working on pca

[mothur.git] / pcoacommand.cpp

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index 4be5ffb8c5b63c4202666aecd57ec58c2be05374..3cd844a36d5a5c253786b4eb29745388b042d2d4 100644 (file)
--- a/pcoacommand.cpp
+++ b/pcoacommand.cpp
@@ -169,12 +169,12 @@ int PCOACommand::execute(){
                vector<double> d;
                vector<double> e;
                vector<vector<double> > G = D;
-               vector<vector<double> > copy_G;
+               //vector<vector<double> > copy_G;
                                
                m->mothurOut("\nProcessing...\n\n");
                
                for(int count=0;count<2;count++){
-                       recenter(offset, D, G);                                 if (m->control_pressed) { return 0; }
+                       linearCalc.recenter(offset, D, G);              if (m->control_pressed) { return 0; }
                        linearCalc.tred2(G, d, e);                              if (m->control_pressed) { return 0; }
                        linearCalc.qtli(d, e, G);                               if (m->control_pressed) { return 0; }
                        offset = d[d.size()-1];
@@ -230,40 +230,6 @@ void PCOACommand::get_comment(istream& f, char begin, char end){
 }      
 /*********************************************************************************************************************************/
 
-void PCOACommand::recenter(double offset, vector<vector<double> > D, vector<vector<double> >& G){
-       try {
-               int rank = D.size();
-               
-               vector<vector<double> > A(rank);
-               vector<vector<double> > C(rank);
-               for(int i=0;i<rank;i++){
-                       A[i].resize(rank);
-                       C[i].resize(rank);
-               }
-               
-               double scale = -1.0000 / (double) rank;
-               
-               for(int i=0;i<rank;i++){
-                       A[i][i] = 0.0000;
-                       C[i][i] = 1.0000 + scale;
-                       for(int j=i+1;j<rank;j++){
-                               A[i][j] = A[j][i] = -0.5 * D[i][j] * D[i][j] + offset;
-                               C[i][j] = C[j][i] = scale;
-                       }
-               }
-               
-               A = linearCalc.matrix_mult(C,A);
-               G = linearCalc.matrix_mult(A,C);
-       }
-       catch(exception& e) {
-               m->errorOut(e, "PCOACommand", "recenter");
-               exit(1);
-       }
-
-}
-
-/*********************************************************************************************************************************/
-
 void PCOACommand::output(string fnameRoot, vector<string> name_list, vector<vector<double> >& G, vector<double> d) {
        try {
                int rank = name_list.size();