X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=2c143e8667786c5740f0aa6324ea4062eab66b76;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hp=190254a96e4c7d7830f8405035933efda4b003ea;hpb=24083a26340293cb3a0e44bcf79edbc9b31f41db;p=mothur.git

diff --git a/mothur.h b/mothur.h
index 190254a..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>
@@ -72,6 +73,8 @@
 	#include <windows.h>
 	#include <psapi.h>
 	#include <direct.h>
+	#include <tchar.h>
+
 #endif
 
 using namespace std;
@@ -83,6 +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 {
@@ -103,6 +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;
@@ -114,9 +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() {}
 };
 /************************************************************/
@@ -125,6 +142,15 @@ struct distlinePair {
 	int end;
 	
 };
+/************************************************************/
+struct seqPriorityNode {
+	int numIdentical;
+	string seq;
+	string name;
+	seqPriorityNode() {}
+	seqPriorityNode(int n, string s, string nm) : numIdentical(n), seq(s), name(nm) {}
+	~seqPriorityNode() {}
+};
 /***************************************************************/
 struct spearmanRank {
 	string name;
@@ -138,6 +164,11 @@ inline bool compareSpearman(spearmanRank left, spearmanRank right){
 	return (left.score > right.score);	
 } 
 //********************************************************************************************************************
+//sorts highest to lowest
+inline bool compareSeqPriorityNodes(seqPriorityNode left, seqPriorityNode right){
+	return (left.numIdentical > right.numIdentical);	
+} 
+//********************************************************************************************************************
 //sorts lowest to highest
 inline bool compareSpearmanReverse(spearmanRank left, spearmanRank right){
 	return (left.score < right.score);	
@@ -172,7 +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>