moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / slibshuff.cpp

diff --git a/slibshuff.cpp b/slibshuff.cpp
deleted file mode 100644 (file)
index 92998e6..0000000
--- a/slibshuff.cpp
+++ /dev/null
@@ -1,116 +0,0 @@
-/*
- *  slibshuff.cpp
- *  Mothur
- *
- *  Created by Pat Schloss on 4/8/09.
- *  Copyright 2009 Patrick D. Schloss. All rights reserved.
- *
- */
-
-#include "slibshuff.h"
-
-/***********************************************************************/
-
-SLibshuff::SLibshuff(FullMatrix* D, int it, float co) : Libshuff(D, it, 0, co){}
-
-/***********************************************************************/
-
-float SLibshuff::evaluatePair(int i, int j){
-       return sCalculate(i,j);
-}
-
-/***********************************************************************/
-
-vector<vector<double> > SLibshuff::evaluateAll(){
-       try{
-               savedMins.resize(numGroups);
-               vector<vector<double> > dCXYValues(numGroups);
-
-               for(int i=0;i<numGroups;i++){
-                       dCXYValues[i].resize(numGroups);
-                       savedMins[i].resize(numGroups);
-                       for(int j=0;j<numGroups;j++){
-                               if(i!=j){
-                                       dCXYValues[i][j] = sCalculate(i,j);     
-                                       savedMins[i][j] = minXY;
-                               }
-
-                               if(savedMins[i][i].size() == 0){
-                                       savedMins[i][i] = minX;
-                               }
-
-                       }
-               }               
-               return dCXYValues;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SLibshuff", "evaluateAll");
-               exit(1);
-       }
-}
-
-/***********************************************************************/
-
-double SLibshuff::sCalculate(int x, int y){
-       try{
-               double sum = 0.0,t=0.0;
-               
-               minX = getMinX(x);
-               
-               if (m->control_pressed) { return sum; }
-               
-               minXY = getMinXY(x,y);
-               
-               if (m->control_pressed) { return sum; }
-
-               sort(minX.begin(), minX.end());
-               
-               if (m->control_pressed) { return sum; }
-               
-               sort(minXY.begin(), minXY.end());
-               
-               if (m->control_pressed) { return sum; }
-
-               int ix=0,iy=0;
-               while( (ix < groupSizes[x]) && (iy < groupSizes[x]) ) {
-                       double h = (ix-iy)/double(groupSizes[x]);
-                       
-                       if(minX[ix] < minXY[iy]) {
-                               sum += (minX[ix] - t)*h*h;
-                               t = minX[ix++];
-                       }
-                       else {
-                               sum += (minXY[iy] - t)*h*h;
-                               t = minXY[iy++];
-                       }
-                       
-               }
-               
-               if(ix < groupSizes[x]) {
-                       
-                       while(ix < groupSizes[x]) {
-                               double h = (ix-iy)/double(groupSizes[x]);
-                               sum += (minX[ix] - t)*h*h;
-                               t = minX[ix++];
-                       }
-                       
-               }
-               else {
-                       
-                       while(iy < groupSizes[x]) {
-                               double h = (ix-iy)/double(groupSizes[x]);
-                               sum += (minXY[iy] - t)*h*h;
-                               t = minXY[iy++];
-                       }
-                       
-               }
-               
-               return sum;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SLibshuff", "sCalculate");
-               exit(1);
-       }
-}
-
-/***********************************************************************/