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Commit aed4aa08 authored by ardalan's avatar ardalan
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exportSBML is now writeSBML

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NAMESPACE
+ 1
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View file @ aed4aa08
...@@ -49,7 +49,7 @@ getSBMLCompartList, ...@@ -49,7 +49,7 @@ getSBMLCompartList,
getSBMLSpeciesList, getSBMLSpeciesList,
getSBMLReactionsList, getSBMLReactionsList,
readSBMLmod, readSBMLmod,
exportSBML, writeSBML,
getSBMLFbcversion, getSBMLFbcversion,
getSBMLmodNotes, getSBMLmodNotes,
getSBMLmodAnnotation getSBMLmodAnnotation
......
R/sybilSBML.R
+ 568
− 568
View file @ aed4aa08
...@@ -330,7 +330,7 @@ deformatGene<-function(idstr) { ...@@ -330,7 +330,7 @@ deformatGene<-function(idstr) {
return(idstr) return(idstr)
} }
exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xml",recoverExtMet=TRUE,printNotes=TRUE,printAnnos=TRUE,validation=FALSE ){ writeSBML<- function(morg=NULL,level=2,version=4,fbcLevel=0,filename="export.xml",recoverExtMet=FALSE,printNotes=TRUE,printAnnos=TRUE,validation=FALSE ){
if(class(morg)!="modelorg"){ if(class(morg)!="modelorg"){
stop("morg has to be of class modelorg\n") stop("morg has to be of class modelorg\n")
} }
...@@ -340,7 +340,7 @@ exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xm ...@@ -340,7 +340,7 @@ exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xm
{ {
# test if Matrix has no double values # test if Matrix has no double values
if( !all( S(morg) == floor(S(morg))) ) warning("Level 1 does not support double values") if( !all( S(morg) == floor(S(morg))) ) warning("Level 1 does not support double values")
FbcLevel=0 fbcLevel=0
if(version != 2) if(version != 2)
{ {
warning("just Level 1 Version 2 will be supported") warning("just Level 1 Version 2 will be supported")
...@@ -348,7 +348,7 @@ exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xm ...@@ -348,7 +348,7 @@ exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xm
} }
}else if (level==2) }else if (level==2)
{ {
FbcLevel=0 fbcLevel=0
if(version >5) if(version >5)
{ {
warning("Level 2 Version 5 will be supported") warning("Level 2 Version 5 will be supported")
...@@ -361,7 +361,7 @@ exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xm ...@@ -361,7 +361,7 @@ exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xm
} }
} }
else if (level==3) else if (level==3)
{ if(FbcLevel >2)FbcLevel=2 { if(fbcLevel >2)fbcLevel=2
if(version != 1) if(version != 1)
{ {
print("Level 3 Version 1 will be supported") print("Level 3 Version 1 will be supported")
...@@ -454,10 +454,10 @@ exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xm ...@@ -454,10 +454,10 @@ exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xm
#Have Gene if not ->no need to write in FBC2 #Have Gene if not ->no need to write in FBC2
if(haveform) if(haveform)
{ {
if(FbcLevel==0)met_notes[i]<-sub("FORMULA: [^<]+",paste("FORMULA: ",met_formula[i], sep = ""), met_notes[i], perl = TRUE) if(fbcLevel==0)met_notes[i]<-sub("FORMULA: [^<]+",paste("FORMULA: ",met_formula[i], sep = ""), met_notes[i], perl = TRUE)
else met_notes[i]<-sub(paste("<",tag,">","FORMULA: [^<]+","</",tag,">",sep = ""),"",met_notes[i], perl = TRUE) else met_notes[i]<-sub(paste("<",tag,">","FORMULA: [^<]+","</",tag,">",sep = ""),"",met_notes[i], perl = TRUE)
} }
else if(FbcLevel==0) met_notes[i]<-gsub("</notes>",paste("<",tag,">","FORMULA: ",met_formula[i],"</",tag,">","\n</notes>",sep = ""),met_notes[i]) else if(fbcLevel==0) met_notes[i]<-gsub("</notes>",paste("<",tag,">","FORMULA: ",met_formula[i],"</",tag,">","\n</notes>",sep = ""),met_notes[i])
} }
if (!is.null(met_charge)) if (!is.null(met_charge))
{ {
