Added halftracepc to the normalization options

computePred.R

@@ -150,6 +150,15 @@ if((normWeightMode=="maxtracepc") | (normWeightMode=="maxpctrace")){
   for (row in 1:nrow(jet)) {
     trace<-append(trace, (jet[row, "pc"]+jet[row, "cv"])/2.0)
     }  
+}else if ((normWeightMode=="halftracepc") | (normWeightMode=="halfpctrace")){
+  print(paste("Using ", normWeightMode))
+  for (row in 1:nrow(jet)) {
+    if(sum(colnames(jet)=="traceMax")==1){
+      trace<-append(trace, (jet[row, "traceMax"]+jet[row, "pc"])/2.0)
+    }else{
+      trace<-append(trace, (jet[row, "trace"]+jet[row, "pc"])/2.0)
+    }
+  }
 } else if ((normWeightMode=="maxcvpc") | (normWeightMode=="maxpccv")){
   print(paste("Using ", normWeightMode))
   for (row in 1:nrow(jet)) {
@@ -234,7 +243,7 @@ if((normWeightMode=="maxtracepc") | (normWeightMode=="maxpctrace")){
 }else{
   print("ERROR: Unknown --normWeightMode selected!")
   print("It can only be 'trace', 'tracemovingaverage', 'pc', 'cv', 'dfi', 'bfactor',")
-  print(" 'maxtracepc', 'maxtracecv', 'maxtracepccv', 'halfcvpc', 'maxtracepchalfpccv',")
+  print(" 'maxtracepc', 'maxtracecv', 'maxtracepccv', 'halfcvpc', 'halftracepc', 'maxtracepchalfpccv',")
   print(" 'maxtracesc', 'maxtracescpc', 'maxtracedfi' or 'maxtracebfactor'!")
 }
 print(trace)

gemme.py

@@ -515,6 +515,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
         (normWeightMode != 'maxtracecvpc') and \
         (normWeightMode != 'halfpccv') and \
         (normWeightMode != 'halfcvpc') and \
+        (normWeightMode != 'halftracepc') and \
         (normWeightMode != 'combinedv1') and \
         (normWeightMode != 'combinedv2') and \
         (normWeightMode != 'combinedv3') and \
@@ -529,7 +530,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
               "       'maxtracebfactor', 'maxtracepcsc', 'maxhalftracepchalftracecvhalfcvpc', "+\
               "       'maxtracecv', 'maxtracepccv', maxtracepchalfpccv"+\
               "       'combinedv1', 'combinedv2', 'combinedv3', 'combinedv4'"+\
-              "       'halfcvpc', 'maxtracehalfcvpc' or maxtracehalftracecvhalfcvpc!")
+              "       'halfcvpc', 'halftracepc', 'maxtracehalfcvpc' or maxtracehalftracecvhalfcvpc!")
         sys.exit(-1)
 
     structure = parsePDB(prot+".pdb")