// reset stat counters
int processCount = 0;
long processTime = 0;
// now create NobleCoder instance and run it
NobleCoder coder = new NobleCoder(terminology);
coder.setHandleAcronymExpansion(handleAcronyms);
coder.setHandleNegation(handleNegation);
//coder.setProcessFilter(NobleCoder.FILTER_DEID|NobleCoder.FILTER_HEADER);
// initialize writers
htmlExporter = new HTMLExporter(outputDir);
csvExporter = new CSVExporter(outputDir);
for(int i=0;i<files.size();i++){
progress("processing report ("+(processCount+1)+") "+files.get(i).getName()+" ... \n");
Document doc = coder.process(files.get(i));
processTime += coder.getProcessTime();
// now output HTML for this report
htmlExporter.export(doc);
csvExporter.export(doc);