...@@ -465,13 +465,13 @@ exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xm ...@@ -465,13 +465,13 @@ exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xm
#Have Subsystem #Have Subsystem
if(havecharge) if(havecharge)
{ {
if(FbcLevel !=0 || (level==2 && version==1 )) if(fbcLevel !=0 || (level==2 && version==1 ))
met_notes[i]<-sub(paste("<",tag,">","CHARGE: [^<]+","</",tag,">",sep = ""),"",met_notes[i], perl = TRUE) met_notes[i]<-sub(paste("<",tag,">","CHARGE: [^<]+","</",tag,">",sep = ""),"",met_notes[i], perl = TRUE)
else met_notes[i]<-sub("CHARGE: [^<]+",paste("CHARGE: ",met_charge[i], sep = ""), met_notes[i], perl = TRUE) else met_notes[i]<-sub("CHARGE: [^<]+",paste("CHARGE: ",met_charge[i], sep = ""), met_notes[i], perl = TRUE)
} }
else if(FbcLevel==0) if(level!=2 && version!=1) met_notes[i]<-gsub("</notes>",paste("<",tag,">","CHARGE: ",met_charge[i],"</",tag,">","\n</notes>",sep = ""),met_notes[i]) else if(fbcLevel==0) if(level!=2 && version!=1) met_notes[i]<-gsub("</notes>",paste("<",tag,">","CHARGE: ",met_charge[i],"</",tag,">","\n</notes>",sep = ""),met_notes[i])
} }
} }
} }
...@@ -504,10 +504,10 @@ exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xm ...@@ -504,10 +504,10 @@ exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xm
#Have Gene if not ->no need to write in FBC2 #Have Gene if not ->no need to write in FBC2
if(havegene) if(havegene)
{ {
if(FbcLevel==2) react_notes[i]<-sub(paste("<",tag,">","GENE[_ ]?ASSOCIATION: [^<]+","</",tag,">",sep = ""),"",react_notes[i], perl = TRUE) if(fbcLevel==2) react_notes[i]<-sub(paste("<",tag,">","GENE[_ ]?ASSOCIATION: [^<]+","</",tag,">",sep = ""),"",react_notes[i], perl = TRUE)
else react_notes[i]<-sub("GENE[_ ]?ASSOCIATION: [^<]+",paste("GENE_ASSOCIATION: ",gpr(morg)[i], sep = ""), react_notes[i], perl = TRUE) else react_notes[i]<-sub("GENE[_ ]?ASSOCIATION: [^<]+",paste("GENE_ASSOCIATION: ",gpr(morg)[i], sep = ""), react_notes[i], perl = TRUE)
} }
else if(FbcLevel!=2)react_notes[i]<-gsub("</notes>",paste("<",tag,">","GENE_ASSOCIATION: ",gpr(morg)[i],"</",tag,">","\n</notes>",sep = ""),react_notes[i]) else if(fbcLevel!=2)react_notes[i]<-gsub("</notes>",paste("<",tag,">","GENE_ASSOCIATION: ",gpr(morg)[i],"</",tag,">","\n</notes>",sep = ""),react_notes[i])
#Have Subsystem #Have Subsystem
if(havesub)react_notes[i]<-sub("SUBSYSTEM: [^<]+",paste("SUBSYSTEM: ",newsubS[i], sep = ""), react_notes[i], perl = TRUE) if(havesub)react_notes[i]<-sub("SUBSYSTEM: [^<]+",paste("SUBSYSTEM: ",newsubS[i], sep = ""), react_notes[i], perl = TRUE)
...@@ -532,7 +532,7 @@ exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xm ...@@ -532,7 +532,7 @@ exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xm
success <-.Call("exportSBML", PACKAGE = "sybilSBML", success <-.Call("exportSBML", PACKAGE = "sybilSBML",
as.integer(version), as.integer(version),
as.integer(level), as.integer(level),
as.integer(FbcLevel), as.integer(fbcLevel),
as.character(filename), as.character(filename),
SYBIL_SETTINGS("MAXIMUM"), SYBIL_SETTINGS("MAXIMUM"),
as.character(mod_desc(morg)), as.character(mod_desc(morg)),
......
man/exportSBML.Rd → man/writeSBML.Rd
+ 118
− 119
View file @ aed4aa08
\name{exportSBML} \name{writeSBML}
\alias{exportSBML} \alias{writeSBML}
\encoding{utf8} \encoding{utf8}
\title{Exports a Metabolic Network in SBML Format} \title{Exports a Metabolic Network in SBML Format}
\description{ \description{
The function exports a metabolic network from S4 object of the class \code{\link{modelorg}} in SBML format. The function The function exports a metabolic network from S4 object of the class \code{\link{modelorg}} in SBML format. The function returns TRUE if the SBML file is successfully built.
returns a success message if exported to SBML file is successfully built.
