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

[mothur.git] / dlibshuff.cpp

diff --git a/dlibshuff.cpp b/dlibshuff.cpp
deleted file mode 100644 (file)
index 4947e05..0000000
--- a/dlibshuff.cpp
+++ /dev/null
@@ -1,95 +0,0 @@
-/*
- *  DLibshuff.cpp
- *  Mothur
- *
- *  Created by Pat Schloss on 4/8/09.
- *  Copyright 2009 Patrick D. Schloss. All rights reserved.
- *
- */
-
-#include "dlibshuff.h"
-
-/***********************************************************************/
-
-DLibshuff::DLibshuff(FullMatrix* D, int it, float step, float co) : Libshuff(D, it, step, co){
-
-       numDXs = int(cutOff / stepSize);
-
-}
-
-/***********************************************************************/
-
-float DLibshuff::evaluatePair(int i, int j){
-       return dCalculate(i,j);
-}
-
-/***********************************************************************/
-
-vector<vector<double> > DLibshuff::evaluateAll(){
-       savedMins.resize(numGroups);
-       vector<vector<double> > dCXYValues(numGroups);
-       
-       for(int i=0;i<numGroups;i++){
-               savedMins[i].resize(numGroups);
-               dCXYValues[i].resize(numGroups);
-               for(int j=0;j<numGroups;j++){
-                       if(i!=j){       dCXYValues[i][j] = dCalculate(i,j);     }
-                       savedMins[i][i] = minX;
-                       savedMins[i][j] = minXY;
-               }
-       }
-       
-       return dCXYValues;
-}
-
-/***********************************************************************/
-
-double DLibshuff::dCalculate(int x, int y){
-       
-       double sum = 0;
-       
-       minX = getMinX(x);
-       
-       if (m->control_pressed) { return sum; }
-       
-       minXY = getMinXY(x, y);
-       
-       if (m->control_pressed) { return sum; }
-       
-       vector<int> nx = calcN(minX);
-       
-       if (m->control_pressed) { return sum; }
-       
-       vector<int> nxy = calcN(minXY);
-       
-       if (m->control_pressed) { return sum; }
-
-       for(int i=0;i<numDXs;i++){
-               float h = (nx[i] - nxy[i]) / (float) groupSizes[x];
-               sum += h * h * stepSize;
-       }
-
-       return sum;
-}
-
-/***********************************************************************/
-
-vector<int> DLibshuff::calcN(vector<double> minVector){
-
-       vector<int> counts(numDXs,0);
-       
-       int precision = int(1 / stepSize);
-       
-       for(int i=0;i<minVector.size();i++){
-               int bin = int (precision * minVector[i]);
-               if(bin < numDXs){       counts[bin]++;  }
-       }
-
-       for(int i=1;i<numDXs;i++){
-               counts[i] += counts[i-1];
-       }
-       
-       return counts;
-}
-
-/***********************************************************************/