X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothur.h;h=32f4778a7c1ee19db25eeb4e1eafaf74fabcd617;hp=e5c389005df83b47e45504433269ac7735f6a8c4;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=bfbc55964f1977da72c2cea984288a427d370a59

diff --git a/mothur.h b/mothur.h
index e5c3890..32f4778 100644
--- a/mothur.h
+++ b/mothur.h
@@ -1,7 +1,6 @@
 #ifndef MOTHUR_H
 #define MOTHUR_H
 
-using namespace std;
 
 
 /*
@@ -13,14 +12,17 @@ using namespace std;
  *
  */
 
-/* This file contains all the standard incudes we use in the project. */
+/* This file contains all the standard incudes we use in the project as well as some common utilities. */
 
+//#include <cstddef>
 
 //io libraries
 #include <iostream>
 #include <iomanip>
 #include <fstream>
 #include <sstream>
+#include <signal.h>
+
 
 //exception
 #include <stdexcept>
@@ -34,11 +36,294 @@ using namespace std;
 #include <map>
 #include <string>
 #include <list>
+#include <string.h>
 
 //math
 #include <cmath>
 #include <math.h>
 #include <algorithm>
+#include <numeric>
+
+//misc
+#include <cerrno>
+#include <ctime>
+#include <limits>
+
+#ifdef USE_MPI
+	#include "mpi.h"
+#endif
+/***********************************************************************/
+
+#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
+		#include <readline/readline.h>
+		#include <readline/history.h>
+	#endif
+
+#else
+	#include <conio.h> //allows unbuffered screen capture from stdin
+	#include <direct.h> //get cwd
+	#include <windows.h>
+	#include <psapi.h>
+	#include <direct.h>
+	#include <tchar.h>
+
+#endif
+
+using namespace std;
+
+#define exp(x) (exp((double) x))
+#define sqrt(x) (sqrt((double) x))
+#define log10(x) (log10((double) x))
+#define log2(x) (log10(x)/log10(2))
+#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;
+	int rvalue;
+	int lcoef;
+	int rcoef;
+	IntNode* left;
+	IntNode* right;
+	
+	IntNode(int lv, int rv, IntNode* l, IntNode* r) : lvalue(lv), rvalue(rv), left(l), right(r) {};
+	IntNode() {};
+};
+
+struct ThreadNode {
+	int* pid;
+	IntNode* left;
+	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;
+	int parent;
+	int smallChild; //used to make linkTable work with list and rabund. represents bin number of this cluster node
+	clusterNode(int num, int par, int kid) : numSeq(num), parent(par), smallChild(kid) {};
+};
+/************************************************************/
+struct seqDist {
+	int seq1;
+	int seq2;
+	double dist;
+	seqDist() {}
+	seqDist(int s1, int s2, double d) : seq1(s1), seq2(s2), dist(d) {}
+	~seqDist() {}
+};
+/************************************************************/
+struct distlinePair {
+	int start;
+	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;
+	float score;
+	
+	spearmanRank(string n, float s) : name(n), score(s) {}
+};
+//***********************************************************************
+inline bool compareIndexes(PDistCell left, PDistCell right){
+	return (left.index > right.index);	
+}
+//********************************************************************************************************************
+inline bool compareSpearman(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){
+	return (left.end < right.end);	
+} 
+//********************************************************************************************************************
+//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
+// works for now, but there should be a way to do it without killing the whole program
+
+class BadConversion : public runtime_error {
+public:
+	BadConversion(const string& s) : runtime_error(s){ }
+};
+
+//**********************************************************************************************************************
+template<typename T>
+void convert(const string& s, T& x, bool failIfLeftoverChars = true){
+	
+		istringstream i(s);
+		char c;
+		if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
+			throw BadConversion(s);
+	
+}
+//**********************************************************************************************************************
+template <typename T> int sgn(T val){ return (val > T(0)) - (val < T(0)); }
+//**********************************************************************************************************************
+
+template<typename T>
+bool convertTestFloat(const string& s, T& x, bool failIfLeftoverChars = true){
+	
+		istringstream i(s);
+		char c;
+		if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
+		{
+			return false;
+		} 
+		return true;
+	
+}
+
+//**********************************************************************************************************************
+
+template<typename T>
+bool convertTest(const string& s, T& x, bool failIfLeftoverChars = true){
+	
+		istringstream i(s);
+		char c;
+		if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
+		{
+			return false;
+		} 
+		return true;
+	
+}
+//**********************************************************************************************************************
+template<typename T>
+string toString(const T&x){
+	
+		stringstream output;
+		output << x;
+		return output.str();
+	
+}
+
+//**********************************************************************************************************************
+
+template<typename T>
+string toHex(const T&x){
+	
+		stringstream output;
+		
+		output << hex << x;
+
+		return output.str();
+	
+}
+//**********************************************************************************************************************
+
+template<typename T>
+string toString(const T&x, int i){
+	
+		stringstream output;
+		
+		output.precision(i);
+		output << fixed << x;
+		
+		return output.str();
+	
+}
+//**********************************************************************************************************************
+
+template<class T>
+T fromString(const string& s){
+	istringstream stream (s);
+	T t;
+	stream >> t;
+	return t;
+}
+
+//**********************************************************************************************************************
 
 #endif