlg"): gets the nr slot.
nr<-: signature(object = "sysBiolAlg"): sets the nr slot.
optimizeProb: signature(object = "sysBiolAlg"): runs optimization on the given problem object (see optimizeProb for details).
problem: signature(object = "sysBiolAlg"): gets the problem slot.
initialize: signature(object = "sysBiolAlg"): default constructor method for objects inheriting from class sysBiolAlg. It gets all data structures necessary to built a problem object (object of class optObj) representing a particular algorithm. This method can be used in constructor methods for subclasses of sysBiolAlg via callNextMethod. In this case, the constructor has to generate all the data structures, pass them to callNextMethod and let the constructor of the superclass do all the work in generating the problem object and interacting with the solver software. See also the Details section.