| NEWS | R Documentation |
removed old file ‘NEWS.Rd’ from top level directory
updated package vignette
slot rhs of class modelorg is not set
file ‘NEWS’ is now in ‘inst/NEWS.Rd’
removed arguments verboseMode, loglevel, logfile
and logfileEnc from function readSBMLmod; use function
sink instead
fixed a bug in .uglyHack: tries no longer to fix SBMLWarnings,
which is not necessary
.uglyHack uses tempfile() to generate corrected
SBML files
fixed a bug in readSBMLmod(): slot subSys was not of
correct data type in rare cases
better SBML id formatting in readSBMLmod()
compatible with sybil version 0.5.12: replaced SparseM with Matrix
some additions to .uglyHack()
fixed a small bug in readSBMLmod(), when parsing sub systems
fixed a small bug in readSBMLmod() concerning the detection of
gpr rules
fixed a bug in readSBMLmod(): genes from reactions which
are excluded from the model are not read
very minor adjustments in readSBMLmod()
readSBMLmod() will continue reading the model,
if rsbml produces warnings. Check warnings in the log file;
arguments loglevel and logfile in readSBMLmod()
updated documentation
added boolean arguments remMet, contrMet,
singletonMet and deadEndmet to readSBMLmod(),
the two boolen arguments remSingleMet and
constrSingleMet are removed, see help("readSBMLmod")
for details
some small changes according to codetools
slots met_single and react_single of class
modelorg are initialized with NA, not FALSE
new arguments for readSBMLmod():
mergeMet, balanceReact, remUnusedMetReact,
remSingleMet, constrSingleMet and tol.
See help("readSBMLmod") for details
a warning is produced, if a metabolite is used only once in S
readSBMLmod() removes unused metabolites and reactions
(rows and lines without any non-zero entries)
readSBMLmod() merges and balances metabolites as in
readTSVmod() from sybil
fixed a bug in readSBMLmod() concerning the number of
metabolite names and metabolite compartments
added NAMESPACE
new boolean parameter bndCnd in readSBMLmod():
If set to TRUE, external metabolites are those,
having the SBML tag boundaryCondition set to TRUE.
If set to FALSE, external metabolites are recogized via
extMetFlag
usage of class sybilLog in readSBMLmod() with four new
parameters. See help("readSBMLmod") for details.
fixed a bug in readSBMLmod():
if an external metabolite id is removed and it occcurs in
a reaction, that particular reaction is read correctly.
new boolean parameter ignoreNoAn in readSBMLmod():
if set to TRUE, any notes and annotation fields in the
listOfReactions in an SBML file are ignored
(default: TRUE).
unused metabolites having no non-zero entry in S, are removed from S
and the metabolites list in instances of class modelorg
updated documentation
added compatibility to sybil version >= 0.4.1:
slot subSys is now of class matrix
fixed a bug in readSBMLmod(): metablite id's differing
only in the number of consecutive '_' are now recogized
as different metabolite id's.
readSBMLmod() can now read the Yeast model in the file
‘Sc_iND750_GlcMM.xml’ from the Palsson group.
If the SBML file contains reactions with metabolites used as reactands and products at the same time, the stoichiometric coefficient for those metabolites is the sum of reactand and product.
fixed some regular expressions when parsing metabolite names and id's
added argument extMetFlag which is used to identify external
metabolites
reads subsystem information also from annotations
initial public release