diff --git a/DESCRIPTION b/DESCRIPTION
index ee31cce95b67a06544b778f85f7775884eaa8e5f..bc9378415e2a4755981a70877eb2d2f264014e2c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: sybil
Type: Package
Title: Efficient Constrained Based Modelling in R
Version: 1.3.4
-Date: 2015-11-16
+Date: 2015-04-18
Authors@R: c(
person(c("C.", "Jonathan"), "Fritzemeier", role = c("cre", "ctb"), email = "clausjonathan.fritzemeier@uni-duesseldorf.de"),
person("Gabriel", "Gelius-Dietrich", role = c("aut")),
diff --git a/R/doubleGeneDel.R b/R/doubleGeneDel.R
index 84b3ac7a19872622050e5c346c519a30f911fb17..760c16809868e8f4f1987e361e5ad2e540ca1e58 100644
--- a/R/doubleGeneDel.R
+++ b/R/doubleGeneDel.R
@@ -195,44 +195,42 @@ doubleGeneDel <- function(model, geneList1, geneList2, lb = NULL, ub = NULL,
# Exclude everything from tmpMAT we do not need.
#tmpMAT <- tmpMAT[geneList1, geneList2, drop = FALSE]
-
- }
- else {
-
- tmpMAT <- matrix(FALSE, nrow = num_genes, ncol = num_genes)
- #diag(tmpMAT) <- TRUE
- for (i in seq(along = geneList1)) {
- tmpMAT[geneList1[i], geneList2[i]] <- TRUE
- }
+ geneList1 <- unique(geneList1)
+ geneList2 <- unique(geneList2)
+
+ # Exclude everything from tmpMAT we do not need.
+ tmpMAT <- tmpMAT[geneList1, geneList2, drop = FALSE]
+
+ # The number of TRUE's in tmpMAT is equal to the number of optimizations
+ num_opt <- sum(tmpMAT == TRUE)
+
+
+ rownames(tmpMAT) <- geneList1
+ colnames(tmpMAT) <- geneList2
+
+ deletions <- which(tmpMAT == TRUE, arr.ind = TRUE)
+
+ kogenesID <- cbind(geneList1[deletions[,"row"]],
+ geneList2[deletions[,"col"]])
+ }
+ else {
+
+# tmpMAT <- matrix(FALSE, nrow = num_genes, ncol = num_genes)
+# #diag(tmpMAT) <- TRUE
+# for (i in seq(along = geneList1)) {
+# tmpMAT[geneList1[i], geneList2[i]] <- TRUE
+# }
+
+ kogenesID <- cbind(geneList1, geneList2)
+
}
- geneList11 <- geneList1
- geneList22 <- geneList2
-
- geneList1 <- unique(geneList1)
- geneList2 <- unique(geneList2)
-
- # Exclude everything from tmpMAT we do not need.
- tmpMAT <- tmpMAT[geneList1, geneList2, drop = FALSE]
-
- # The number of TRUE's in tmpMAT is equal to the number of optimizations
- num_opt <- sum(tmpMAT == TRUE)
-
-
- rownames(tmpMAT) <- geneList1
- colnames(tmpMAT) <- geneList2
- #print(tmpMAT)
- #print(num_opt)
-
#------------------------------------------------------------------------------#
# run optimization #
#------------------------------------------------------------------------------#
- deletions <- which(tmpMAT == TRUE, arr.ind = TRUE)
-
- kogenesID <- cbind(geneList1[deletions[,"row"]],
- geneList2[deletions[,"col"]])
+
kogenes <- lapply(seq_len(nrow(kogenesID)), function(x) kogenesID[x, ])
fd <- .generateFluxdels(model, kogenes)
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index 2875c437eeb4e21e56ff3852c94e77b73c3e79ca..69f03dd906a17cee7b2801898d84310f34375cdd 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -6,6 +6,14 @@
\newcommand{\CRANpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
+
+\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.
+ \item corrected url of openCOBRA in the manual.
+ }
+}
+% ---------------------------------------------------------------------------- %
\section{Changes in version 1.3.3 2015-11-25}{
\itemize{
\item \code{addReact} crashed for irreversible models.
diff --git a/man/sybil-package.Rd b/man/sybil-package.Rd
index b4699acf95fb580e3e498dbda335171161485d10..784dcd7ea1745f1d40cd9fbf67d34285e598ba32 100644
--- a/man/sybil-package.Rd
+++ b/man/sybil-package.Rd
@@ -64,7 +64,7 @@ model <- readTSVmod(prefix = "Ec_core",
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic
reconstructions. \emph{BMC Bioinformatics} \bold{11}, 213.
- The openCOBRA project \url{http://opencobra.sourceforge.net/}.
+ The openCOBRA project \url{https://opencobra.github.io/}.
Becker, S. A., Feist, A. M., Mo, M. L., Hannum, G., Palsson, B. Ø. and
Herrgard, M. J. (2007) Quantitative prediction of cellular metabolism with