From f04aaf315ba00a59c68eb967d780f2d7dae338be Mon Sep 17 00:00:00 2001
From: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@hhu.de>
Date: Wed, 17 Dec 2014 15:08:29 +0100
Subject: [PATCH] bug fixed
---
R/addReact.R | 21 ++++++++++-----------
R/rmReact.R | 12 ++++++++++--
2 files changed, 20 insertions(+), 13 deletions(-)
diff --git a/R/addReact.R b/R/addReact.R
index 3c6ab34..1705cba 100644
--- a/R/addReact.R
+++ b/R/addReact.R
@@ -211,8 +211,14 @@ addReact <- function(model,
# subsystems
if (any(is.na(subSystem))) {
- newsubSys <- rBind(subSys(model),
- rep(FALSE, ncol(subSys(model))))
+ ss <- subSys(model)
+ if(ncol(ss)==0){ # if no subSys defined, rbind (see else) failed
+ dim(ss) <- c(nrow(ss)+1, ncol(ss))
+ newsubSys <- ss
+ }
+ else {
+ newsubSys <- rBind(ss, rep(FALSE, ncol(subSys(model))))
+ }
}
else {
if (is(subSystem, "logical")) {
@@ -230,14 +236,12 @@ addReact <- function(model,
newrxnGeneMat <- rBind(rxnGeneMat(model),
rep(FALSE, ncol(rxnGeneMat(model))))
}
- else if (nrow(rxnGeneMat(model)) > 0) {
+ else { #if (nrow(rxnGeneMat(model)) > 0) {
newrxnGeneMat <- rxnGeneMat(model)
dim(newrxnGeneMat) <- c(nrow(newrxnGeneMat)+1,
ncol(newrxnGeneMat))
}
- else {
- newrxnGeneMat <- rxnGeneMat(model)
- }
+ # do above else always.
if ( (is.na(gprAssoc)) || (gprAssoc == "") ) {
if ((length(gprRules(model)) > 0)) {
@@ -274,14 +278,9 @@ addReact <- function(model,
newrxnGeneMat <- cBind(newrxnGeneMat,
rep(FALSE, nrow(newrxnGeneMat)))
}
-# print("arsch")
}
}
-# print(newrxnGeneMat)
-# print(nCols)
-# print(geneInd)
-
# rxnGeneMat
newrxnGeneMat[nCols, geneInd] <- TRUE
diff --git a/R/rmReact.R b/R/rmReact.R
index c2cc8ce..3e9ff3c 100644
--- a/R/rmReact.R
+++ b/R/rmReact.R
@@ -148,8 +148,16 @@ rmReact <- function(model, react, rm_met = TRUE) {
subSys(mod_out) <- subSys(model)[keepReact, , drop = FALSE]
ag <- unique(unlist(genes(mod_out)))
- ncag <- nchar(ag)
- allGenes(mod_out) <- ag[which(ncag != 0)]
+ # old code tried to assign NULL to allGenes, if no gene was left.
+ if(length(ag)==0){
+ allGenes(mod_out) <- character(0)
+ }
+ else {
+ ncag <- nchar(ag)
+ ag <- ag[which(ncag != 0)]
+ allGenes(mod_out) <- ag
+ }
+
# reaction to gene mapping
#SrGMbin <- rxnGeneMat(mod_out) != 0
--
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