| NEWS | R Documentation |
Changes to functions modelorg2ExPA and promptSysBiolAlg,
where closeAllConnections was called on.exit of the function.
The two functions now only close the connections that they have opened.
It is now possible to use the functions setSolverParm and
getSolverParm in combination with package clpAPI to set the
number of iterations, to set or get the maximum number of iterations or
maximum number of seconds and to check, if the maximum number of iterations
(or time) was hit. See also setSolverParm-methods and
getSolverParm-methods in the manual.
Updated URLs in DESCRIPTION, inst/CITATION and inst/NEWS.Rd and corrected keyword definition for CRAN submission. \
Minor changes removing invalid URLs for CRAN submission. \
Minor code change in addExchReact for CRAN submission, where
logical operator || encountered and used argument of length more than one.
\
Minor bug fix for function getRedCosts in optObj_cplexAPI.
\
Maintainer change to Mayo Roettger <mayo.roettger@hhu.de>. \
Package sybilSBML gets rejected on CRAN, but can be downloaded at https://www.cs.hhu.de/en/research-groups/computational-cell-biology/software.html.
Documentation for react-class and related methods.
\
addReact is now a method of the modelorg class.
Preparation for sybilNLO.
New reaction object for easy merging and splitting of models. See reactClass.
Typo in setting methods generated an character vector object.
\
Minor changes for CRAN submission.
The function genrateWT caused a problem when setting only solverParm and no solver.
rmReact handles now react_attr and met_attr corretly, if there is just one column.
The function mod2irrev crashed when using models with just one gene.
After rmReact the columns of rxnGeneMat and
allGenes-slot did not match.
upgradeModelorg was not working correctly, when all gprRules
are empty.
modelorg-class has changed and thus a slot version was introduced.
the method upgradeModelorg can convert from earlier instances of this
class. This method is only needed if modelorg-Objects were loaded
with load from disk.
gprRules were stored in an impractical format. This lead to bugs
in rmReact and further geneDel.
updated the manual of various files.
doubleGeneDel messed up the order of deletions when using exlicit gene lists.
corrected url of openCOBRA in the manual.
addReact crashed for irreversible models.
New Algorithm fbaEasyConstraint and mtfEasyConstraint
implemented. With these new sysBiolAlg-Classes it is easier to add
linear constraints to a model. See package vignette or manual for more details.
switch needs the first parameter explicitly named.
rmReact error, if resulting model had only one gene left, corrected.
deadEndMetabolite() could miss deadEndMetabolites if reactions differ in stoichiometry e.g. 1 and 2.
readTSVmod had a mistake in the documentation about singletons.
changed maintainer
.parseBoolean now gives a warning, but handles empty gpr in a intuitive way.
findExchangeReact can now deal with real big matrices (>30.000 columns).
additional example for readProb and writeProb.
modified multiDel to not use require
doubleFluxDel had a bug if react1 or react2 contained duplicated entries.
documentation of hasEffect in optsol_genedel is now clearer.
fixed a bug in class modelorg and function addReact when
the modelorg object is initially empty
for method optimizeProb of class modelorg: if arguments
lb, ub or obj_coef are of length one, they are used
for all elements given in react
function geneDel returns a more illustrative error message if a gene
association is malformed
fixed a bug in optimizer which returns the wrong objective value in rare cases
added boolean parameter fldind to methods optimizeProb
and applyChanges which controls the usage of parameter react
function findExchReact gives a propper warning, if no exchange
reactions can be found and returns NULL in this case
fixed a bug in function addReact which accours when more than
one new gene per reaction is added to the model
function checkSolStat recognizes return code
CPXMIP_OPTIMAL_TOL (102): ‘integer optimal, tolerance’
as ‘successfully solved’
added parameter absMAX to the constructor methods of classes
sysBiolAlg_lmoma, sysBiolAlg_mtf and
sysBiolAlg_room, which is used as a maximum value for upper variable
and contraint bounds
for method optimizeProb of class modelorg: if both
arguments gene and react are not NULL, a warning
will be given that react is ignored
added file ‘CITATION’
added methods singletonMetabolites and
deadEndMetabolites to class modelorg to find dead end
or singleton metabolites in metabolic networks
fixed a bug in function findExchReact which accours when a
model is in irreversible format
added methods setRowsNames, getRowsNames,
