readdistcommand.cpp

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