Removed unnecessary combinedv[1-4] normWeightMode options.

computePred.R

@@ -186,46 +186,6 @@ if((normWeightMode=="maxtracepc") | (normWeightMode=="maxpctrace")){
       trace<-append(trace, jet[row, "trace"])
     } 
   }
-}else if (normWeightMode=="combinedv1"){
-  print("Using only combinedv1")
-  for (row in 1:nrow(jet)) {
-    if(sum(colnames(jet)=="combinedv1")==1){
-      trace<-append(trace, jet[row, "combinedv1"])
-    }else{
-      print("No field called combinedv1 in the JET output!")
-      quit(status=-1)
-    } 
-  }
-}else if (normWeightMode=="combinedv2"){
-  print("Using only combinedv2")
-  for (row in 1:nrow(jet)) {
-    if(sum(colnames(jet)=="combinedv2")==1){
-      trace<-append(trace, jet[row, "combinedv2"])
-    }else{
-      print("No field called combinedv2 in the JET output!")
-      quit(status=-1)
-    } 
-  }
-}else if (normWeightMode=="combinedv3"){
-  print("Using only combinedv3")
-  for (row in 1:nrow(jet)) {
-    if(sum(colnames(jet)=="combinedv3")==1){
-      trace<-append(trace, jet[row, "combinedv3"])
-    }else{
-      print("No field called combinedv3 in the JET output!")
-      quit(status=-1)
-    } 
-  }
-}else if (normWeightMode=="combinedv4"){
-  print("Using only combinedv4")
-  for (row in 1:nrow(jet)) {
-    if(sum(colnames(jet)=="combinedv4")==1){
-      trace<-append(trace, jet[row, "combinedv4"])
-    }else{
-      print("No field called combinedv4 in the JET output!")
-      quit(status=-1)
-    } 
-  }
 }else if (normWeightMode=="tracemovingaverage"){
   print("Using only tracemovingaverage")
   for (row in 1:nrow(jet)) {

sgemme.py

@@ -839,10 +839,6 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
         (normWeightMode != 'halfpccv') and \
         (normWeightMode != 'halfcvpc') and \
         (normWeightMode != 'halftracepc') and \
-        (normWeightMode != 'combinedv1') and \
-        (normWeightMode != 'combinedv2') and \
-        (normWeightMode != 'combinedv3') and \
-        (normWeightMode != 'combinedv4') and \
         (normWeightMode != 'maxtracehalfcvpc') and \
         (normWeightMode != 'maxtracehalftracecvhalfcvpc') and \
         (normWeightMode != 'maxhalftracepchalftracecvhalfcvpc') and \
@@ -854,8 +850,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
               "       'maxtracepc', 'maxtracedfi', 'maxpccv', 'maxtracesc',"+\
               "       'maxtracebfactor', 'maxtracepcsc', 'maxhalftracepchalftracecvhalfcvpc', "+\
               "       'maxtracecv', 'maxtracepccv', maxtracepchalfpccv"+\
-              "       'combinedv1', 'combinedv2', 'combinedv3', 'combinedv4'"+\
-              "       'halfcvpc', 'halftracepc', 'maxtracehalfcvpc', 'maxtracehalftracecvhalfcvpc' or 'jetormax'!")
+              "       'halfcvpc', 'halftracepc', 'maxtracehalfcvpc', 'maxtracehalftracecvhalfcvpc' or 'ssjetormax'!")
         sys.exit(-1)
 
     structure = parsePDB(prot+".pdb")