setColsNames and getColsNames to classes extending
class optObj
added function phpp for phenotypic phase plane analysis
added class optsol_phpp
added argument rng to function robAna
fixed a bug in function optimizer which accours when setting
arguments setToZero to TRUE and verboseMode to
a value larger than two
updated function promptSysBiolAlg, including now a very basic
example how to set column, row and problem names in problem objects of
class sysBiolAlg and optObj
fixed a bug in function addReact which accours if the model
does not contain a GPR association
some adjustments in classes extending class optObj:
methods loadLPprob, addRowsToProb and
changeRowsBnds works in the same way for each solver (see the
corresponding manual pages for details)
added parameters writeProbToFileName and pname to
constructor methods of classes extending class sysBiolAlg
fixed a bug in method changeRowBnds of class
optObj_lpSolveAPI
suggests on glpkAPI (version >= 1.2.8)
suggests on clpAPI (version >= 1.2.4)
added parameter scaleDist to the constructor method of class
sysBiolAlg_moma, which provides a fine tuning method of the
impact of particular reactions on the objective function of the
MOMA algorithm
suggests on glpkAPI (version >= 1.2.7)
suggests on clpAPI (version >= 1.2.3)
variable and constraint names can now be set in objects of class
sysBiolAlg and optObj
added a new parameter USE_NAMES
added arguments cnames and rnames to method
loadLPprob for classes extending class optObj
added argument rnames to method addRowsToProb for
classes extending class optObj
added arguments cnames and rnames to method
initialize of class sysBiolAlg
added arguments useNames, cnames and rnames to
method initialize of classes sysBiolAlg_fba,
sysBiolAlg_fv,sysBiolAlg_lmoma,sysBiolAlg_moma,
sysBiolAlg_mtf and sysBiolAlg_room.
in method printMetabolite of class modelorg:
metabolite id's beginning with a digit or period are prefixed by the
letter "r" and reaction id's beginning with a digit or period
are prefixed by the letter "x"
function readTSVmod checks input files for empty fields
added method changeUptake to class modelorg to change
media conditions in metabolic networks
fixed a bug in functions .generateWT and doubleGeneDel
which accours if argument solver was given as variable name and not
as character value directly
added argument termOut to method initialize of class
sysBiolAlg enabling or disabling terminal output of the
mathematical programming software
function checkSolStat no longer returns an optimal MILP
solution generated by IBM ILOG CPLEX as non-optimal
some refinements for the regular expressions in function
readTSVmod to identify stoichiometric coefficients and
compartment flags of metabolites
added argument linInd to function doubleReact
return value of function doubleReact is now FALSE if
no identical reactions are found, otherwise a list of id's
corresponding to the reaction id's of identical reactions
default value for argument wtflux in method initialize
of class sysBiolAlg_moma is NULL
new parameter to the MOMA algorithm (quadratic version): argument
Qmat in method initialize of class
sysBiolAlg_moma gives the quadratic part of the objective
function
new parameter to the MOMA algorithm (linear version): argument
obj_coefD in method initialize of class
sysBiolAlg_lmoma contains the non-zero part of the objective
function
fixed a bug in function doubleGeneDel which appears if
argument exLethal is set to TRUE
removed old file ‘NEWS.Rd’ from top level directory
fixed a bug in the calculation of default objective values in the
mtf algorithm
method histogram of class optsol plots the return value
of mod_obj, not lp_obj
removed argument MoreArgs from method optimizeProb of
class modelorg
slots dels and fluxdels of class optsol_fluxdel
and class optsol_genedel are matrices of class character
class sysBiolAlg has new methods applyChanges and
resetChanges for altering objects of class sysBiolAlg
temporarily
replaced method optimizeProb of class sysBiolAlg_room by
methods applyChanges and resetChanges
constructor method of class sysBiolAlg has new arguments
retAlgPar and algPar used for saving algorithm specific
parameters in objects extending class sysBiolAlg
added slot maxobj and method changeMaxObj to class
sysBiolAlg_mtf
fixed a bug in algorithm mtf: modifications in the model (like
gene knock-outs) were ignored during the calculation of the optimized
objective value
argument algorithm to function optimizer can now also be
"mtf" or "fv"
added class netFlux and constructor function getNetFlux
to order exchange reaction rates according to their sign
function optimizer returns a list and no longer an object
extending class optsol.
