pat's fixes to pca command

[mothur.git] / linearalgebra.cpp

diff --git a/linearalgebra.cpp b/linearalgebra.cpp
index 6970c6429481f94cb5d9b7a26bd990407410ff8d..e19861912d9c7fc78f9b2cbbb87ecd76e9388ba9 100644 (file)
--- a/linearalgebra.cpp
+++ b/linearalgebra.cpp
@@ -696,4 +696,30 @@ double LinearAlgebra::calcKendall(vector< vector<double> >& euclidDists, vector<
 
 /*********************************************************************************************************************************/
 
+vector<vector<double> > LinearAlgebra::getObservedEuclideanDistance(vector<vector<double> >& relAbundData){
 
+       int numSamples = relAbundData.size();
+       int numOTUs = relAbundData[0].size();
+       
+       vector<vector<double> > dMatrix(numSamples);
+       for(int i=0;i<numSamples;i++){
+               dMatrix[i].resize(numSamples);
+       }
+       
+       for(int i=0;i<numSamples;i++){
+               for(int j=0;j<numSamples;j++){
+                       
+                       double d = 0;
+                       for(int k=0;k<numOTUs;k++){
+                               d += pow((relAbundData[i][k] - relAbundData[j][k]), 2.0000);
+                       }
+                       dMatrix[i][j] = pow(d, 0.50000);
+                       dMatrix[j][i] = dMatrix[i][j];
+                       
+               }
+       }
+       return dMatrix;
+       
+}
+
+/*********************************************************************************************************************************/