X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;h=2c143e8667786c5740f0aa6324ea4062eab66b76;hb=a6cf29fa4dac0909c7582cb1094151d34093ee76;hp=337e5b33a6b1d8100effe484c230d42c7fd93f58;hpb=173a1a82a4e4aa6bef8e4ba77bce342fb9c6563e;p=mothur.git

diff --git a/mothur.h b/mothur.h
index 337e5b3..2c143e8 100644
--- a/mothur.h
+++ b/mothur.h
@@ -36,11 +36,13 @@
 #include <map>
 #include <string>
 #include <list>
+#include <string.h>
 
 //math
 #include <cmath>
 #include <math.h>
 #include <algorithm>
+#include <numeric>
 
 //misc
 #include <cerrno>
@@ -52,10 +54,12 @@
 #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>
+	#include <sys/types.h>
+	#include <sys/stat.h>
 	#include <unistd.h>
 	
 	#ifdef USE_READLINE
@@ -68,6 +72,8 @@
 	#include <direct.h> //get cwd
 	#include <windows.h>
 	#include <psapi.h>
+	#include <direct.h>
+	#include <tchar.h>
 
 #endif
 
@@ -80,6 +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 {
@@ -100,6 +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;
@@ -111,9 +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() {}
 };
 /************************************************************/
@@ -123,6 +143,37 @@ 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);	
@@ -152,7 +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>
@@ -219,5 +271,15 @@ 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