#description: Inverse log ratios in a data set into a child data set

#Import some handy Java classes
from java.lang import String
from java.lang import Math

#set replacement value for 0.0 entries
replVal = -200

#get dimensions of dataset
n=data.getDataLength()
m=data.getDataWidth()

   
#clone the dataset that we will modify
a = data.clone()


#Set some fields Icon og Navn
a.setIcon("data")
a.setFile("Jython script calculated inversed log ratios")


#calculate the new data set
dat = data.getData()

newdata = []

for i in range(n):
   newline = []
   for j in range(m):
      if dat[i][j] == 0.0:
         new_log_ratio = replVal
      else:
         new_log_ratio = 0 - dat[i][j]
      newline=newline + [ new_log_ratio ]

   newdata = newdata + [newline]


#insert the cloned dataset object into the project tree of JE
a.removeFromParent()
main.addNode(a,data)
a.unLink(0)


#insert the new data into the cloned dataset  object
a.setData(newdata)


#Update id fields and headers
colInfos = a.getColInfos();
newcolumnID = []
for j in range(m):
   newColumn =["inv "+colInfos[j][0]]
   newcolumnID=newcolumnID+[newColumn]

a.setColInfos(newcolumnID)

a.setColInfoHeaders( ["New identifiers"] )