Am not sure i completely understand what you're trying to achieve, but you are probably trying to do this :
while ((line = bufferReader.readLine()) != null)
{
bufferdata+= System.getProperty("line.separator") + line;
if(startSaving)
{
modifieddata += System.getProperty("line.separator") + line;
}
else
{
originaldata += System.getProperty("line.separator") + line;
}
if(line.isEmpty())
{
startSaving = true;
}
}
if(modifieddata.isEmpty())
{
modifieddata = originaldata.trim();
}
else
{
modifieddata = modifieddata.trim();
}
String[] array = new String[]{modifieddata, originaldata};
//Close the buffer reader
bufferReader.close();
// return array;