removed method logOptimizationNE of class sybilLog
requires R version 2.14.2 or higher
method getFluxDist of class optsol get additional
argument opt to access specific optimization results
removed argument needId from function checkReactId
removed slot has_id and method hasId from
class reactId
removed constructor function reactId for objects of class
reactId, use function checkReactId instead
added function editEnvir: the environment editor for metabolic
networks
method shrinkMatrix can get objects of class reactId
removed deprecated functions simpleFBA and prepProbObj
removed deprecated generics loadProblemData,
loadProblemDataLM, loadProblemDataMTF
and loadMatrix
removed deprecated class optsol_simpleFBA
some updates in the vignette
class reactId is reorganized: it has new slots mod_id,
mod_key, react_num and has_id and new methods
hasId and [, also the implementation of method
show has changed
new class reactId_Exch extending class react_id
function findExchReact now returns an object of class
reactId_Exch when getting an object of class modelorg
instead of a list
class modelorg, class reactId, class optsol and
class optsolSummary have new slot mod_key containing a
character string functioning as a unique key to a model object
fixed a small bug in method printObjFunc of class
modelorg
fixed a small bug in function fluxVar which has occurred when
not all reactions given in a model where analyzed
function fluxVar has new argument exex in order to
exclude exchange reactions from the analysis
class optsol_fluxVar has a new method blReact which does
essentially the same as function blockedReact
function blockedReact is now deprecated
class optsol has a new slot obj_func containing the
objective function of the used model as a character string
method optimizeProb of class modelorg returns an object
of class optsol_optimizeProb as default behaviour (argument
retOptSol is TRUE, default)
function geneDel now returns NULL instead of NA
if a gene deletion has no effect
default value for arguments gene, react, lb,
ub and obj_coef in methods optimizeProb is
NULL
in optimizeProb all changes to variable bounds must be set
explicitly, there is no default anymore
added method shrinkMatrix to class modelorg for
retrieving subsets of the stoichiometric matrix
changed argument alg in method initialize of class
sysBiolAlg to sbalg
changed argument alg in function optimizer
to algorithm
slot lp_dir of class optsol is now of type factor
solver names "glpk", "cplex" and "clp" are not
used anymore, use "glpkAPI", "cplexAPI" and
"clpAPI" instead
added method readProb to class optObj
removed slot rhs from class modelorg, because this
parameter is algorithm dependent and not model dependent
added new class optsolSummary
the function printObjFunc is now a generic and has a method in
class modelorg
the function checkOptSol is now a generic and has a method in
class optsol and class optsolSummary
added methods printMetabolite and printReaction to
class modelorg
added method nnzero to class fluxDistribution
fixed a bug in backupProb methods
fixed a small bug in checkDefaultMethod
moved method mod_obj from class optsol_fluxdel to the
base class optsol
added deprecated class optsol_simpleFBA for compatibility
with other packages depending on sybil
fixed file ‘DESCRIPTION’
some performance improvements in function fluxVar
new function modelorg2ExPA
some very minor improvements in sybilStack (stack [LIFO] and queue [FIFO])
solver names glpk, cplex and clp are deprecated,
use glpkAPI, cplexAPI and clpAPI instead
classes optObj_glpk, optObj_cplex and optObj_clp
are renamed to optObj_glpkAPI, optObj_cplexAPI and
optObj_clpAPI
fixed a small bug in SYBIL_SETTINGS appearing if parameters
were set several times
argument solverParm can be list or data.frame
argument fmt to the generic writeProb is now ff
added support for mixed interger optimization problems with glpkAPI and cplexAPI
added support for quadratic optimization problems with cplexAPI
added methods changeMatrixRow, loadLPprob and
loadQobj to class optObj
cplexAPI must be version 1.2.3 or higher, if used
added function addSolver in order to make additional solver
packages available
added argument arrowlength to function readTSVmod
added arguments probType and loadPackage to function
checkDefaultMethod
class optsol_doublefluxdel and class
optsol_doublegenedel are not available anymore, class
optsol_fluxdel and class optsol_genedel are used instead
added new method mod_obj to class optsol\_fluxdel, which
returns
c^T v
with c being the vector of
objective coefficients in the model (object of class modelorg)
and v being the flux
distribution as a result of the optimization. In contrast, method
lp_obj always returns the value of the objective function
of the used algorithm after optimization.
