X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=slibshuff.cpp;fp=slibshuff.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=92998e66ac1eadb442b5b0afc0cfee33835f902a;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/slibshuff.cpp b/slibshuff.cpp
deleted file mode 100644
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);
-	}
-}
-
-/***********************************************************************/