} }
\usage{ \usage{
exportSBML(morg=NULL,level=2,version=4,FbcLevel=0, writeSBML(morg=NULL,level=2,version=4,fbcLevel=0,
filename="export.xml", filename="export.xml",
recoverExtMet=TRUE, recoverExtMet=FALSE,
printNotes=TRUE, printNotes=TRUE,
printAnnos=TRUE, printAnnos=TRUE,
validation=FALSE) validation=FALSE)
...@@ -32,7 +31,7 @@ ...@@ -32,7 +31,7 @@
A single integer value containing the SBML version for the exporting SBML file. \cr A single integer value containing the SBML version for the exporting SBML file. \cr
Default: \code{4}. Default: \code{4}.
} }
\item{FbcLevel}{ \item{fbcLevel}{
A single integer value containing the fbc package version for the exporting SBML file. \cr A single integer value containing the fbc package version for the exporting SBML file. \cr
Default: \code{2}. Default: \code{2}.
} }
...@@ -42,7 +41,7 @@ ...@@ -42,7 +41,7 @@
} }
\item{recoverExtMet}{ \item{recoverExtMet}{
Boolean: recover external metabolites and refer them to compartment \code{"BOUNDARY"}.\cr Boolean: recover external metabolites and refer them to compartment \code{"BOUNDARY"}.\cr
Default: \code{TRUE}. Default: \code{FALSE}.
} }
\item{printNotes}{ \item{printNotes}{
Boolean: print Notes from original SBML file .\cr Boolean: print Notes from original SBML file .\cr
...@@ -66,7 +65,7 @@ ...@@ -66,7 +65,7 @@
} }
\value{ \value{
A single character string for a success message. A single boolean value for a successful export .
} }
\references{ \references{
...@@ -100,7 +99,7 @@ ...@@ -100,7 +99,7 @@
\note{ \note{
The function \code{exportSBML} makes use of the library The function \code{writeSBML} makes use of the library
\code{libSBML} (\url{http://www.sbml.org}). \code{libSBML} (\url{http://www.sbml.org}).
} }
...@@ -112,7 +111,7 @@ ...@@ -112,7 +111,7 @@
dir <- system.file(package = "sybilSBML", "extdata") dir <- system.file(package = "sybilSBML", "extdata")
file <- file.path(dir, "ecoli_core_model.xml") file <- file.path(dir, "ecoli_core_model.xml")
mod <- readSBMLmod(file, bndCond = FALSE) mod <- readSBMLmod(file, bndCond = FALSE)
exportSBML(mod,level=3,version=1,FbcLevel=2) writeSBML(mod,level=3,version=1,fbcLevel=2)
} }
\keyword{ IO } \keyword{ IO }
......
src/sybilSBML.c
+ 10
− 5
View file @ aed4aa08
...@@ -2291,11 +2291,16 @@ SEXP exportSBML (SEXP version, SEXP level,SEXP FbcLevel, SEXP filename,SEXP sybi ...@@ -2291,11 +2291,16 @@ SEXP exportSBML (SEXP version, SEXP level,SEXP FbcLevel, SEXP filename,SEXP sybi
// write SBML file // write SBML file
int result = writeSBML(sbmlDoc, fname); int result = writeSBML(sbmlDoc, fname);
SEXP out = R_NilValue; SEXP out = R_NilValue;
if (result) out = Rf_mkString(append_strings("Wrote file",fname," ")); if (result)
else out = Rf_mkString(append_strings("Failed to write",fname," ")); {
printf("Wrote file %s \n",fname);
out = Rf_ScalarLogical(1);
//UNPROTECT(1); }
else
{
printf("Cloud not write file %s \n",fname);
out = Rf_ScalarLogical(0);
}
return out; return out;
} }
......
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