Removed some commented/unused code from computePred.R

computePred.R

@@ -283,122 +283,6 @@ write.table(evolDist,paste0(prot,"_pred_evolEpi.txt"))
 print("done")
 
 print("running normalization...")
-#normWeightMode="trace+pc+cv"
-#normWeightMode="trace+pc"
-#normWeightMode="trace+cv"
-#normWeightMode="trace"
-#print(normWeightMode)
-#In future, you may need to comment line 44 to use this functionality if you do
-#weighting not just in normalization.
-#This part of the code obtains max values of Trace, PC, or CV for weighting the 
-#normalized results. 
-
-# trace = c()
-# if((normWeightMode=="maxtracepc") | (normWeightMode=="maxpctrace")){
-#   print(paste("Using ", normWeightMode))
-#   for (row in 1:nrow(jet)) { 
-#     if(sum(colnames(jet)=="traceMax")==1){
-#       trace<-append(trace, max(jet[row, "traceMax"], jet[row, "pc"]))
-#     }else{
-#         trace<-append(trace, max(jet[row, "trace"], jet[row, "pc"]))
-#     }
-#   }
-# } else if ((normWeightMode=="maxtracecv") | (normWeightMode=="maxcvtrace")){
-#   print(paste("Using ", normWeightMode))
-#   for (row in 1:nrow(jet)) {
-#     if(sum(colnames(jet)=="traceMax")==1){
-#       trace<-append(trace, max(jet[row, "traceMax"], jet[row, "cv"]))
-#     }else{
-#         trace<-append(trace, max(jet[row, "trace"], jet[row, "cv"]))
-#     } 
-#   }
-# } else if ((normWeightMode=="maxtracedfi") | (normWeightMode=="maxdfitrace")){
-#   print(paste("Using ", normWeightMode))
-#   for (row in 1:nrow(jet)) {
-#     if(sum(colnames(jet)=="traceMax")==1){
-#       trace<-append(trace, max(jet[row, "traceMax"], jet[row, "dfi"]))
-#     }else{
-#         trace<-append(trace, max(jet[row, "trace"], jet[row, "dfi"]))
-#     } 
-#   }
-# } else if ((normWeightMode=="maxtracebfactor") | (normWeightMode=="maxbfactortrace")){
-#   print(paste("Using ", normWeightMode))
-#   for (row in 1:nrow(jet)) {
-#     if(sum(colnames(jet)=="traceMax")==1){
-#       trace<-append(trace, max(jet[row, "traceMax"], jet[row, "bfactor"]))
-#     }else{
-#         trace<-append(trace, max(jet[row, "trace"], jet[row, "bfactor"]))
-#     } 
-#   }
-# }else if ((normWeightMode=="maxtracepccv")|(normWeightMode=="maxtracecvpc")){
-#   print(paste("Using ", normWeightMode))
-#   for (row in 1:nrow(jet)) {
-#     if(sum(colnames(jet)=="traceMax")==1){
-#       trace<-append(trace, max(jet[row, "traceMax"], max(jet[row, "pc"], jet[row, "cv"])))
-#     }else{
-#       trace<-append(trace, max(jet[row, "trace"], max(jet[row, "pc"], jet[row, "cv"])))
-#     }
-#   }
-# } else if ((normWeightMode=="maxtracehalfpccv")|(normWeightMode=="maxtracehalfcvpc")){
-#   print(paste("Using ", normWeightMode))
-#   for (row in 1:nrow(jet)) {
-#     if(sum(colnames(jet)=="traceMax")==1){
-#       trace<-append(trace, max(jet[row, "traceMax"], (jet[row, "pc"]+jet[row, "cv"])/2.0 ))
-#     }else{
-#       trace<-append(trace, max(jet[row, "trace"], (jet[row, "pc"]+jet[row, "cv"])/2.0 ))
-#     }
-#   }
-# }else if ((normWeightMode=="halfcvpc") | (normWeightMode=="halfpccv")){
-#   print(paste("Using ", normWeightMode))
-#   for (row in 1:nrow(jet)) {
-#     trace<-append(trace, (jet[row, "pc"]+jet[row, "cv"])/2.0)
-#     }  
-# } else if ((normWeightMode=="maxcvpc") | (normWeightMode=="maxpccv")){
-#   print(paste("Using ", normWeightMode))
-#   for (row in 1:nrow(jet)) {
-#     trace<-append(trace, max(jet[row, "pc"], jet[row, "cv"]))
-#     }  
-# }else if (normWeightMode=="trace"){
-#   print("Using only JET2 traces")
-#   for (row in 1:nrow(jet)) {
-#     if(sum(colnames(jet)=="traceMax")==1){
-#       trace<-append(trace, jet[row, "traceMax"])
-#     }else{
-#       trace<-append(trace, jet[row, "trace"])
-#     } 
-#   }
-# }else if (normWeightMode=="tracemovingaverage"){
-#   print("Using only tracemovingaverage")
-#   for (row in 1:nrow(jet)) {
-#     trace<-append(trace, jet[row, "tracemovingaverage"]) 
-#   }
-#   print("Here is the tracemovingaverage!")
-#   print(trace)
-# }else if (normWeightMode=="cv"){
-#   print("Using only CV traces")
-#   for (row in 1:nrow(jet)) {
-#     trace<-append(trace, jet[row, "cv"]) 
-#   }
-# }else if (normWeightMode=="pc"){
-#   print("Using only PC traces")
-#   for (row in 1:nrow(jet)) {
-#     trace<-append(trace, jet[row, "pc"]) 
-#   }
-# }else if (normWeightMode=="dfi"){
-#   print("Using only DFI values")
-#   for (row in 1:nrow(jet)) {
-#     trace<-append(trace, jet[row, "dfi"]) 
-#   }
-# }else if (normWeightMode=="bfactor"){
-#   print("Using only Bfactor values")
-#   for (row in 1:nrow(jet)) {
-#     trace<-append(trace, jet[row, "bfactor"]) 
-#   }
-# }else{
-#   print("ERROR: Unknown --normWeightMode selected!")
-#   print("It can only be 'trace', 'tracemovingaverage', 'pc', 'cv', 'dfi', 'bfactor', 'maxtracepc', 'maxtracecv', 'maxtracepccv', 'halfcvpc', 'maxtracedfi' or 'maxtracebfactor'!")
-# }
-#print(trace)
 
 if(simple){
   #Independent model normalization