X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=50344e24bfea85e8b7c4b829b5136e3e63d34fc7;hb=16abd6271c455bd01b34ff89a2e3641bef0fa128;hp=2e2299ec2ad6fa1938a2f49e1f8601993b232cbd;hpb=8173238f9f94af9baab8471de58bed7c8830948d;p=mothur.git

diff --git a/mothur.h b/mothur.h
index 2e2299e..50344e2 100644
--- a/mothur.h
+++ b/mothur.h
@@ -36,6 +36,7 @@
 #include <map>
 #include <string>
 #include <list>
+#include <string.h>
 
 //math
 #include <cmath>
@@ -56,6 +57,7 @@
 	#include <sys/wait.h>
 	#include <sys/time.h>
 	#include <sys/resource.h>
+	#include <sys/types.h>
 	#include <sys/stat.h>
 	#include <unistd.h>
 	
@@ -69,6 +71,8 @@
 	#include <direct.h> //get cwd
 	#include <windows.h>
 	#include <psapi.h>
+	#include <direct.h>
+	#include <tchar.h>
 
 #endif
 
@@ -81,6 +85,7 @@ using namespace std;
 #define isnan(x) ((x) != (x))
 #define isinf(x) (fabs(x) == std::numeric_limits<double>::infinity())
 
+
 typedef unsigned long ull;
 
 struct IntNode {
@@ -101,6 +106,19 @@ 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;
@@ -124,6 +142,37 @@ struct distlinePair {
 	
 };
 /************************************************************/
+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;
+	float score;
+	
+	spearmanRank(string n, float s) : name(n), score(s) {}
+};
+//********************************************************************************************************************
+//sorts highest to lowest
+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);	
+} 
+/************************************************************/
 //sorts lowest to highest
 inline bool compareDistLinePairs(distlinePair left, distlinePair right){
 	return (left.end < right.end);	
@@ -153,7 +202,8 @@ 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>
@@ -220,5 +270,15 @@ string toString(const T&x, int i){
 }
 //**********************************************************************************************************************
 
+template<class T>
+T fromString(const string& s){
+	istringstream stream (s);
+	T t;
+	stream >> t;
+	return t;
+}
+
+//**********************************************************************************************************************
+
 #endif