raredisplay.cpp

   1 /*
   2  *  raredisplay.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 11/18/08.
   6  *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "raredisplay.h"
  11
  12 /***********************************************************************/
  13
  14 void RareDisplay::init(string label){
  15         try {
  16                 this->label = label;
  17                 if(nIters != 1){
  18                         tempInFile.clear();
  19                         openOutputFile(tempOutName, tempOutFile);
  20                         openInputFile(tempInName, tempInFile);
  21                 }
  22                 else{
  23                         openOutputFile(tempOutName, tempOutFile);
  24                 }
  25         }
  26         catch(exception& e) {
  27                 errorOut(e, "RareDisplay", "init");
  28                 exit(1);
  29         }
  30 }
  31
  32 /***********************************************************************/
  33
  34 void RareDisplay::update(SAbundVector* rank){
  35         try {
  36                 int newNSeqs = rank->getNumSeqs();
  37                 vector<double> data = estimate->getValues(rank);
  38
  39                 if(nIters != 1){
  40
  41                         double oldNSeqs, oldMean, oldVar;
  42
  43                         tempInFile >> oldNSeqs >> oldMean >> oldVar;
  44
  45                         double oldS = oldVar * ( nIters - 2 );
  46                         double delta = data[0] - oldMean;
  47                         double newMean = oldMean + delta / nIters;
  48                         double newS = oldS + delta * ( data[0] - newMean );
  49                         double newVar = newS / ( nIters - 1 );
  50
  51                         tempOutFile << newNSeqs << '\t' << newMean << '\t' << newVar << endl;
  52                 }
  53                 else{
  54                         tempOutFile << newNSeqs << '\t' << data[0] << '\t' << 0 << endl;
  55                 }
  56         }
  57         catch(exception& e) {
  58                 errorOut(e, "RareDisplay", "update");
  59                 exit(1);
  60         }
  61 }
  62
  63 /***********************************************************************/
  64 void RareDisplay::update(vector<SharedRAbundVector*> shared, int numSeqs, int numGroupComb) {
  65         try {
  66                 vector<double> data = estimate->getValues(shared);
  67                 double newNSeqs = data[0];
  68
  69                 if(nIters != 1){
  70                         double oldNSeqs, oldMean, oldVar;
  71
  72                         tempInFile >> oldNSeqs >> oldMean >> oldVar;
  73
  74                         double oldS = oldVar * ( nIters - 2 );
  75                         double delta = data[0] - oldMean;
  76                         double newMean = oldMean + delta / nIters;
  77                         double newS = oldS + delta * ( data[0] - newMean );
  78                         double newVar = newS / ( nIters - 1 );
  79
  80                         tempOutFile << newNSeqs << '\t' << newMean << '\t' << newVar << endl;
  81                 }
  82                 else{
  83                         tempOutFile << newNSeqs << '\t' << data[0] << '\t' << 0 << endl;
  84                 }
  85         }
  86         catch(exception& e) {
  87                 errorOut(e, "RareDisplay", "update");
  88                 exit(1);
  89         }
  90 }
  91
  92 /***********************************************************************/
  93
  94 void RareDisplay::reset(){
  95         try {
  96                 if(nIters != 1){
  97                         tempOutFile.close();
  98                         tempInFile.close();
  99                 }
 100                 else{
 101                         tempOutFile.close();
 102                 }
 103
 104                 nIters++;
 105
 106                 remove(tempInName.c_str());
 107                 renameOk = rename(tempOutName.c_str(), tempInName.c_str());
 108
 109                 //checks to make sure user was able to rename and remove successfully
 110                 if (renameOk != 0) { mothurOut("Unable to rename the necessary temp files."); mothurOutEndLine(); }
 111         }
 112         catch(exception& e) {
 113                 errorOut(e, "RareDisplay", "reset");
 114                 exit(1);
 115         }
 116 }
 117
 118 /***********************************************************************/
 119
 120 void RareDisplay::close(){
 121         try {
 122
 123                 output->initFile(label);
 124
 125                 openInputFile(tempInName, tempInFile);
 126
 127                 while(!tempInFile.eof()){
 128                         int nSeqs;
 129                         tempInFile >> nSeqs;
 130
 131                         vector<double> data(3,0);
 132                         double variance = 0;
 133
 134                         tempInFile >> data[0];
 135                         tempInFile >> variance;
 136
 137                         double ci = 1.96 * pow(variance, 0.5);
 138                         data[1] = data[0] - ci;
 139                         data[2] = data[0] + ci;
 140
 141                         output->output(nSeqs, data);
 142
 143                         gobble(tempInFile);
 144                 }
 145                 tempInFile.close();
 146
 147                 remove(tempInName.c_str());
 148                 remove(tempOutName.c_str());
 149
 150                 nIters = 1;
 151                 output->resetFile();
 152         }
 153         catch(exception& e) {
 154                 errorOut(e, "RareDisplay", "close");
 155                 exit(1);
 156         }
 157 }
 158
 159 /***********************************************************************/
 160