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 #include "readphylip.h"
  12 #include "readcolumn.h"
  13
  14 ReadDistCommand::ReadDistCommand(){
  15         try {
  16                 globaldata = GlobalData::getInstance();
  17
  18                 filename = globaldata->inputFileName;
  19                 format = globaldata->getFormat();
  20
  21                 if (format == "column") { read = new ReadColumnMatrix(filename); }
  22                 else if (format == "phylip") { read = new ReadPhylipMatrix(filename); }
  23                 else if (format == "matrix") {
  24                                 groupMap = new GroupMap(globaldata->getGroupFile());
  25                                 groupMap->readMap();
  26                                 //if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap;  }
  27                                 globaldata->gGroupmap = groupMap;
  28                 }
  29
  30                 if (format != "matrix" ) {
  31                         if(globaldata->getPrecision() != ""){
  32                                 convert(globaldata->getPrecision(), precision);
  33                         }
  34
  35                         if(globaldata->getCutOff() != ""){
  36                                 convert(globaldata->getCutOff(), cutoff);
  37                                 cutoff += (5 / (precision * 10.0));
  38                         }
  39                         read->setCutoff(cutoff);
  40
  41                         if(globaldata->getNameFile() != ""){
  42                                 nameMap = new NameAssignment(globaldata->getNameFile());
  43                                 nameMap->readMap(1,2);
  44                         }
  45                         else{
  46                                 nameMap = NULL;
  47                         }
  48                 }
  49
  50         }
  51         catch(exception& e) {
  52                 cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function ReadDistCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  53                 exit(1);
  54         }
  55         catch(...) {
  56                 cout << "An unknown error has occurred in the ReadDistCommand class function ReadDistCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  57                 exit(1);
  58         }
  59 }
  60
  61 //**********************************************************************************************************************
  62 ReadDistCommand::~ReadDistCommand(){
  63         delete read;
  64         delete nameMap;
  65 }
  66
  67 //**********************************************************************************************************************
  68 int ReadDistCommand::execute(){
  69         try {
  70
  71                 if (format == "matrix") {
  72                         ifstream in;
  73                         openInputFile(filename, in);
  74                         matrix = new FullMatrix(in); //reads the matrix file
  75                         //memory leak prevention
  76                         //if (globaldata->gMatrix != NULL) { delete globaldata->gMatrix;  }
  77                         globaldata->gMatrix = matrix; //save matrix for coverage commands
  78                 }else {
  79                         read->read(nameMap);
  80                         globaldata->gListVector = read->getListVector();
  81                         globaldata->gSparseMatrix = read->getMatrix();
  82                 }
  83                 return 0;
  84         }
  85         catch(exception& e) {
  86                 cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  87                 exit(1);
  88         }
  89         catch(...) {
  90                 cout << "An unknown error has occurred in the ReadDistCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  91                 exit(1);
  92         }
  93 }