added functions addAlgorithm, checkAlgorithm and
getsybilenv
added a new class sysBiolAlg including a general constructor
function sysBiolAlg and subclasses sysBiolAlg_fba,
sysBiolAlg_fv, sysBiolAlg_lmoma, sysBiolAlg_moma,
sysBiolAlg_mtf and sysBiolAlg_room. These classes
contain instances of class optObj, prepared for specific
algorithms like ROOM or MOMA
support for algorithms MOMA and ROOM in class sysBiolAlg
added method optimizeProb as a replacement for function
simpleFBA: unused argument checkIds is removed, new
arguments gene and MoreArgs were added.
added function promptSysBiolAlg which generates a skeletal
structure for new classes inhereting from sysBiolAlg
functions prepProbObj and simpleFBA are deprecated and
will be removed soon, use sysBiolAlg and optimizeProb
instead
methods loadMatrix, loadProblemData,
loadProblemDataLM and loadProblemDataMTF are deprecated
and will be removed soon, use loadLPprob instead
class optsol makes now use of the package lattice to
plot histograms (use histogram() instead of hist())
updated package vignette
renamed parameter SOLVER_CTRL_PARAM to SOLVER_CTRL_PARM
renamed argument param in SYBIL_SETTINGS() to
parm
file ‘NEWS’ is now in ‘inst/NEWS.Rd’
added argument absCtrl to the plot method in
class optsol_robAna
in readTSVmod, if a model description file is missing, the
basename of the reaction list is used as model id, not the complete
path to the file if fpath is used, or the reaction list is not in
the working directory
removed arguments verboseMode, loglevel, logfile
and logfileEnc from function readTSVmod; use function
sink instead
removed arguments loglevel, logfile and
logfileEnc from function optimizer; use function
sink instead
added method show to class sybilError
methods logOptimization and logOptimizationNE of class
sybilLog need argument i giving a consecutive number
methods logComment, logOptimization,
logOptimizationNE and logOptimizationTH of class
sybilLog now also write to stdout (by cat) if
verblevel is > 2
fixed a bug in mod2irrev(): slots met_de and
react_de of class modelorg (in the reversible model)
are no longer ignored
added function addReact() to add or change reactions in a
given model
added function addExchReact() to add exchange reactions for
metabolites to a given model
minor changes in printObjFunc()
SYBIL_SETTINGS(parm) gives an error if parm is not a valid
parameter name
function findExchReact() now returns indices of metabolite id's
having an exchange reaction
compatible to clpAPI (version >= 1.2.0)
removed sybilSBML from Suggests field and removed undocumented
function readModel()
added method dim to class modelorg
renamed method setColsBndsObjCoefs to
changeColsBndsObjCoefs
updated documentation
depends on glpkAPI (version >= 1.2.1)
needs cplexAPI (version >= 1.2.0)
switched from SparseM to Matrix (version >= 1.0-4), a consequence is a dependency on R (version >= 2.12.0)
completely new implementation of SYBIL_SETTINGS
reorganization of files: one class >= one file
use Collate field in file ‘DESCRIPTION’
LIFO/FIFO (stack/queue) implementation with new functions
stinit(), stclear(), stpush(),
stpop(),
stunshift(), stshift(), stseek(),
stfirst(),
stlist(), stlength() and stexists()
a few compatibility changes in readTSVmod() for output of
BiGG database: added arguments
quoteChar, commentChar and oneSubSystem
added argument minimalSet to modelorg2tsv()
added function geneDeletion() for n gene deletions
fixed a bug in doubleGeneDel() when allComb = FALSE
added geneDeletion to multiDel()
added argument checkId to geneDel()
arguments poCmd and prCmd to optimizer and
simpleFBA must be of type list
some improvements in sybilLogClass
optimizer() now makes use of class sybilLog
removed arguments resolve and resolveParm from
optimizer()
removed sybil parameters LP_ALT_METHOD and
SOLVER_ALT_CTRL_PARAM from SYBIL_SETTINGS()
renamed sybil parameter LP_SOLVER to SOLVER
renamed sybil parameter LP_METHOD to METHOD
moved methods length and hist from class
optsol_fluxdel to class optsol
added slot num_of_prob in class checksol
fixed a bug in class optObj when setting parameters to
lpSolveAPI
