changeing the input method is no longer necessary

RBBGCMuso/R/calibMuso.R

@@ -113,10 +113,14 @@ calibMuso <- function(settings=setupMuso(), calibrationPar=NULL,
     ##change the epc file if and only if there are given parameters
        
     if(!is.null(parameters)){
-        changemulline(filePaths = epcInput,
+        changemulline(filePaths = epc[2],
                       calibrationPar = calibrationPar,
                       contents = parameters,
-                      fileOut = toModif,
+                      src = if(file.exists(bck)){
+                          bck
+                      } else {
+                          NULL
+                      })
                        # fileToChange = fileToChange,)
     }
     

RBBGCMuso/R/changeMuso.R

@@ -7,45 +7,30 @@
 #' @keywords internal
 #' 
 
-changemulline <- function(filePaths, calibrationPar, contents, fileOut, fileToChange, modifyOriginal=FALSE){
+
-    selectFileToWrite <- function(filePaths, fileTochange){
+changemulline <- function(filePaths, calibrationPar, contents, src){
-        if(fileToChange == "epc"){
+    # browser()
-            return(1)
+    if(is.null(src)){
-        } else{
+        src <- filePaths
-            return(2)            
     }
     
+    fileStringVector <- readLines(src)
+    Map(function(index, content){
+           fileStringVector <<- changeByIndex(index, content, fileStringVector)
+
+    }, calibrationPar, contents)
+    writeLines(fileStringVector, filePaths)
+    
 }
 
-    if(xor(is.list(calibrationPar), is.list(contents)) ){
+changeNth <- function (string,place,replacement) {
-        stop("If you change epc and ini files also, you have to use list for calibrationPar, and paramateters.")
+    trimws(gsub(sprintf("^((.*?\\s+){%s})(.*?\\s+)", place), sprintf("\\1%s ", replacement), paste0(string," "), perl=TRUE),
+           which="right")
 }
 
-    if(!is.element(fileToChange,c("ini","epc","both"))){
+changeByIndex <- function (rowIndex, parameter, fileStringVector){
-        stop("RBBGCMuso can only change ini or epc file, so fileToChange can be 'epc/ini/both'")
+    h <- round((rowIndex*100) %% 10)
+    i <- as.integer(rowIndex)
+    fileStringVector[i] <- changeNth(fileStringVector[i], h, parameter)        
+    fileStringVector
 }
-
-    if(fileToChange == "epc" | fileToChange == "ini"){
-        parMat<-matrix(c(calibrationPar, contents),nrow=length(calibrationPar))
-        if(nrow(parMat)!=1){
-            parMat <- parMat[order(parMat[,1]),]
-        }
-        changeMusoC(inFile = filePaths[selectFileToWrite(filePaths, fileToChange)],
-                    outFile = fileOut[selectFileToWrite(filePaths, fileToChange)],
-                    parMat)
-    }
-    
-    if(fileToChange == "both"){
-        parMat[[1]]<-cbind(calibrationPar[[1]], contents[[1]])
-        parMat[[1]]<- parMat[[1]][order(parMat[[1]][,1]),]
-        parMat[[2]]<-cbind(calibrationPar[[2]], contents[[2]])
-        parmat[[2]]<- parMat[[2]][order(parMat[[2]][,1]),]
-        
-        browser()
-        changeMusoC(filePaths[1],fileOut[1],parMat[[1]] )
-        changeMusoC(filePaths[2],fileOut[2],parMat[[2]] )
-    }
-
-}
-
-