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# Indent <string> using <count> tabs.
indent <- function(string,count)
{
if (count == 0)
return(string)
return(paste(paste(rep("\t",count),collapse=""), string, sep=""))
}
# Export a Boolean network <network> to an sbml-qual file <fileName>.
# If <generateDNFs>, a new symbolic representation for the interactions
# is generated on the basis of the truth tables (in disjunctive normal form).
# Otherwise, the $expression elements of the interactions are parsed.
# If <saveFixed> is true, constant transition functions are exported for fixed genes
# instead of their true transition functions
toSBML <- function(network, file, generateDNFs=FALSE, saveFixed = TRUE)
{
symbolic <- inherits(network,"SymbolicBooleanNetwork")
stopifnot(inherits(network,"BooleanNetwork") || symbolic)
if (symbolic)
{
if (any(network$timeDelays > 1))
stop("SBML does not support networks with time delays!")
parseTrees <- network$interactions
}
else
{
parseTrees <- NULL
if (generateDNFs == FALSE)
# Check whether all interactions have suitable string representations
{
tryCatch(
{
# parse the string representations
parseTrees <- lapply(network$interactions,
function(int)parseBooleanFunction(int$expression))
},
error=function(e)
{
warning(paste("The transition functions of this network did not contain valid symbolic expressions!",
"Generating DNF representations from the truth tables!"))
# There was an error parsing a string representation => generate DNFs
generateDNFs <<- TRUE
})
}
if (generateDNFs != FALSE)
# build new representations of the functions in disjunctive normal form
{
network$interactions <- lapply(network$interactions, function(interaction)
{
table <- allcombn(2, length(interaction$input)) - 1
interaction$expression <- getDNF(interaction$func,
network$genes[interaction$input],
generateDNFs)
return(interaction)
})
# parse the DNF representations
parseTrees <- lapply(network$interactions,
function(int)parseBooleanFunction(int$expression))
}
names(parseTrees) <- network$genes
}
# generate a network identifier from the file name
id <- sub(".sbml", "", basename(file), fixed=TRUE)
id <- gsub("[^a-zA-Z0-9_]+","_",id)
# open a string connection
output <- NULL
f <- textConnection("output", encoding="UTF-8", open="w", local=TRUE)
# write document header
cat(file=f, "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
cat(file=f, "<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" level=\"3\" version=\"1\" xmlns:qual=\"http://www.sbml.org/sbml/level3/version1/qual/version1\" qual:required=\"true\">\n")
cat(file=f, "\t<model id=\"", id, "\">\n", sep="")
# write default compartment
cat(file=f, "\t\t<listOfCompartments>\n")
cat(file=f, "\t\t\t<compartment id=\"default\" constant=\"true\"/>\n")
cat(file=f, "\t\t</listOfCompartments>\n")
# write genes
cat(file=f, "\t\t<qual:listOfQualitativeSpecies>\n")
for (gene in network$genes)
{
if ((saveFixed && network$fixed[gene] != -1) ||
(!symbolic && network$interactions[[gene]]$input[1] == 0))
{
if (saveFixed && network$fixed[gene] != -1)
level <- network$fixed[gene]
else
level <- network$interactions[[gene]]$func[1]
cat(file=f, "\t\t\t<qual:qualitativeSpecies qual:compartment=\"default\"",
" qual:constant=\"true\" qual:id=\"", gene,
"\" qual:name=\"", gene,
"\" qual:initialLevel=\"", level,
"\" qual:maxLevel=\"", level,
"\"/>\n", sep="")
}
else
cat(file=f, "\t\t\t<qual:qualitativeSpecies qual:compartment=\"default\"",
" qual:constant=\"false\" qual:id=\"", gene,
"\" qual:name=\"", gene, "\" qual:maxLevel=\"1\"/>\n", sep="")
}
cat(file=f, "\t\t</qual:listOfQualitativeSpecies>\n")
