X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.h;fp=mothur.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=2c143e8667786c5740f0aa6324ea4062eab66b76;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/mothur.h b/mothur.h
deleted file mode 100644
index 2c143e8..0000000
--- a/mothur.h
+++ /dev/null
@@ -1,285 +0,0 @@
-#ifndef MOTHUR_H
-#define MOTHUR_H
-
-
-
-/*
- *  mothur.h
- *  Mothur
- *
- *  Created by Sarah Westcott on 2/19/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-/* 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>
-#include <exception>
-#include <cstdlib> 
-
-
-//containers
-#include <vector>
-#include <set>
-#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;
-
-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 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 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);	
-} 
-//********************************************************************************************************************
-//sorts lowest to highest
-inline bool compareSequenceDistance(seqDist left, seqDist right){
-	return (left.dist < right.dist);	
-} 
-/***********************************************************************/
-
-// 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
-