Commit 7231dce5 authored by Habil, Ardalan (arhab001)'s avatar Habil, Ardalan (arhab001)
Browse files

BUG compartment FIX

parent cf61cc58
...@@ -413,7 +413,7 @@ if (is.null(compartmentsList)) { ...@@ -413,7 +413,7 @@ if (is.null(compartmentsList)) {
} }
missingId(compartmentsList) missingId(compartmentsList)
sybil::mod_compart(mod) <- compartmentsList[["id"]] comp_tmp_id <- compartmentsList[["id"]]
#------------------------------------------------------------------------------# #------------------------------------------------------------------------------#
...@@ -1056,6 +1056,27 @@ if(newSybil) ...@@ -1056,6 +1056,27 @@ if(newSybil)
} }
#------------------------------------------------------------------------------#
# compartments Attr @Ardalan #
#------------------------------------------------------------------------------#
# Define SKIP_COMPARTMENT FALSE= HAS NO REFERENCE
met_comp_tmp <- metabolitesList[["compartment"]][met_id_pos][SKIP_METABOLITE]
SKIP_COMPARTMENT<- comp_tmp_id %in% unique(met_comp_tmp)
sybil::mod_compart(mod) <- comp_tmp_id[SKIP_COMPARTMENT]
numcom<-length(mod_compart(mod))
comannotation <- compartmentsList[["annotation"]][SKIP_COMPARTMENT]
comnotes <- compartmentsList[["notes"]][SKIP_COMPARTMENT]
if(newSybil)
{
sybil::comp_attr(mod) <-data.frame(row.names=1:numcom)
if( !is.null(comannotation) && length(comannotation)==numcom )sybil::comp_attr(mod)[['annotation']]<-comannotation
if( !is.null(comnotes) && length(comnotes)==numcom )sybil::comp_attr(mod)[['notes']]<-comnotes
}
#------------------------------------------------------------------------------# #------------------------------------------------------------------------------#
# metabolite id's # # metabolite id's #
#------------------------------------------------------------------------------# #------------------------------------------------------------------------------#
...@@ -1071,7 +1092,7 @@ sybil::met_id(mod) <- gsub("-", "_", met_id_tmp, fixed = TRUE) ...@@ -1071,7 +1092,7 @@ sybil::met_id(mod) <- gsub("-", "_", met_id_tmp, fixed = TRUE)
# metabolite compartments # # metabolite compartments #
#------------------------------------------------------------------------------# #------------------------------------------------------------------------------#
met_comp_tmp <- metabolitesList[["compartment"]][met_id_pos][SKIP_METABOLITE] #met_comp_tmp <- metabolitesList[["compartment"]][met_id_pos][SKIP_METABOLITE]
sybil::met_comp(mod) <- match(met_comp_tmp, sybil::mod_compart(mod)) sybil::met_comp(mod) <- match(met_comp_tmp, sybil::mod_compart(mod))
...@@ -1149,20 +1170,6 @@ if(newSybil) ...@@ -1149,20 +1170,6 @@ if(newSybil)
} }
#------------------------------------------------------------------------------#
# compartments Attr @Ardalan #
#------------------------------------------------------------------------------#
sybil::mod_compart(mod) <- sybil::mod_compart(mod)[sort(unique(sybil::met_comp(mod)))]
numcom<-length(mod_compart(mod))
comannotation <- compartmentsList[["annotation"]]
comnotes <- compartmentsList[["notes"]]
if(newSybil)
{
sybil::comp_attr(mod) <-data.frame(row.names=1:numcom)
if( !is.null(comannotation) && length(comannotation)==numcom )sybil::comp_attr(mod)[['annotation']]<-comannotation
if( !is.null(comnotes) && length(comnotes)==numcom )sybil::comp_attr(mod)[['notes']]<-comnotes
}
#------------------------------------------------------------------------------# #------------------------------------------------------------------------------#
......
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