Initial revision

[mothur.git] / raredisplay.cpp

diff --git a/raredisplay.cpp b/raredisplay.cpp
new file mode 100644 (file)
index 0000000..e2c75e9
--- /dev/null
+++ b/raredisplay.cpp
@@ -0,0 +1,175 @@
+/*
+ *  raredisplay.cpp
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 11/18/08.
+ *  Copyright 2008 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "raredisplay.h"
+
+/***********************************************************************/
+
+void RareDisplay::init(string label){
+       try {
+               this->label = label;
+               if(nIters != 1){
+                       openOutputFile(tempOutName, tempOutFile);
+                       openInputFile(tempInName, tempInFile);
+               }
+               else{
+                       openOutputFile(tempOutName, tempOutFile);
+               }
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the RareDisplay class Function init. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the RareDisplay class function init. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
+
+/***********************************************************************/
+
+void RareDisplay::update(SAbundVector* rank){
+       try {
+               int newNSeqs = rank->getNumSeqs();
+               vector<double> data = estimate->getValues(rank);
+
+               if(nIters != 1){
+
+                       double oldNSeqs, oldMean, oldVar;
+               
+                       tempInFile >> oldNSeqs >> oldMean >> oldVar;
+               
+                       double oldS = oldVar * ( nIters - 2 );
+                       double delta = data[0] - oldMean;
+                       double newMean = oldMean + delta / nIters;
+                       double newS = oldS + delta * ( data[0] - newMean );
+                       double newVar = newS / ( nIters - 1 );
+
+                       tempOutFile << newNSeqs << '\t' << newMean << '\t' << newVar << endl;
+               }
+               else{
+                       tempOutFile << newNSeqs << '\t' << data[0] << '\t' << 0 << endl;
+               }
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the RareDisplay class Function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the RareDisplay class function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+};
+
+/***********************************************************************/
+void RareDisplay::update(SharedRAbundVector* shared1, SharedRAbundVector* shared2, int numSeqs, int numGroupComb) {
+       try {
+               vector<double> data = estimate->getValues(shared1, shared2); 
+               double newNSeqs = data[0];
+               
+               if(nIters != 1){
+                       double oldNSeqs, oldMean, oldVar;
+               
+                       tempInFile >> oldNSeqs >> oldMean >> oldVar;
+               
+                       double oldS = oldVar * ( nIters - 2 );
+                       double delta = data[0] - oldMean;
+                       double newMean = oldMean + delta / nIters;
+                       double newS = oldS + delta * ( data[0] - newMean );
+                       double newVar = newS / ( nIters - 1 );
+
+                       tempOutFile << newNSeqs << '\t' << newMean << '\t' << newVar << endl;
+               }
+               else{
+                       tempOutFile << newNSeqs << '\t' << data[0] << '\t' << 0 << endl;
+               }
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the RareDisplay class Function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the RareDisplay class function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+};
+
+/***********************************************************************/
+
+void RareDisplay::reset(){
+       try {
+               if(nIters != 1){
+                       tempOutFile.close();
+                       tempInFile.close();
+               }
+               else{
+                       tempOutFile.close();
+               }
+       
+               nIters++;
+       
+               remove(tempInName.c_str());
+               rename(tempOutName.c_str(), tempInName.c_str());        
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the RareDisplay class Function reset. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the RareDisplay class function reset. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
+
+/***********************************************************************/
+
+void RareDisplay::close(){
+       try {
+               output->initFile(label);
+       
+               openInputFile(tempInName, tempInFile);
+       
+               while(!tempInFile.eof()){
+                       int nSeqs;
+                       tempInFile >> nSeqs;
+               
+                       vector<double> data(3,0);
+                       double variance = 0;
+               
+                       tempInFile >> data[0];
+                       tempInFile >> variance;
+               
+                       double ci = 1.96 * pow(variance, 0.5);
+                       data[1] = data[0] - ci;
+                       data[2] = data[0] + ci;
+               
+                       output->output(nSeqs, data);
+               
+                       gobble(tempInFile);
+               }
+               tempInFile.close();
+       
+               remove(tempInName.c_str());
+               remove(tempOutName.c_str());
+       
+               nIters = 1;
+               output->resetFile();
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the RareDisplay class Function close. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the RareDisplay class function close. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
+
+/***********************************************************************/
+