changes to modelorg for version 2.0

R/addReact.R

@@ -54,9 +54,7 @@ addReact <- function(model,
         stop("needs an object of class modelorg!")
     }
 	
-	if(!.hasSlot(model, "version")){
-		validObject(model)
-	}
+	stopifnot(checkVersion(model))
 
     if (length(met) != length(Scoef)) {
         stop("arguments 'met' and 'Scoef' must have the same length")

R/geneDel.R

@@ -41,9 +41,7 @@ geneDel <- function(model, genes, checkId = FALSE) {
       stop("needs an object of class modelorg!")
   }
   
-  if(!.hasSlot(model, "version")){
-  	validObject(model)
-  }
+  stopifnot(checkVersion(model))
   
   if (isTRUE(checkId)) {
       if (is(genes, "character")) {
@@ -99,9 +97,10 @@ geneDel <- function(model, genes, checkId = FALSE) {
 #print(reactInd)
   
   #x <- logical(length(allGenes(model)))
-  x <- rep(TRUE, length(allGenes(model)))
+  xAll <- rep(TRUE, length(allGenes(model)))
   #print(x)
-  x[geneInd] <- FALSE
+  xAll[geneInd] <- FALSE
+  names(xAll) <- allGenes(model)
   constReact <- logical(length(reactInd))
 #print(constReact)
 
@@ -112,10 +111,15 @@ geneDel <- function(model, genes, checkId = FALSE) {
   # If that's the case, the reaction needs gene bla.
 
   ru <- gprRules(model)[reactInd]
+  ge <- genes(model)[reactInd]
   for(i in 1:length(reactInd)) {
       #print(reactInd[i])
       #print(ru[i])
       #ev <- eval(parse(text = ru[i]))
+      
+      #define x for eval:
+      x <- xAll[ge[[i]]]
+      
       ev <- tryCatch(eval(parse(text = ru[i])), error = function(e) e)
       if (is(ev, "simpleError")) {
           stop("wrong gene association:",

R/modelorgClass.R

@@ -604,6 +604,7 @@ setMethod("optimizeProb", signature(object = "modelorg"),
              prCmd = NA, poCmd = NA,
              prCil = NA, poCil = NA, ...) {
 
+		stopifnot(checkVersion(object))
 
         if (!is.null(gene)) {
             if (!is.null(react)) {
@@ -1097,13 +1098,13 @@ setMethod("singletonMetabolites", signature(object = "modelorg"),
 setMethod("checkVersion", signature(object = "modelorg"),
 	function(object) {
 		if(!.hasSlot(object, "version")){
-			stop("No version slot found. Please use upgradeModelorg on object")
+			return("No version slot found. Please use upgradeModelorg with object")
 		}
 		
 		if(compareVersion(version(object), SYBIL_SETTINGS("MODELORG_VERSION")) == 0){
 			return(TRUE)
 		}
-		stop(paste0("modelorg has version ", object(version), ", but you need at least version ", version))
+		return(paste0("modelorg has version ", version(object), ", but you need at least version ", version))
 	}
 )
 

R/rmReact.R

@@ -42,9 +42,7 @@ rmReact <- function(model, react, rm_met = TRUE) {
 		stop("needs an object of class modelorg!")
 	}
 	
-	if(!.hasSlot(model, "version")){
-		validObject(model)
-	}
+	stopifnot(checkVersion(model))
 	
 	# check this, propably working wrong
 	if (is.na(match(is(react)[1], c("reactId", "numeric", "integer", "character")))) {

R/validmodelorg.R

@@ -38,13 +38,10 @@
         return("needs an object of class modelorg!")
     }
     
-    if(compareVersion(version(object), SYBIL_SETTINGS("MODELORG_VERSION")) != 0){
-		if(compareVersion(version(object), SYBIL_SETTINGS("MODELORG_VERSION")) == -1){
-			return("You are using an old version of the modelorg-Class. Use upgradeModelorg to get a compatible object!")
-		}
-		if(compareVersion(version(object), SYBIL_SETTINGS("MODELORG_VERSION")) == 1){
-			return("You are using a new version of the modelorg-Class. Plase upgrade your sybil package!")
-		}
+    versionCheck <- checkVersion(object)
+    
+    if(!isTRUE(versionCheck)){
+    	return(versionCheck)
     }
     
     if ((length(mod_id(object)) != 1) || (length(mod_name(object)) != 1)) {