# write transition functions
cat(file=f, "\t\t<qual:listOfTransitions>\n")
for (gene in network$genes)
{
if ((!saveFixed || network$fixed[[gene]] == -1) &&
(symbolic || network$interactions[[gene]]$input[1] != 0))
{
cat(file=f, "\t\t\t<qual:transition qual:id=\"tr_", gene,
"\" qual:name=\"Interactions targeting ", gene, "\">\n", sep="")
cat(file=f, "\t\t\t\t<qual:listOfInputs>\n")
if (symbolic)
inputs <- getInputs(network$interactions[[gene]])
else
inputs <- network$genes[network$interactions[[gene]]$input]
for (input in inputs)
cat(file=f, "\t\t\t\t\t<qual:input qual:qualitativeSpecies=\"", input,
"\" qual:transitionEffect=\"none\"/>\n", sep="")
cat(file=f, "\t\t\t\t</qual:listOfInputs>\n")
cat(file=f, "\t\t\t\t<qual:listOfOutputs>\n")
cat(file=f, "\t\t\t\t\t<qual:output qual:qualitativeSpecies=\"", gene,
"\" qual:transitionEffect=\"assignmentLevel\"/>\n", sep="")
cat(file=f, "\t\t\t\t</qual:listOfOutputs>\n")
cat(file=f, "\t\t\t\t<qual:listOfFunctionTerms>\n")
cat(file=f, "\t\t\t\t\t<qual:functionTerm qual:resultLevel=\"1\">\n")
cat(file=f, "\t\t\t\t\t\t<math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n")
parseTree <- parseTrees[[gene]]
cat(file=f, MathMLFromParseTree(parseTree, indentLevel=7))
cat(file=f, "\t\t\t\t\t\t</math>\n")
cat(file=f, "\t\t\t\t\t</qual:functionTerm>\n")
cat(file=f, "\t\t\t\t\t<qual:defaultTerm qual:resultLevel=\"0\"/>\n")
cat(file=f, "\t\t\t\t</qual:listOfFunctionTerms>\n")
cat(file=f, "\t\t\t</qual:transition>\n")
}
}
# finish document
cat(file=f, "\t\t</qual:listOfTransitions>\n")
cat(file=f, "\t</model>\n")
cat(file=f, "</sbml>\n")
close(f)
# open file and write the complete XML string
f <- file(file, encoding="UTF-8", open="w")
cat(file=f,output,sep="\n")
close(f)
}
# Build a MathML representation of a parse tree <tree>
# that represents a symbolic Boolean expression.
# Indentation of the XML nodes starts with <indentLevel>.
# Returns a string with MathML code.
MathMLFromParseTree <- function(tree,indentLevel=0)
{
res <- switch(tree$type,
operator =
{
if (tree$operator %in% c("timeis","timegt","timelt"))
stop(sprintf("Operator \"%s\" not supported in SBML!", tree$operator));
if (tree$operator %in% c("maj","sumis","sumlt","sumgt"))
# convert special predicates to general Boolean formulae
tree <- expandCountPredicate(tree)
if (tree$negated)
paste(indent("<apply>\n", indentLevel),
indent("<not/>\n", indentLevel+1),
indent("<apply>\n" ,indentLevel+1),
indent({if (tree$operator=="|" || tree$operator=="any")
{"<or/>\n"} else{"<and/>\n"}}, indentLevel+2),
paste(sapply(tree$operands,MathMLFromParseTree, indentLevel+2),
collapse=""),
indent("</apply>\n", indentLevel+1),
indent("</apply>\n", indentLevel), sep="")
else
paste(indent("<apply>\n", indentLevel),
indent({if (tree$operator=="|" || tree$operator=="any")
{"<or/>\n"} else{"<and/>\n"}}, indentLevel+1),
paste(sapply(tree$operands, MathMLFromParseTree, indentLevel+1),
collapse=""),
indent("</apply>\n", indentLevel), sep="")
},
atom =
{
if ((tree$name == "0" && !tree$negated) || (tree$name == "1" && tree$negated))
indent("<cn type=\"integer\">0</cn>\n", indentLevel)
else
if ((tree$name == "1" && !tree$negated) || (tree$name == "0" && tree$negated))
indent("<cn type=\"integer\">1</cn>\n", indentLevel)
else
paste(indent("<apply>\n",indentLevel),
indent("<eq/>\n", indentLevel+1),
indent(paste("<ci>",tree$name,"</ci>\n",sep=""),indentLevel+1),
indent(paste("<cn type=\"integer\">", {if (tree$negated) 0 else 1},
"</cn>\n", sep=""), indentLevel+1),
indent("</apply>\n",indentLevel), sep="")
})
return(res)
}
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