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                                 if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap;  }
  25                                 globaldata->gGroupmap = groupMap;
  26                 }
  27
  28                 if (format != "matrix" ) {
  29                         if(globaldata->getPrecision() != ""){
  30                                 convert(globaldata->getPrecision(), precision);
  31                         }
  32
  33                         if(globaldata->getCutOff() != ""){
  34                                 convert(globaldata->getCutOff(), cutoff);
  35                                 cutoff += (5 / (precision * 10.0));
  36                         }
  37                         read->setCutoff(cutoff);
  38
  39                         if(globaldata->getNameFile() != ""){
  40                                 nameMap = new NameAssignment(globaldata->getNameFile());
  41                                 nameMap->readMap(1,2);
  42                         }
  43                         else{
  44                                 nameMap = NULL;
  45                         }
  46                 }
  47
  48         }
  49         catch(exception& e) {
  50                 cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function ReadDistCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  51                 exit(1);
  52         }
  53         catch(...) {
  54                 cout << "An unknown error has occurred in the ReadDistCommand class function ReadDistCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  55                 exit(1);
  56         }
  57 }
  58
  59 //**********************************************************************************************************************
  60 ReadDistCommand::~ReadDistCommand(){
  61         delete read;
  62         delete nameMap;
  63 }
  64
  65 //**********************************************************************************************************************
  66 int ReadDistCommand::execute(){
  67         try {
  68
  69                 if (format == "matrix") {
  70                         ifstream in;
  71                         openInputFile(filename, in);
  72                         matrix = new FullMatrix(in); //reads the matrix file
  73                         //memory leak prevention
  74                         if (globaldata->gMatrix != NULL) { delete globaldata->gMatrix;  }
  75                         globaldata->gMatrix = matrix; //save matrix for coverage commands
  76                 }else {
  77                         read->read(nameMap);
  78                         globaldata->gListVector = read->getListVector();
  79                         globaldata->gSparseMatrix = read->getMatrix();
  80                 }
  81                 return 0;
  82         }
  83         catch(exception& e) {
  84                 cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  85                 exit(1);
  86         }
  87         catch(...) {
  88                 cout << "An unknown error has occurred in the ReadDistCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  89                 exit(1);
  90         }
  91 }