5 * Created by Sarah Westcott on 1/21/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "deconvolutecommand.h"
12 /**************************************************************************************/
13 int DeconvoluteCommand::execute() {
15 globaldata = GlobalData::getInstance();
17 //prepare filenames and open files
18 filename = globaldata->getFastaFile();
19 outputFileName = (getRootName(filename) + "names");
20 openInputFile(filename, in);
21 openOutputFile(outputFileName, out);
23 //constructor reads in file and store internally
24 fastamap = new FastaMap();
26 //two columns separated by tabs sequence name and then sequence
27 fastamap->readFastaFile(in);
29 //print out new names file
30 //file contains 2 columns separated by tabs. the first column is the groupname(name of first sequence found.
31 //the second column is the list of names of identical sequences separated by ','.
37 cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
41 cout << "An unknown error has occurred in the DeconvoluteCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
45 /**************************************************************************************/