X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=2c143e8667786c5740f0aa6324ea4062eab66b76;hb=e0b6040c7b6ad4ecdad4aa90b4326c0528379178;hp=f8ec32363516bcc6543569b57f313505796acef7;hpb=fc1ed1ae1b022719176910ab71993bd6535810ad;p=mothur.git

diff --git a/mothur.h b/mothur.h
index f8ec323..2c143e8 100644
--- a/mothur.h
+++ b/mothur.h
@@ -42,6 +42,7 @@
 #include <cmath>
 #include <math.h>
 #include <algorithm>
+#include <numeric>
 
 //misc
 #include <cerrno>
@@ -53,7 +54,7 @@
 #endif
 /***********************************************************************/
 
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 	#include <sys/wait.h>
 	#include <sys/time.h>
 	#include <sys/resource.h>
@@ -85,6 +86,7 @@ using namespace std;
 #define isnan(x) ((x) != (x))
 #define isinf(x) (fabs(x) == std::numeric_limits<double>::infinity())
 
+
 typedef unsigned long ull;
 
 struct IntNode {
@@ -105,6 +107,19 @@ struct ThreadNode {
 	IntNode* right;
 };
 
+struct diffPair {
+	float	prob;
+	float	reverseProb;
+	
+	diffPair() {
+		prob = 0; reverseProb = 0;
+	}
+	diffPair(float p, float rp) {
+		prob = p;
+		reverseProb = rp;
+	}
+};
+
 /************************************************************/
 struct clusterNode {
 	int numSeq;
@@ -116,9 +131,9 @@ struct clusterNode {
 struct seqDist {
 	int seq1;
 	int seq2;
-	float dist;
+	double dist;
 	seqDist() {}
-	seqDist(int s1, int s2, float d) : seq1(s1), seq2(s2), dist(d) {}
+	seqDist(int s1, int s2, double d) : seq1(s1), seq2(s2), dist(d) {}
 	~seqDist() {}
 };
 /************************************************************/
@@ -188,7 +203,8 @@ void convert(const string& s, T& x, bool failIfLeftoverChars = true){
 			throw BadConversion(s);
 	
 }
-
+//**********************************************************************************************************************
+template <typename T> int sgn(T val){ return (val > T(0)) - (val < T(0)); }
 //**********************************************************************************************************************
 
 template<typename T>