reportfile.cpp

   1 /*
   2  *  reportfile.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 12/19/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "mothur.h"
  11 #include "mothurout.h"
  12 #include "reportfile.h"
  13
  14 /**************************************************************************************************/
  15
  16 ReportFile::ReportFile(){
  17         try {
  18                 m = MothurOut::getInstance();
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "ReportFile", "ReportFile");
  22                 exit(1);
  23         }
  24 }
  25
  26 /**************************************************************************************************/
  27
  28 ReportFile::ReportFile(ifstream& repFile, string repFileName){
  29         try {
  30                 m = MothurOut::getInstance();
  31
  32                 m->openInputFile(repFileName, repFile);
  33                 m->getline(repFile);
  34         }
  35         catch(exception& e) {
  36                 m->errorOut(e, "ReportFile", "ReportFile");
  37                 exit(1);
  38         }
  39 }
  40
  41
  42 /**************************************************************************************************/
  43
  44 ReportFile::ReportFile(ifstream& repFile){
  45         try {
  46
  47                 m = MothurOut::getInstance();
  48
  49                 repFile >> queryName;
  50                 repFile >> queryLength;
  51                 repFile >> templateName;
  52                 repFile >> templateLength;
  53                 repFile >> searchMethod;
  54                 repFile >> dummySearchScore;
  55                 repFile >> alignmentMethod;
  56                 repFile >> queryStart;
  57                 repFile >> queryEnd;
  58                 repFile >> templateStart;
  59                 repFile >> templateEnd;
  60                 repFile >> pairwiseAlignmentLength;
  61                 repFile >> gapsInQuery;
  62                 repFile >> gapsInTemplate;
  63                 repFile >> longestInsert;
  64                 repFile >> simBtwnQueryAndTemplate;
  65
  66                 if(dummySearchScore != "nan"){
  67                         istringstream stream(dummySearchScore);
  68                         stream >> searchScore;
  69                 }
  70                 else{
  71                         searchScore = 0;
  72                 }
  73
  74                 m->gobble(repFile);
  75         }
  76         catch(exception& e) {
  77                 m->errorOut(e, "ReportFile", "ReportFile");
  78                 exit(1);
  79         }
  80
  81 }
  82
  83 /**************************************************************************************************/