sybil (version 2.0.0)

optObj-class: Class "optObj"

Description

Structure of the class "optObj". Objects extending optObj returned by the constructor function optObj. These objects are used as part of class '>sysBiolAlg.

Objects from the Class

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

Slots

oobj:

Object of class "pointerToProb" containing a pointer to a problem object (see section Note).

solver:

Object of class "character" containing the name of the solver software (see SYBIL_SETTINGS for suitable values).

method:

Object of class "character" containing the method (algorithm) used by the solver software (see SYBIL_SETTINGS for suitable values).

probType:

Object of class "character" giving the problem type (see optObj argument pType for suitable values).

Methods

dim

signature(x = "optObj"): returns a vector d of length two with d[1] and d[2] containing the number of rows and columns of the constraint matrix.

method

signature(object = "optObj"): gets the method slot.

probType

signature(object = "optObj"): gets the probType slot.

solver

signature(object = "optObj"): gets the solver slot.

Further usefull Functions

checkSolStat:

checkSolStat(stat, solver = SYBIL_SETTINGS("SOLVER"))

Returns the indices of problems with a non-optimal solution status, or NA if it is not possible to retrieve a solution status.

stat

Vector of integer values containing the solution status.

solver

Single character string specifying the used solver (see SYBIL_SETTINGS).

getMeanReturn:

getMeanReturn(code, solver = SYBIL_SETTINGS("SOLVER"))

Translates the return value (code) of a solver in a human readable string. Returns NA if hte translation is not possible.

getMeanStatus:

getMeanStatus(code, solver = SYBIL_SETTINGS("SOLVER"), env = NULL)

Translates the soluton status value (code) of a solver in a human readable string. Returns NA if hte translation is not possible. Argument env is for use with IBM ILOG CPLEX holding an object of class cplexPtr pointing to a IBM ILOG CPLEX environment.

wrong_type_msg:

wrong_type_msg(lp)

prints a warning message, if slot oobj from lp (an instance of class optObj) does not contain a pointer to a valid solver. See also SYBIL_SETTINGS for possible solvers.

wrong_solver_msg:

wrong_solver_msg(lp, method, printOut = TRUE)

if printOut == TRUE, it will print a warning message, if method is not available for solver in lp.

Additional methods used by classes extending class <code>optObj</code>

addCols:

add columns to the problem object.

addRows:

add rows to the problem object.

addRowsCols:

add rows and columns to the problem object.

addColsToProb:

add new columns (variables) to the problem object.

addRowsToProb:

add new rows (constraints) to the problem object.

backupProb:

copies a problem object into a new problem object.

changeColsBnds:

change column (variable) bounds in the problem object.

changeColsBndsObjCoefs:

change column (variable) bounds and objective coefficients in the problem object.

changeMatrixRow:

change a row in the constraint matrix of the problem object.

changeObjCoefs:

change objective coefficients in the problem object.

changeRowsBnds:

change row bounds in the problem object.

delProb:

delete (free) memory associated to the pointer to the problem object.

getColPrim:

get primal value of variables after optimization.

getColsLowBnds:

get lower bounds of variables.

getColsUppBnds:

get upper bounds of variables.

getFluxDist:

get all primal values of variables after optimization (resulting flux distribution).

getNumCols:

get number of columns in the problem object.

getNumNnz:

get number of non zero elements in the constraint matrix of the problem object.

getNumRows:

get number of rows in the problem object.

getObjCoefs:

get objective coefficients in the problem object.

getObjDir:

get direction of optimization.

getObjVal:

get value of the objective function after optimization.

getRedCosts:

get reduced costs of all variables after optimization.

getRowsLowBnds:

get lower row bounds of the problem object.

getRowsUppBnds:

get lower bounds of the rows (constraints) of the problem object.

getSolStat:

get solution status after optimization.

getSolverParm:

get current parameter settings of the used solver.

initProb:

initialize problem object.

loadLPprob:

load data to the problem object. Use this method to generate problem objects.

loadQobj:

load quadratic part of the objective function to the problem object.

readProb:

read problem object from file (e.g. lp formated).

scaleProb:

scaling of the constraint matrix.

sensitivityAnalysis:

perform sensitivity analysis.

setObjDir:

set direction of optimization.

setRhsZero:

set right hand side of the problem object to zero: \(\mbox{\boldmath$Sv$\unboldmath} = 0\).

setSolverParm:

set parameters for the used solver.

solveLp:

run optimization with the solver mentioned in slot solver and with the method given by slot method.

writeProb:

write problem object to file (e.g. in lp format).

Details

The intention of class optObj is, to provide a flexible user interface to several optimization software products. The methods here working on the slot oobj are interface functions to low level functions invoking corresponding C functions. Basically, the user has not to care about the nature of the solver, or solver-specific functions. That is done by the class.

See Also

The constructor function sysBiolAlg for objects extending class '>sysBiolAlg; The constructor function optObj; SYBIL_SETTINGS and checkDefaultMethod.

Examples

# NOT RUN {
  showClass("optObj")
# }