Revert to previous commit

[mothur.git] / raredisplay.cpp

diff --git a/raredisplay.cpp b/raredisplay.cpp
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+++ b/raredisplay.cpp
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+/*
+ *  raredisplay.cpp
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 11/18/08.
+ *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "raredisplay.h"
+
+/***********************************************************************/
+
+void RareDisplay::init(string label){
+       try {
+               this->label = label;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "RareDisplay", "init");
+               exit(1);
+       }
+}
+
+/***********************************************************************/
+
+void RareDisplay::update(SAbundVector* rank){
+       try {
+               int newNSeqs = rank->getNumSeqs();
+               vector<double> data = estimate->getValues(rank);
+
+               if(nIters != 1){
+
+                       double oldS = var[index] * ( nIters - 2 );
+                       double delta = data[0] - results[index];
+                       double newMean = results[index] + delta / nIters;
+                       double newS = oldS + delta * ( data[0] - newMean );
+                       double newVar = newS / ( nIters - 1 );
+
+                       seqs[index] = newNSeqs;
+                       results[index] = newMean; 
+                       var[index] = newVar;
+                       
+                       index++;  
+               }
+               else{
+                       seqs.push_back(newNSeqs); 
+                       results.push_back(data[0]);
+                       var.push_back(0.0);
+               }
+       }
+       catch(exception& e) {
+               m->errorOut(e, "RareDisplay", "update");
+               exit(1);
+       }
+}
+
+/***********************************************************************/
+void RareDisplay::update(vector<SharedRAbundVector*> shared, int numSeqs, int numGroupComb) {
+       try {
+               vector<double> data = estimate->getValues(shared); 
+               double newNSeqs = data[0];
+               
+               if(nIters != 1){
+               
+                       double oldS = var[index] * ( nIters - 2 );
+                       double delta = data[0] - results[index];
+                       double newMean = results[index] + delta / nIters;
+                       double newS = oldS + delta * ( data[0] - newMean );
+                       double newVar = newS / ( nIters - 1 );
+                       seqs[index] = newNSeqs;
+                       results[index] = newMean; 
+                       var[index] = newVar;
+                       
+                       index++;  
+               }
+               else{
+                       
+                       seqs.push_back(newNSeqs); 
+                       results.push_back(data[0]);
+                       var.push_back(0.0);
+
+               }
+       }
+       catch(exception& e) {
+               m->errorOut(e, "RareDisplay", "update");
+               exit(1);
+       }
+}
+
+/***********************************************************************/
+
+void RareDisplay::reset(){
+       try {
+               nIters++;
+               index = 0;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "RareDisplay", "reset");
+               exit(1);
+       }
+}
+
+/***********************************************************************/
+
+void RareDisplay::close(){
+       try {
+               
+               output->initFile(label);
+       
+               for (int i = 0; i < seqs.size(); i++) {
+               
+                       vector<double> data(3,0);
+                       double variance = var[i];
+                       
+                       data[0] = results[i];
+                       
+                       double ci = 1.96 * pow(variance, 0.5);
+                       data[1] = data[0] - ci;
+                       data[2] = data[0] + ci;
+               
+                       output->output(seqs[i], data);
+               }
+               
+               nIters = 1;
+               index = 0;
+               
+               seqs.clear();
+               results.clear();
+               var.clear();
+               
+               output->resetFile();
+       }
+       catch(exception& e) {
+               m->errorOut(e, "RareDisplay", "close");
+               exit(1);
+       }
+}
+/***********************************************************************/
+
+void RareDisplay::inputTempFiles(string filename){
+       try {
+               ifstream in;
+               m->openInputFile(filename, in);
+               
+               int thisIters;
+               in >> thisIters; m->gobble(in);
+               
+               for (int i = 0; i < seqs.size(); i++) {
+                       double tempresult, tempvar;
+                       in >> tempresult >> tempvar; m->gobble(in);
+                       
+                       //find weighted result
+                       results[i] = ((nIters * results[i]) + (thisIters * tempresult)) / (float)(nIters + thisIters);
+                       
+                       var[i] = ((nIters * var[i]) + (thisIters * tempvar)) / (float)(nIters + thisIters);
+               }
+               
+               in.close();
+       }
+       catch(exception& e) {
+               m->errorOut(e, "RareDisplay", "inputTempFiles");
+               exit(1);
+       }
+}
+
+/***********************************************************************/
+
+void RareDisplay::outputTempFiles(string filename){
+       try {
+               ofstream out;
+               m->openOutputFile(filename, out);
+               
+               out << nIters << endl;
+               
+               for (int i = 0; i < seqs.size(); i++) {
+                       out << results[i] << '\t' << var[i] << endl;
+               }
+               
+               out.close();
+       }
+       catch(exception& e) {
+               m->errorOut(e, "RareDisplay", "outputTempFiles");
+               exit(1);
+       }
+}
+
+
+/***********************************************************************/
+