X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothur.h;h=32f4778a7c1ee19db25eeb4e1eafaf74fabcd617;hp=190254a96e4c7d7830f8405035933efda4b003ea;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=24083a26340293cb3a0e44bcf79edbc9b31f41db

diff --git a/mothur.h b/mothur.h
index 190254a..32f4778 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;
@@ -83,7 +86,9 @@ using namespace std;
 #define isnan(x) ((x) != (x))
 #define isinf(x) (fabs(x) == std::numeric_limits<double>::infinity())
 
+
 typedef unsigned long ull;
+typedef unsigned short intDist;
 
 struct IntNode {
 	int lvalue;
@@ -103,6 +108,40 @@ 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 PDistCell{
+	ull index;
+	float dist;
+	PDistCell() :  index(0), dist(0) {};
+	PDistCell(ull c, float d) :  index(c), dist(d) {}
+};
+/***********************************************************************/
+struct consTax{
+	string name;
+    string taxonomy;
+    int abundance;
+	consTax() :  name(""), taxonomy("unknown"), abundance(0) {};
+	consTax(string n, string t, int a) :  name(n), taxonomy(t), abundance(a) {}
+};
+/***********************************************************************/
+struct consTax2{
+    string taxonomy;
+    int abundance;
+	consTax2() :  taxonomy("unknown"), abundance(0) {};
+	consTax2(string t, int a) :  taxonomy(t), abundance(a) {}
+};
 /************************************************************/
 struct clusterNode {
 	int numSeq;
@@ -114,9 +153,9 @@ 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 +164,24 @@ 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 compGroup {
+	string group1;
+	string group2;
+	compGroup() {}
+	compGroup(string s, string nm) : group1(s), group2(nm) {}
+    string getCombo() { return group1+"-"+group2; }
+	~compGroup() {}
+};
 /***************************************************************/
 struct spearmanRank {
 	string name;
@@ -132,16 +189,26 @@ struct spearmanRank {
 	
 	spearmanRank(string n, float s) : name(n), score(s) {}
 };
+//***********************************************************************
+inline bool compareIndexes(PDistCell left, PDistCell right){
+	return (left.index > right.index);	
+}
 //********************************************************************************************************************
-//sorts highest to lowest
 inline bool compareSpearman(spearmanRank left, spearmanRank right){
-	return (left.score > right.score);	
+	return (left.score < right.score);	
 } 
 //********************************************************************************************************************
-//sorts lowest to highest
-inline bool compareSpearmanReverse(spearmanRank left, spearmanRank right){
-	return (left.score < right.score);	
+//sorts highest to lowest
+inline bool compareSeqPriorityNodes(seqPriorityNode left, seqPriorityNode right){
+	if (left.numIdentical > right.numIdentical) {
+        return true;
+    }else if (left.numIdentical == right.numIdentical) {
+        if (left.seq > right.seq) { return true; }
+        else { return false; }
+    }
+    return false;	
 } 
+ 
 /************************************************************/
 //sorts lowest to highest
 inline bool compareDistLinePairs(distlinePair left, distlinePair right){
@@ -151,7 +218,15 @@ inline bool compareDistLinePairs(distlinePair left, distlinePair right){
 //sorts lowest to highest
 inline bool compareSequenceDistance(seqDist left, seqDist right){
 	return (left.dist < right.dist);	
-} 
+}
+//********************************************************************************************************************
+//returns sign of double
+inline double sign(double temp){
+	//find sign
+    if (temp > 0)       { return 1.0;   }
+    else if (temp < 0)  { return -1.0;  }
+    return 0;
+}
 /***********************************************************************/
 
 // snagged from http://www.parashift.com/c++-faq-lite/misc-technical-issues.html#faq-39.2
@@ -172,7 +247,8 @@ 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>