changes while testing

[mothur.git] / sharedthetayc.cpp

diff --git a/sharedthetayc.cpp b/sharedthetayc.cpp
index 6f3f25001a73208caa74dc438a0b9c7652f70531..864c6e63712cdc78d2cc0320ff2869c6deff196f 100644 (file)
--- a/sharedthetayc.cpp
+++ b/sharedthetayc.cpp
@@ -14,29 +14,29 @@ EstOutput ThetaYC::getValues(vector<SharedRAbundVector*> shared) {
        try {   
                data.resize(3,0.0000);
                
-               float Atotal = 0;
-               float Btotal = 0;
-               float thetaYC = 0;
-               float pi = 0;
-               float qi = 0;
-               float a = 0;
-               float b = 0;
-               float d = 0;
+               double Atotal = 0;
+               double Btotal = 0;
+               double thetaYC = 0;
+               double pi = 0;
+               double qi = 0;
+               double a = 0;
+               double b = 0;
+               double d = 0;
                
-               float sumPcubed = 0;
-               float sumQcubed = 0;
-               float sumPQsq = 0;
-               float sumPsqQ = 0;
+               double sumPcubed = 0;
+               double sumQcubed = 0;
+               double sumPQsq = 0;
+               double sumPsqQ = 0;
                
                //get the total values we need to calculate the theta denominator sums
-               for (int i = 0; i < shared[0]->size(); i++) {
+               for (int i = 0; i < shared[0]->getNumBins(); i++) {
                        //store in temps to avoid multiple repetitive function calls
-                       Atotal += (float)shared[0]->getAbundance(i);
-                       Btotal += (float)shared[1]->getAbundance(i);
+                       Atotal += (double)shared[0]->getAbundance(i);
+                       Btotal += (double)shared[1]->getAbundance(i);
                }
                
                //calculate the theta denominator sums
-               for (int j = 0; j < shared[0]->size(); j++) {
+               for (int j = 0; j < shared[0]->getNumBins(); j++) {
                        //store in temps to avoid multiple repetitive function calls
                        pi = shared[0]->getAbundance(j) / Atotal;
                        qi = shared[1]->getAbundance(j) / Btotal;
@@ -55,21 +55,30 @@ EstOutput ThetaYC::getValues(vector<SharedRAbundVector*> shared) {
                
                if (isnan(thetaYC) || isinf(thetaYC)) { thetaYC = 0; }
                
-               float varA = 4 / Atotal * (sumPcubed - a * a);
-               float varB = 4 / Btotal * (sumQcubed - b * b);
-               float varD = sumPQsq / Atotal + sumPsqQ / Btotal - d * d * (1/Atotal + 1/Btotal);
-               float covAD = 2 / Atotal * (sumPsqQ - a * d);
-               float covBD = 2 / Btotal * (sumPQsq - b* d);
+               double varA = 4 / Atotal * (sumPcubed - a * a);
+               double varB = 4 / Btotal * (sumQcubed - b * b);
+               double varD = sumPQsq / Atotal + sumPsqQ / Btotal - d * d * (1/Atotal + 1/Btotal);
+               double covAD = 2 / Atotal * (sumPsqQ - a * d);
+               double covBD = 2 / Btotal * (sumPQsq - b* d);
                
-               float varT = d * d * (varA + varB) / pow(a + b - d, (float)4.0) + pow(a+b, (float)2.0) * varD / pow(a+b-d, (float)4.0)
-                                               - 2.0 * (a + b) * d / pow(a + b - d, (float)4.0) * (covAD + covBD);
+               double varT = d * d * (varA + varB) / pow(a + b - d, (double)4.0) + pow(a+b, (double)2.0) * varD / pow(a+b-d, (double)4.0)
+                                               - 2.0 * (a + b) * d / pow(a + b - d, (double)4.0) * (covAD + covBD);
                
-               float ci = 1.95 * sqrt(varT);
+               double ci = 1.95 * sqrt(varT);
                
                data[0] = thetaYC;
                data[1] = thetaYC - ci;
                data[2] = thetaYC + ci;
                
+               if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
+               if (isnan(data[1]) || isinf(data[1])) { data[1] = 0; }
+               if (isnan(data[2]) || isinf(data[2])) { data[2] = 0; }
+               
+               data[0] = 1.0 - data[0];
+        double hold = data[1];
+        data[1] = 1.0 - data[2];
+        data[2] = 1.0 - hold;
+        
                return data;
        }
        catch(exception& e) {