readdistphylipfilecommand.cpp

   1 /*
   2  *  readdistphylipfilecommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "readdistphylipfilecommand.h"
  11
  12 //**********************************************************************************************************************
  13
  14 ReadDistPhylipFileCommand::ReadDistPhylipFileCommand(){
  15         try {
  16                 globaldata = GlobalData::getInstance();
  17
  18                 filename = globaldata->inputFileName;
  19
  20                 format = globaldata->getFormat();
  21                 read = new ReadPhylipMatrix(filename);
  22
  23                 if(globaldata->getPrecision() != ""){
  24                         convert(globaldata->getPrecision(), precision);
  25                 }
  26
  27                 if(globaldata->getCutOff() != ""){
  28                         convert(globaldata->getCutOff(), cutoff);
  29                         cutoff += (5 / (precision * 10.0));
  30                 }
  31                 read->setCutoff(cutoff);
  32
  33                 if(globaldata->getNameFile() != ""){
  34                         nameMap = new NameAssignment(globaldata->getNameFile());
  35                         nameMap->readMap(1,2);
  36                 }
  37                 else{
  38                         nameMap = NULL;
  39                 }
  40         }
  41         catch(exception& e) {
  42                 cout << "Standard Error: " << e.what() << " has occurred in the ReadDistPhylipFileCommand class Function ReadDistPhylipFileCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  43                 exit(1);
  44         }
  45         catch(...) {
  46                 cout << "An unknown error has occurred in the ReadDistPhylipFileCommand class function ReadDistPhylipFileCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  47                 exit(1);
  48         }
  49 }
  50
  51 //**********************************************************************************************************************
  52
  53 ReadDistPhylipFileCommand::~ReadDistPhylipFileCommand(){
  54         delete read;
  55         delete nameMap;
  56 }
  57
  58 //**********************************************************************************************************************
  59
  60 int ReadDistPhylipFileCommand::execute(){
  61         try {
  62                 read->read(nameMap);
  63                 globaldata->setListVector(read->getListVector());
  64                 globaldata->setSparseMatrix(read->getMatrix());
  65                 return 0;
  66         }
  67         catch(exception& e) {
  68                 cout << "Standard Error: " << e.what() << " has occurred in the ReadDistPhylipFileCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  69                 exit(1);
  70         }
  71         catch(...) {
  72                 cout << "An unknown error has occurred in the ReadDistPhylipFileCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  73                 exit(1);
  74         }
  75 }