X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurfisher.cpp;fp=mothurfisher.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=7acefb2087533546b6089afb984005ec8db64d45;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/mothurfisher.cpp b/mothurfisher.cpp
deleted file mode 100644
index 7acefb2..0000000
--- a/mothurfisher.cpp
+++ /dev/null
@@ -1,193 +0,0 @@
-/*
- *  mothurfisher.cpp
- *  Mothur
- *
- *  Created by westcott on 7/8/11.
- *  Copyright 2011 Schloss Lab. All rights reserved.
- *
- */
-
-//translated to c++ using source code http://www.langsrud.com/stat/fisher.htm as a reference
-
-#include "mothurfisher.h"
-/***********************************************************/
-double MothurFisher::fexact(double n11_, double n12_, double n21_, double n22_) {
-	try {
-		sleft = 0.0; sright = 0.0; sless = 0.0; slarg = 0.0;
-		
-		if(n11_<0) n11_ *= -1;
-		if(n12_<0) n12_ *= -1;
-		if(n21_<0) n21_ *= -1;
-		if(n22_<0) n22_ *= -1; 
-		
-		double n1_ = n11_+n12_;
-		double n_1 = n11_+n21_;
-		double n   = n11_ +n12_ +n21_ +n22_;
-		exact(n11_,n1_,n_1,n);
-		double twotail = sleft+sright;
-		
-		if(twotail>1) twotail=1;
-		double result = twotail;
-		return result; 
-		
-	}catch(exception& e) {
-		m->errorOut(e, "MothurFisher", "fexact");
-		exit(1);
-	}	
-}
-/***********************************************************/
-double MothurFisher::lngamm(double z) {
-	// Reference: "Lanczos, C. 'A precision approximation 
-	// of the gamma function', J. SIAM Numer. Anal., B, 1, 86-96, 1964."
-	// Translation of  Alan Miller's FORTRAN-implementation
-	// See http://lib.stat.cmu.edu/apstat/245
-	try {
-		double x = 0;
-		x += 0.1659470187408462e-06/(z+7);
-		x += 0.9934937113930748e-05/(z+6);
-		x -= 0.1385710331296526    /(z+5);
-		x += 12.50734324009056     /(z+4);
-		x -= 176.6150291498386     /(z+3);
-		x += 771.3234287757674     /(z+2);
-		x -= 1259.139216722289     /(z+1);
-		x += 676.5203681218835     /(z);
-		x += 0.9999999999995183;
-		
-		return(log(x)-5.58106146679532777-z+(z-0.5)*log(z+6.5));
-		
-	}catch(exception& e) {
-		m->errorOut(e, "MothurFisher", "lngamm");
-		exit(1);
-	}	
-}
-
-/***********************************************************/
-double MothurFisher::lnfact(double n){
-	try {
-		if(n <= 1) return(0);
-		return(lngamm(n+1));
-	}catch(exception& e) {
-		m->errorOut(e, "MothurFisher", "lnfact");
-		exit(1);
-	}	
-}
-/***********************************************************/
-double MothurFisher::lnbico(double n, double k){
-	try {
-		return(lnfact(n)-lnfact(k)-lnfact(n-k));
-	}catch(exception& e) {
-		m->errorOut(e, "MothurFisher", "lnbico");
-		exit(1);
-	}
-}
-/***********************************************************/
-double MothurFisher::hyper_323(double n11, double n1_, double n_1, double n){
-	try {
-		return(exp(lnbico(n1_,n11)+lnbico(n-n1_,n_1-n11)-lnbico(n,n_1)));
-	}catch(exception& e) {
-		m->errorOut(e, "MothurFisher", "hyper_323");
-		exit(1);
-	}
-}
-/***********************************************************/
-double MothurFisher::myhyper(double n11){
-	try {
-		double hyper0Result = hyper0(n11,0,0,0);
-		return hyper0Result;
-	}catch(exception& e) {
-		m->errorOut(e, "MothurFisher", "myhyper");
-		exit(1);
-	}
-}
-/***********************************************************/
-double MothurFisher::hyper0(double n11i, double n1_i, double n_1i, double ni) {
-	try {
-		if (!((n1_i != 0)&&(n_1i != 0)&&(ni != 0))) {
-			if(!(((int)n11i % 10) == 0)){
-				if(n11i==sn11+1)  
-				{
-					sprob *= ((sn1_-sn11)/(n11i))*((sn_1-sn11)/(n11i+sn-sn1_-sn_1));
-					sn11 = n11i;
-					return sprob;
-				}
-				if(n11i==sn11-1)
-				{
-					sprob *= ((sn11)/(sn1_-n11i))*((sn11+sn-sn1_-sn_1)/(sn_1-n11i));
-					sn11 = n11i;
-					return sprob;
-				}
-			}
-			sn11 = n11i;
-		}else{
-			sn11 = n11i;
-			sn1_=n1_i;
-			sn_1=n_1i;
-			sn=ni;
-		}
-		
-		sprob = hyper_323(sn11,sn1_,sn_1,sn);
-		return sprob;
-		
-	}catch(exception& e) {
-		m->errorOut(e, "MothurFisher", "hyper0");
-		exit(1);
-	}
-}
-/***********************************************************/
-double MothurFisher::exact(double n11, double n1_, double n_1, double n){
-	try {
-		double p,i,j,prob;
-		double max=n1_;
-		if(n_1<max) max=n_1;
-		double min = n1_+n_1-n;
-		if(min<0) min=0;
-		if(min==max)
-		{
-			sless = 1;
-			sright= 1;
-			sleft = 1;
-			slarg = 1;
-			return 1;
-		}
-		prob=hyper0(n11,n1_,n_1,n);
-		sleft=0;
-		p=myhyper(min);
-		for(i=min+1; p<0.99999999*prob; i++)
-		{
-			sleft += p;
-			p=myhyper(i);
-		}
-		i--;
-		if(p<1.00000001*prob) sleft += p;
-		else i--;
-		sright=0;
-		p=myhyper(max);
-		for(j=max-1; p<0.99999999*prob; j--)
-		{
-			sright += p;
-			p=myhyper(j);
-		}
-		j++;
-		if(p<1.00000001*prob) sright += p;
-		else j++;
-		if(abs(i-n11)<abs(j-n11)) 
-		{
-			sless = sleft;
-			slarg = 1 - sleft + prob;
-		} 
-		else 
-		{
-			sless = 1 - sright + prob;
-			slarg = sright;
-		}
-		return prob;
-		
-	}catch(exception& e) {
-		m->errorOut(e, "MothurFisher", "exact");
-		exit(1);
-	}
-}
-/***********************************************************/
-
-
-