#ifndef MOTHUR_H
#define MOTHUR_H
-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>
#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
projects / mothur.git / blobdiff