From 3d586b729d5862c9deab97852b0da8712454bf56 Mon Sep 17 00:00:00 2001
From: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@hhu.de>
Date: Tue, 17 May 2016 14:52:41 +0200
Subject: [PATCH] updated documentation for version modelorg
---
NAMESPACE | 1 +
R/upgradeModelorg.R | 2 +-
inst/NEWS.Rd | 13 ++++++++-
man/SYBIL_SETTINGS.Rd | 13 ++++++---
man/checkVersion-methods.Rd | 58 +++++++++++++++++++++++++++++++++++++
man/modelorg-class.Rd | 13 +++++++++
man/upgradeModelorg.Rd | 46 +++++++++++++++++++++++++++++
7 files changed, 140 insertions(+), 6 deletions(-)
create mode 100644 man/checkVersion-methods.Rd
create mode 100644 man/upgradeModelorg.Rd
diff --git a/NAMESPACE b/NAMESPACE
index 737bebc..e782ef4 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -7,6 +7,7 @@ import(lattice)
importFrom("grDevices", "colorRampPalette", "grey")
importFrom("graphics", "arrows", "hist", "points", "polygon", "segments")
importFrom("utils", "combn", "edit", "read.table", "str", "write.table")
+importFrom("utils", "compareVersion")
exportPattern("^[^\\.]")
diff --git a/R/upgradeModelorg.R b/R/upgradeModelorg.R
index f85fa69..54031c1 100644
--- a/R/upgradeModelorg.R
+++ b/R/upgradeModelorg.R
@@ -38,7 +38,7 @@ upgradeModelorg <- function(object){
# just add version slot and run again.
object@version <- "2.0"
- rules <- lapply(gpr(object), sybil:::.parseBoolean)
+ rules <- lapply(gpr(object), .parseBoolean)
genes(object) <- sapply(rules, "[[", "gene")
gprRules(object) <- sapply(rules, "[[", "rule")
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index 69f03dd..37e5130 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -6,7 +6,18 @@
\newcommand{\CRANpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
-
+\section{Changes in version 2.0.0 2016-05-17}{
+ \itemize{
+ \item \code{modelorg}-class has changed and thus a slot \code{version} was introduced.
+ the method \code{upgradeModelorg} can convert from earlier instances of this
+ class. This method is only needed if \code{modelorg}-Objects were loaded
+ with \code{load} from disk.
+ \item \code{gprRules} were stored in an impractical format. This lead to bugs
+ in \code{rmReact} and further \code{geneDel}.
+ \item updated the manual of various files.
+ }
+}
+% ---------------------------------------------------------------------------- %
\section{Changes in version 1.3.4 2016-04-18}{
\itemize{
\item \code{doubleGeneDel} messed up the order of deletions when using exlicit gene lists.
diff --git a/man/SYBIL_SETTINGS.Rd b/man/SYBIL_SETTINGS.Rd
index 75810ed..471edb6 100644
--- a/man/SYBIL_SETTINGS.Rd
+++ b/man/SYBIL_SETTINGS.Rd
@@ -93,14 +93,15 @@
for a particular \code{"SOLVER"}, the corresponding default value will
be used in such a case.
}
- \item{\code{"TOLERANCE"}}{
- Tolerance value.\cr
- Default: \code{1E-6}.
- }
\item{\code{"MAXIMUM"}}{
Absolute maximum value.\cr
Default: \code{1000}.
}
+ \item{\code{"MODELORG_VERSION"}}{
+ Currtent version of \code{modelorg}-Class.\cr
+ Value: \code{"2.0"}.\cr
+ This value must not be changed.
+ }
\item{\code{"ALGORITHM"}}{
Algorithm to use in order to analyze metabolic networks.
Possible values are:
@@ -145,6 +146,10 @@
(e.g. GLPK).\cr
Default: \code{as.data.frame(NA)}.
}
+ \item{\code{"TOLERANCE"}}{
+ Tolerance value.\cr
+ Default: \code{1E-6}.