added arguments connect and colconnect to the
plot mathod of class optsol_fluxVar
updated package vignette
fixed a bug in readTSVmod() when reading closed networks
.createReactionString() now adds the compartment id to the
metabolite id if it is not already there
if the metabolite id's do not contain the compartment abbreviation in
square brackets, the compartment names are used by
modelorg2tsv()
added arguments exclM and exclR to
.singletonMetabolite()
in readTSVmod(): upper and lower bounds which are larger
than abs(def_bnd) are set to abs(def_bnd)
added slots met_de and react_de to modelorg
added Boolean arguments remMet, contrMet,
singletonMet and deadEndmet to readTSVmod(), the
two Boolean arguments remSingleMet and constrSingleMet
are removed, see help("readTSVmod") for details
fixed a bug in constructor of class sybilError
depends on cplexAPI (version >= 1.1.7)
checkOptSol() is compatible with cplexAPI
(version 1.1.7) in combination with IBM ILOG CPLEX (version 12.3)
slots met_single and react_single of class
modelorg are initialized with NA, not FALSE
some minor changes in readTSVmod() according to
codetools
fixed a bug in class logFileFH
added slots met_single and react_single to class
modelorg
new arguments for readTSVmod():
mergeMet, balanceReact, remUnusedMetReact,
remSingleMet, constrSingleMet and tol see
help("readTSVmod") for details
method logError of class sybilLog returns object of
class sybilError
fixed a bug in .printNamedList()
added class sybilLog
added logging in readTSVmod(), see help("readTSVmod")
for details and new arguments
added NAMESPACE
fixed a minor bug in findExchReact()
fixed a bug in method show for class SYBIL_SETTINGS
fixed a bug in .validModelorg()
changes in readTSVmod():
If a metabolite is used more than once as product or educt of a particular reaction, it is merged:
a + (2) a
is converted to
(3) a
and a warning will be given.
If a metabolite is used first as educt and then as product of a particular reaction, the reaction is balanced:
(2) b + a -> b + c
is converted to
b + a -> c
The stoichiometric matrix S is scanned for metabolites, which are used only once in S. If there are some, a warning will be given.
The stoichiometric matrix S is scanned for reactions, which are not used in S. If there are some, a warning will be given and the corresponding reactions will be removed from the model.
Some improvements in parsing the reaction string: if more than one reaction arrow is found, a warning is given and the reaction will be removed from the model.
support for low level interface glpkAPI (version 1.1.2)
support for low level interface clpAPI (version 1.1.1)
support for low level interface cplexAPI (version 1.1.1)
added new slot in class optObj: probType.
The constructor function optObj() has a new argument
pType, with lp as default value (linear programming).
updated documentation
slot subSys in class modelorg is now of class
matrix, so one reaction can belong to more than one subsystem,
for example:
cytosol | mitochondria | external |
|
v_1 | TRUE | FALSE | FALSE |
v_2 | TRUE | TRUE | FALSE |
v_3 | FALSE | TRUE | FALSE |
b_1 | FALSE | FALSE | TRUE |
b_2 | FALSE | FALSE | TRUE |
In slot subSys, only the column names are named according to
the subsystem. The rows do not have names, the first row corresponds
to the first reaction in slot react_id, the second row to the
second reaction id, and so forth.
added method getRedCost to class optObj.
SBML compatibility is moved to the package sybilSBML, making sybil independend from rsbml. The new package sybilSBML requires a working rsbml installation (available from Bioconductor).
added functions modelorg2tsv() and readTSVmod() in order
to handle ‘tsv’ files compatible to the
BiGG database
fixed a bug in optimizer() when pre/post-processing
should be performed, but no optimization was done.
added argument solverParm in fluxVar(), argument
... is passed to simpleFBA() now
cleaning of class optObj:
new classes extending optObj:
optObj_glpk, optObj_clp, optObj_cplex
and optObj_lpSolveAPI
methods setRhsZero and setColsBndsObjCoefs are not
usable for initial model creation (this is a feature, not a bug).
