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                 else if (format == "matrix") {
  22                                 groupMap = new GroupMap(globaldata->getGroupFile());
  23                                 groupMap->readMap();
  24                                 globaldata->gGroupmap = groupMap;
  25                 }
  26
  27                 if (format != "matrix" ) {
  28                         if(globaldata->getPrecision() != ""){
  29                                 convert(globaldata->getPrecision(), precision);
  30                         }
  31
  32                         if(globaldata->getCutOff() != ""){
  33                                 convert(globaldata->getCutOff(), cutoff);
  34                                 cutoff += (5 / (precision * 10.0));
  35                         }
  36                         read->setCutoff(cutoff);
  37
  38                         if(globaldata->getNameFile() != ""){
  39                                 nameMap = new NameAssignment(globaldata->getNameFile());
  40                                 nameMap->readMap(1,2);
  41                         }
  42                         else{
  43                                 nameMap = NULL;
  44                         }
  45                 }
  46
  47         }
  48         catch(exception& e) {
  49                 cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function ReadDistCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  50                 exit(1);
  51         }
  52         catch(...) {
  53                 cout << "An unknown error has occurred in the ReadDistCommand class function ReadDistCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  54                 exit(1);
  55         }
  56 }
  57
  58 //**********************************************************************************************************************
  59 ReadDistCommand::~ReadDistCommand(){
  60         delete read;
  61         delete nameMap;
  62 }
  63
  64 //**********************************************************************************************************************
  65 int ReadDistCommand::execute(){
  66         try {
  67
  68                 if (format == "matrix") {
  69                         ifstream in;
  70                         openInputFile(filename, in);
  71                         matrix = new FullMatrix(in); //reads the matrix file
  72                         globaldata->gMatrix = matrix; //save matrix for coverage commands
  73                 }else {
  74                         read->read(nameMap);
  75                         globaldata->setListVector(read->getListVector());
  76                         globaldata->setSparseMatrix(read->getMatrix());
  77                 }
  78                 return 0;
  79         }
  80         catch(exception& e) {
  81                 cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  82                 exit(1);
  83         }
  84         catch(...) {
  85                 cout << "An unknown error has occurred in the ReadDistCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  86                 exit(1);
  87         }
  88 }