+ }
}
}
diff --git a/man/checkVersion-methods.Rd b/man/checkVersion-methods.Rd
new file mode 100644
index 0000000..528c275
--- /dev/null
+++ b/man/checkVersion-methods.Rd
@@ -0,0 +1,58 @@
+\name{checkVersion-methods}
+
+\docType{methods}
+\encoding{utf8}
+
+\alias{checkVersion}
+\alias{checkVersion-methods}
+\alias{checkVersion,modelorg}
+\alias{checkVersion,modelorg-method}
+
+\title{checks Version of modelorg}
+
+\description{
+ Checks the Version of the modelorg.
+}
+
+\usage{
+\S4method{checkVersion}{modelorg}(object)
+}
+
+\section{Methods}{
+ \describe{
+ \item{\code{signature(object = "modelorg")}}{
+ method to use with objects of class \code{\linkS4class{modelorg}}.
+ }
+ }
+}
+
+\arguments{
+ \item{object}{
+ An object of class \code{\linkS4class{modelorg}} or of class
+ \code{\linkS4class{summaryOptsol}}.
+ }
+}
+
+\details{
+ This method checks whether this instance of a modelorg-Class is of the currently
+ used version. All methods of sybil create the correct version of modelorg, but
+ if objects saved to disk may be of an older version. Current version can be
+ obtained by \code{SYBIL_SETTINGS("VERSION")}.
+}
+
+\author{
+ Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
+}
+
+
+\value{
+ Returns \code{TRUE} if the version is correct. Otherwise returns a character
+ stating the reason.
+}
+
+\seealso{
+ Class \code{\linkS4class{modelorg}},
+ method \code{\link{upgradeModelorg}} and \code{\link{SYBIL_SETTINGS}}
+}
+
+\keyword{methods}
diff --git a/man/modelorg-class.Rd b/man/modelorg-class.Rd
index 2b34679..c76921d 100644
--- a/man/modelorg-class.Rd
+++ b/man/modelorg-class.Rd
@@ -118,6 +118,10 @@
\alias{uppbnd,modelorg-method}
\alias{uppbnd<-}
\alias{uppbnd}
+\alias{version<-,modelorg-method}
+\alias{version,modelorg-method}
+\alias{version<-}
+\alias{version}
\encoding{utf8}
@@ -160,6 +164,9 @@
\item{\code{mod_name}:}{
Object of class \code{"character"} indicating the model name.
}
+ \item{\code{version}:}{
+ Object of class \code{"character"} indicating the model version.
+ }
\item{\code{mod_id}:}{
Object of class \code{"character"} indicating the model id.
}
@@ -430,6 +437,12 @@
\item{\code{uppbnd}:}{
\code{signature(object = "modelorg")}: gets the \code{uppbnd} slot.
}
+ \item{\code{version<-}:}{
+ \code{signature(object = "modelorg")}: sets the \code{version} slot.
+ }
+ \item{\code{version}:}{
+ \code{signature(object = "modelorg")}: gets the \code{version} slot.
+ }
}
}
diff --git a/man/upgradeModelorg.Rd b/man/upgradeModelorg.Rd
new file mode 100644
index 0000000..45073b3
--- /dev/null
+++ b/man/upgradeModelorg.Rd
@@ -0,0 +1,46 @@
+\name{upgradeModelorg}
+\alias{upgradeModelorg}
+
+\encoding{utf8}
+
+\title{
+ Upgrade modelorg to newer version.
+}
+\description{
+ Performs necessary changes to the object to promote it to a newer version.
+}
+\usage{
+ upgradeModelorg(object)
+}
+
+\arguments{
+ \item{object}{
+ An object of class \code{\linkS4class{modelorg}}.
+ }
+}
+
+\details{
+ This method performs the necessary changes on a modelorg object to promote
+ it to a newer version.
+
+ Changes from previous modelorg version (no version slot set) to version 2.0:
+ Representation in the gprRules slot is now incompatible to the earlier versions.
+}
+
+\value{
+ An object of class \code{\linkS4class{modelorg}}, matching the current
+ version requirements used by sybil.
+}
+
+\author{
+ Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
+}
+
+
+\examples{
+ data(Ec_core)
+ upgradeModelorg(Ec_core)
+}
+
+\keyword{upgrade, version}
+
--
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