pca command

[mothur.git] / pcoacommand.cpp

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index 9375144bcb342faf364a38eee6eca63226099659..d1d919c93d5f43086658a86cf79f11a09de8ae9f 100644 (file)
--- a/pcoacommand.cpp
+++ b/pcoacommand.cpp
@@ -30,7 +30,6 @@ PCOACommand::PCOACommand(){
                vector<string> tempOutNames;
                outputTypes["pcoa"] = tempOutNames;
                outputTypes["loadings"] = tempOutNames;
-               outputTypes["corr"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "PCOACommand", "PCOACommand");
@@ -102,7 +101,6 @@ PCOACommand::PCOACommand(string option)  {
                        vector<string> tempOutNames;
                        outputTypes["pcoa"] = tempOutNames;
                        outputTypes["loadings"] = tempOutNames;
-                       outputTypes["corr"] = tempOutNames;
                        
                        //required parameters
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
@@ -192,11 +190,11 @@ int PCOACommand::execute(){
                        
                        for (int i = 1; i < 4; i++) {
                                                        
-                               vector< vector<double> > EuclidDists = calculateEuclidianDistance(G, i); //G is the pcoa file
+                               vector< vector<double> > EuclidDists = linearCalc.calculateEuclidianDistance(G, i); //G is the pcoa file
                                
                                if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
                                
-                               double corr = calcPearson(EuclidDists, D); //G is the pcoa file, D is the users distance matrix
+                               double corr = linearCalc.calcPearson(EuclidDists, D); //G is the pcoa file, D is the users distance matrix
                                
                                m->mothurOut("Pearson's coefficient using " + toString(i) + " axis: " + toString(corr)); m->mothurOutEndLine();
                                
@@ -217,114 +215,6 @@ int PCOACommand::execute(){
        }
 }
 /*********************************************************************************************************************************/
-vector< vector<double> > PCOACommand::calculateEuclidianDistance(vector< vector<double> >& axes, int dimensions){
-       try {
-               //make square matrix
-               vector< vector<double> > dists; dists.resize(axes.size());
-               for (int i = 0; i < dists.size(); i++) {  dists[i].resize(axes.size(), 0.0); }
-                       
-               if (dimensions == 1) { //one dimension calc = abs(x-y)
-                       
-                       for (int i = 0; i < dists.size(); i++) {
-                               
-                               if (m->control_pressed) { return dists; }
-                               
-                               for (int j = 0; j < i; j++) {
-                                       dists[i][j] = abs(axes[i][0] - axes[j][0]);
-                                       dists[j][i] = dists[i][j];
-                               }
-                       }
-                       
-               }else if (dimensions == 2) { //two dimension calc = sqrt ((x1 - y1)^2 + (x2 - y2)^2)
-                       
-                       for (int i = 0; i < dists.size(); i++) {
-                               
-                               if (m->control_pressed) { return dists; }
-                               
-                               for (int j = 0; j < i; j++) {
-                                       double firstDim = ((axes[i][0] - axes[j][0]) * (axes[i][0] - axes[j][0]));
-                                       double secondDim = ((axes[i][1] - axes[j][1]) * (axes[i][1] - axes[j][1]));
-
-                                       dists[i][j] = sqrt((firstDim + secondDim));
-                                       dists[j][i] = dists[i][j];
-                               }
-                       }
-                       
-               }else if (dimensions == 3) { //two dimension calc = sqrt ((x1 - y1)^2 + (x2 - y2)^2 + (x3 - y3)^2)
-                       
-                       for (int i = 0; i < dists.size(); i++) {
-                               
-                               if (m->control_pressed) { return dists; }
-                               
-                               for (int j = 0; j < i; j++) {
-                                       double firstDim = ((axes[i][0] - axes[j][0]) * (axes[i][0] - axes[j][0]));
-                                       double secondDim = ((axes[i][1] - axes[j][1]) * (axes[i][1] - axes[j][1]));
-                                       double thirdDim = ((axes[i][2] - axes[j][2]) * (axes[i][2] - axes[j][2]));
-                                       
-                                       dists[i][j] = sqrt((firstDim + secondDim + thirdDim));
-                                       dists[j][i] = dists[i][j];
-                               }
-                       }
-                       
-               }else { m->mothurOut("[ERROR]: too many dimensions, aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
-               
-               return dists;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "PCOACommand", "calculateEuclidianDistance");
-               exit(1);
-       }
-}
-/*********************************************************************************************************************************/
-double PCOACommand::calcPearson(vector< vector<double> >& euclidDists, vector< vector<double> >& userDists){
-       try {
-               
-               //find average for - X
-               vector<float> averageEuclid; averageEuclid.resize(euclidDists.size(), 0.0);
-               for (int i = 0; i < euclidDists.size(); i++) {
-                       for (int j = 0; j < euclidDists[i].size(); j++) {
-                               averageEuclid[i] += euclidDists[i][j];  
-                       }
-               }
-               for (int i = 0; i < averageEuclid.size(); i++) {  averageEuclid[i] = averageEuclid[i] / (float) euclidDists.size();   }
-               
-               //find average for - Y
-               vector<float> averageUser; averageUser.resize(userDists.size(), 0.0);
-               for (int i = 0; i < userDists.size(); i++) {
-                       for (int j = 0; j < userDists[i].size(); j++) {
-                               averageUser[i] += userDists[i][j];  
-                       }
-               }
-               for (int i = 0; i < averageUser.size(); i++) {  averageUser[i] = averageUser[i] / (float) userDists.size();  }
-               
-               double numerator = 0.0;
-               double denomTerm1 = 0.0;
-               double denomTerm2 = 0.0;
-               
-               for (int i = 0; i < euclidDists.size(); i++) {
-                       
-                       for (int k = 0; k < i; k++) {
-                               
-                               float Yi = userDists[i][k];
-                               float Xi = euclidDists[i][k];
-                                       
-                               numerator += ((Xi - averageEuclid[k]) * (Yi - averageUser[k]));
-                               denomTerm1 += ((Xi - averageEuclid[k]) * (Xi - averageEuclid[k]));
-                               denomTerm2 += ((Yi - averageUser[k]) * (Yi - averageUser[k]));
-                       }
-               }
-               
-               double denom = (sqrt(denomTerm1) * sqrt(denomTerm2));
-               double r = numerator / denom;
-               
-               return r;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "PCOACommand", "calculateEuclidianDistance");
-               exit(1);
-       }
-}
-/*********************************************************************************************************************************/
 
 void PCOACommand::get_comment(istream& f, char begin, char end){
        try {