5 * Created by Sarah Westcott on 1/20/09.
6 * Copyright 2009 Schloss Lab UMASS AMherst. All rights reserved.
10 #include "readotucommand.h"
12 //**********************************************************************************************************************
13 ReadOtuCommand::ReadOtuCommand(){
15 globaldata = GlobalData::getInstance();
16 filename = globaldata->inputFileName;
17 read = new ReadPhilFile(filename);
18 if (globaldata->getFormat() == "shared") {
19 //read in group map info.
20 groupMap = new GroupMap(globaldata->getGroupFile());
24 cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
28 cout << "An unknown error has occurred in the ReadOtuCommand class function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
33 //**********************************************************************************************************************
35 ReadOtuCommand::~ReadOtuCommand(){
39 //**********************************************************************************************************************
41 int ReadOtuCommand::execute(){
43 read->read(&*globaldata);
44 if (globaldata->getFormat() == "shared") {
46 globaldata->gGroupmap = groupMap;
48 shared = new SharedCommand();
50 parselist = new ParseListCommand();
56 cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
60 cout << "An unknown error has occurred in the ReadOtuCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
64 //**********************************************************************************************************************