+++ /dev/null
-#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
-
projects / mothur.git / blobdiff