Use addRows and addCols here.
added stack like functions
added function multiDel(): multicore support for
oneGeneDel(), doubleGeneDel(), oneFluxDel()
and doubleFluxDel()
fixed a bug in fluxVar()
removed file ‘NAMESPACE’
blockedReact() now works also for irreversible models.
some improvements in readSBMLmod()
depends on rsbml version >= 2.4.0
first public beta release
some things were renamed:
class postAnalysis is now class ppProc
function postProcessing() is now function
.ppProcessing()
slot postAna in class optsol_simpleFBA is now
slot postProc
argument ppCmd in function simpleFBA() is now
argument poCmd
added slot preProc in class optsol_simpleFBA()
added argument prCmd in function simpleFBA():
same purpose as argument poCmd, but the commands are
executed immideately before solving the optimization problem.
added slot lethal to class optsol_doublefluxdel
added method ind2id() to class optsol_fluxdel,
optsol_genedel and optsol_doublegenedel
some minor improvements in doubleGeneDel()
added classes sybilError and postAnalysis
added function postProcessing()
added slot postAna in class optsol_simpleFBA
added method sensitivityAnalysis in class optObj
added argument ppCmd in simpleFBA():
The argument ppCmd should be a character vector. If it has a
length = 1, it will be treated as a function name, if it has
length > 1, it will be treated as function name (ppCmd[1])
plus arguments (ppCmd[-1]). Basically, ppCmd is treated as
a command, executed on the problem object (object of class optObj),
after the problem has been solved. The first element of ppCmd will
be used as function name, all other elements as arguments to that
function. The command will be joint with ‘,’ and
‘()’:
ppCmd[1] "(" ppCmd[-1] ")"
and ppCmd[-1] will be joind with ‘,’.
The string “LP_PROB” will be used as a placeholder for the
variable name of the problem object. If “LP_PROB” is used
in ppCmd, it will be replaced. The result of the execution of
ppCmd will be stored in an object of class postAnalysis
in the slot postAna of class optsol_simpleFBA.
Some examples:
perform sensitivity analysis with GLPK:
simpleFBA(<model>, ppCmd = "sensitivityAnalysis")
Here, ppCmd has length = 1,
“sensitivityAnalysis” will be treated as a function name
and executed on the problem object.
access reduced costs in conjunction with IBM ILOG CPLEX:
simpleFBA(<model>, solver = "cplex",
ppCmd = c("getDjCPLEX",
"LP_PROB@oobj$env", "LP_PROB@oobj$lp",
"0", "react_num(<model>)-1"))
In that example, ppCmd has length > 1, the first element
is the function name, the others are the arguments. For IBM ILOG CPLEX,
slot oobj of objects of class optObj is a list,
containing a pointer to the cplex environment env and a second
pointer to the problem object lp. The third and fourth argument
are begin and end for the function getDjCPLEX().
Remember: in IBM ILOG CPLEX, the first element has index 0!
Instances of class postAnalysis have two slots:
a single character string containing the executed command
the result of the post processing. If an error occured,
pa contains the error message and is of class
sybilError
fixed a bug in optimizer():
flux distribution was not saved when argument rebuildModel is
set to TRUE and the used algorithm is
“linearMOMA”
option resolve = TRUE in optimizer() is working again.
setting of parameters to lp solver with SYBIL_SETTINGS is
working again.
improved function blockedReact().
fixed a bug in changeObjCoefs()
fixed a bug in onlyChangeGPR()
fixed a bug in changeGPR()
added function changeGPR()
fixed a small bug in readSBMLmod()
fixed a bug in optimizer() in conjunction with IBM ILOG CPLEX
and parameter copyModel = TRUE
fixed a bug in optObj_Class:
loadProblemDataML() produced an error when
solver = "lpSolveAPI" and alg = "linearMOMA_COBRA"
method loadProblemDataMTF in optObj_Class failed when
IBM ILOG CPLEX is used
fixed a bug in mod2irrev(): slot rev2irrev contained
wrong entries.
argument resolve in optimizer() is not working in this
version!
completely rewritten function simpleFBA(); new (changed)
arguments:
(default: NA) fluxes with changed lower and upper
bounds
(default: NA) new lower bounds for fluxes in argument
react
(default: NA) new upper bounds for fluxes in argument
react
(default: FALSE) Boolean, if set to
TRUE, after FBA, the sum of all flux rates will be minimized
(default: FALSE) Boolean, if set to TRUE,
a minimized distance to a wild type flux distribution will be
generated
(default: NA) a single flux value (if
argument minTotalFlux is set to TRUE) for on optimized
objective function, or a flux vector (if argument minDist is
set to TRUE) for an optimized flux distribution.
