-/*
- * readdistphylipfilecommand.cpp
- * Dotur
- *
- * Created by Sarah Westcott on 1/2/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "readdistphylipfilecommand.h"
-
-//**********************************************************************************************************************
-
-ReadDistPhylipFileCommand::ReadDistPhylipFileCommand(){
- try {
- globaldata = GlobalData::getInstance();
-
- filename = globaldata->inputFileName;
-
- format = globaldata->getFormat();
- read = new ReadPhylipMatrix(filename);
-
- if(globaldata->getPrecision() != ""){
- convert(globaldata->getPrecision(), precision);
- }
-
- if(globaldata->getCutOff() != ""){
- convert(globaldata->getCutOff(), cutoff);
- cutoff += (5 / (precision * 10.0));
- }
- read->setCutoff(cutoff);
-
- if(globaldata->getNameFile() != ""){
- nameMap = new NameAssignment(globaldata->getNameFile());
- nameMap->readMap(1,2);
- }
- else{
- nameMap = NULL;
- }
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReadDistPhylipFileCommand class Function ReadDistPhylipFileCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ReadDistPhylipFileCommand class function ReadDistPhylipFileCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-ReadDistPhylipFileCommand::~ReadDistPhylipFileCommand(){
- delete read;
- delete nameMap;
-}
-
-//**********************************************************************************************************************
-
-int ReadDistPhylipFileCommand::execute(){
- try {
- read->read(nameMap);
- globaldata->setListVector(read->getListVector());
- globaldata->setSparseMatrix(read->getMatrix());
- return 0;
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReadDistPhylipFileCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ReadDistPhylipFileCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}