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 #include "readmatrix.hpp"
  14
  15 ReadDistCommand::ReadDistCommand(){
  16         try {
  17                 globaldata = GlobalData::getInstance();
  18
  19                 filename = globaldata->inputFileName;
  20                 format = globaldata->getFormat();
  21
  22                 if (format == "column") { read = new ReadColumnMatrix(filename); }
  23                 else if (format == "phylip") { read = new ReadPhylipMatrix(filename); }
  24                 else if (format == "matrix") {
  25                                 groupMap = new GroupMap(globaldata->getGroupFile());
  26                                 groupMap->readMap();
  27                                 //if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap;  }
  28                                 globaldata->gGroupmap = groupMap;
  29                 }
  30
  31                 if (format != "matrix" ) {
  32                         if(globaldata->getPrecision() != ""){
  33                                 convert(globaldata->getPrecision(), precision);
  34                         }
  35
  36                         if(globaldata->getCutOff() != ""){
  37                                 convert(globaldata->getCutOff(), cutoff);
  38                                 cutoff += (5 / (precision * 10.0));
  39                         }
  40                         read->setCutoff(cutoff);
  41
  42                         if(globaldata->getNameFile() != ""){
  43                                 nameMap = new NameAssignment(globaldata->getNameFile());
  44                                 nameMap->readMap(1,2);
  45                         }
  46                         else{
  47                                 nameMap = NULL;
  48                         }
  49                 }
  50
  51         }
  52         catch(exception& e) {
  53                 cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function ReadDistCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  54                 exit(1);
  55         }
  56         catch(...) {
  57                 cout << "An unknown error has occurred in the ReadDistCommand class function ReadDistCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  58                 exit(1);
  59         }
  60 }
  61
  62 //**********************************************************************************************************************
  63 ReadDistCommand::~ReadDistCommand(){
  64         delete read;
  65         delete nameMap;
  66 }
  67
  68 //**********************************************************************************************************************
  69 int ReadDistCommand::execute(){
  70         try {
  71
  72                 if (format == "matrix") {
  73                         ifstream in;
  74                         openInputFile(filename, in);
  75                         matrix = new FullMatrix(in); //reads the matrix file
  76                         //memory leak prevention
  77                         //if (globaldata->gMatrix != NULL) { delete globaldata->gMatrix;  }
  78                         globaldata->gMatrix = matrix; //save matrix for coverage commands
  79                 }else {
  80                         read->read(nameMap);
  81                         //to prevent memory leak
  82                         if (globaldata->gListVector != NULL) { delete globaldata->gListVector;  }
  83                         globaldata->gListVector = read->getListVector();
  84                         if (globaldata->gSparseMatrix != NULL) { delete globaldata->gSparseMatrix;  }
  85                         globaldata->gSparseMatrix = read->getMatrix();
  86                 }
  87                 return 0;
  88         }
  89         catch(exception& e) {
  90                 cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  91                 exit(1);
  92         }
  93         catch(...) {
  94                 cout << "An unknown error has occurred in the ReadDistCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  95                 exit(1);
  96         }
  97 }