If wtFluxes is NA, FBA will be performed. If arguments
minDist or minTotalFlux are TRUE and wtFluxes is
NA, the needed values will be calculated by FBA.
added method backupProb() in class optObj:
the functions
copyProbGLPK()/cloneProbCPLEX() will be used here, which
return a pointer to the new problem object
the functions
saveModelCLP()/write.lp() will be used here, which write
the specified problem to file. That file will be deleted after
building the new problem out of those. That may cause a lot IO.
new arguments to optimizer() [can be passed to
optimizer() by argument ... in e.g.
oneGeneDel() or doubleGeneDel()]:
(default: FALSE) Boolean. If set to
TRUE, the problem object will be recreated for every
optimization. That will increase the running time significantly!
(default: FALSE) Boolean. If set to TRUE,
the problem object will be taken from a backup copy. That backup copy
will be created prior to the very first optimization from the modelorg
object.
argument alg in optimizer() works now for all solvers
added the used algorithm in the logfile
added dependency on SparseM
added options exLethal and tol to doubleGeneDel()
argument alg in optimizer(): can be “FBA”
(default), “linearMOMA” or
“linearMOMA_COBRA”; works only with GLPK
added method length for objects of class optsol_fluxdel
added method “[” for objects of class
optsol_fluxdel
added argument alg in optimizer(): can be
“FBA” (default) or “linearMOMA”;
works only with glpk
added slot algorithm and methods algorithm and
algorithm<- for objects of class optsol_fluxdel
containing the name of the used algorithm.
added slot TOLERANCE in SYBIL_SETTINGS
added slot MAXIMUM in SYBIL_SETTINGS
added slot ALGORITHM in SYBIL_SETTINGS
added slot OPT_DIRECTION in SYBIL_SETTINGS
fixed a bug in optObj_Class, method changeColsBnds when
using ILOG CPLEX as solver
in optObj_Class the methods getColsLowBnds and
getColsUppBnds now use getLowBndsIdsCPLEX and
getUppBndsIdsCPLEX respectively when using ILOG CPLEX as solver
fixed a bug in nonZeroElements():
empty rows and columns are now handled correctly when argument
maorder is set to “column” or “row”
added support for low level interface sybilCPLEX (version 0.0.2)
minor changes applied to ‘uglyHack.R’ in order to support libsbml version 3.4.1
added setting LP_ALT_METHOD, used for resolve in
optimizer() and refineSol()
added class SYBIL_SETTINGS which contains default settings,
currently for the default lp solver and corresponding method.
The class contains the relevant set/get methods to fit the
content to ones needs.
added method addRowsCols to class optObj
added support for low level interface lpSolveAPI (version 5.5.0.14)
added support for low level interface sybilCLP (version 0.0.1)
argument resolve in oneFluxDel(), oneGeneDel(),
doubleFluxDel() and doubleGeneDel()
default: NA
if resolve is enabled, value should be a valid method
depending on the desired solver (e.g. “exact” in
case of solver = "glpk")
renamed optObj-method setColsBnds to changeColsBnds
renamed optObj-method setRowsBnds to changeRowsBnds
renamed optObj-method setObjCoefs to changeObjCoefs
argument resolve in optimizer() and refineSol():
no longer Boolean
default: NA
if non optimal solutions should be resolved: set to method resolve should use
argument logfile in optimizer() and refineSol():
no longer Boolean
default: NA
if a logfile should printed, logfile will be the filename
argument scaling in optimizer() and refineSol():
no longer Boolean
default: NA
if the model should be scaled, scaling will be the scaling method
added solver and method in ‘logfile’
added argument checkOptSolObj to function optimizer():
print a warning, in cases where solution status != 0
in objects of class optsol (default: FALSE)
added slots chlb and chub to class optsol:
containing lower and upper bounds of changed flux rates.
replace method: ch?b<-
get method: ch?b
support for low level interface sybilGLPK (version 0.1.0)