working on nmds command

[mothur.git] / linearalgebra.cpp

diff --git a/linearalgebra.cpp b/linearalgebra.cpp
index 5de5a71dc35c1ab8888ff28ab8d7e92107f8cc72..6b56597f10501b4720d77b28ca08961d2c35554e 100644 (file)
--- a/linearalgebra.cpp
+++ b/linearalgebra.cpp
@@ -27,7 +27,7 @@ vector<vector<double> > LinearAlgebra::matrix_mult(vector<vector<double> > first
                
                product.resize(first_rows);
                for(int i=0;i<first_rows;i++){
-                       product[i].resize(first_cols);
+                       product[i].resize(second_cols);
                }
                
                for(int i=0;i<first_rows;i++){
@@ -172,7 +172,7 @@ int LinearAlgebra::qtli(vector<double>& d, vector<double>& e, vector<vector<doub
                                        if(fabs(e[myM])+dd == dd) break;
                                }
                                if(myM != l){
-                                       if(iter++ == 30) cerr << "Too many iterations in tqli\n";
+                                       if(iter++ == 3000) cerr << "Too many iterations in tqli\n";
                                        g = (d[l+1]-d[l]) / (2.0 * e[l]);
                                        r = pythag(g, 1.0);
                                        g = d[myM] - d[l] + e[l] / (g + SIGN(r,g));
@@ -234,6 +234,7 @@ int LinearAlgebra::qtli(vector<double>& d, vector<double>& e, vector<vector<doub
        }
 }
 /*********************************************************************************************************************************/
+//groups by dimension
 vector< vector<double> > LinearAlgebra::calculateEuclidianDistance(vector< vector<double> >& axes, int dimensions){
        try {
                //make square matrix
@@ -252,38 +253,70 @@ vector< vector<double> > LinearAlgebra::calculateEuclidianDistance(vector< vecto
                                }
                        }
                        
-               }else if (dimensions == 2) { //two dimension calc = sqrt ((x1 - y1)^2 + (x2 - y2)^2)
+               }else if (dimensions > 1) { //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]));
+                                       double sum = 0.0;
+                                       for (int k = 0; k < dimensions; k++) {
+                                               sum += ((axes[i][k] - axes[j][k]) * (axes[i][k] - axes[j][k]));
+                                       }
                                        
-                                       dists[i][j] = sqrt((firstDim + secondDim));
+                                       dists[i][j] = sqrt(sum);
                                        dists[j][i] = dists[i][j];
                                }
                        }
                        
-               }else if (dimensions == 3) { //two dimension calc = sqrt ((x1 - y1)^2 + (x2 - y2)^2 + (x3 - y3)^2)
+               }
+               
+               return dists;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "LinearAlgebra", "calculateEuclidianDistance");
+               exit(1);
+       }
+}
+/*********************************************************************************************************************************/
+//returns groups by dimensions from dimensions by groups
+vector< vector<double> > LinearAlgebra::calculateEuclidianDistance(vector< vector<double> >& axes){
+       try {
+               //make square matrix
+               vector< vector<double> > dists; dists.resize(axes[0].size());
+               for (int i = 0; i < dists.size(); i++) {  dists[i].resize(axes[0].size(), 0.0); }
+               
+               if (axes.size() == 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++) {
-                                       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] = abs(axes[0][i] - axes[0][j]);
+                                       dists[j][i] = dists[i][j];
+                               }
+                       }
+                       
+               }else if (axes.size() > 1) { //two dimension calc = sqrt ((x1 - y1)^2 + (x2 - y2)^2)...
+                       
+                       for (int i = 0; i < dists[0].size(); i++) {
+                               
+                               if (m->control_pressed) { return dists; }
+                               
+                               for (int j = 0; j < i; j++) {
+                                       double sum = 0.0;
+                                       for (int k = 0; k < axes.size(); k++) {
+                                               sum += ((axes[k][i] - axes[k][j]) * (axes[k][i] - axes[k][j]));
+                                       }
                                        
-                                       dists[i][j] = sqrt((firstDim + secondDim + thirdDim));
+                                       dists[i][j] = sqrt(sum);
                                        dists[j][i] = dists[i][j];
                                }
                        }
                        
-               }else { m->mothurOut("[ERROR]: too many dimensions, aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
+               }
                
                return dists;
        }