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mothur.h
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mothur.h
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#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>
//boost libraries
#ifdef USE_BOOST
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/filter/gzip.hpp>
#endif
//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>
/***********************************************************************/
#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 <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 CommonHeader {
unsigned int magicNumber;
string version;
unsigned long long indexOffset;
unsigned int indexLength;
unsigned int numReads;
unsigned short headerLength;
unsigned short keyLength;
unsigned short numFlowsPerRead;
int flogramFormatCode;
string flowChars; //length depends on number flow reads
string keySequence; //length depends on key length
CommonHeader(){ magicNumber=0; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlowsPerRead=0; flogramFormatCode='s'; }
~CommonHeader() { }
};
/**********************************************************/
struct Header {
unsigned short headerLength;
unsigned short nameLength;
unsigned int numBases;
unsigned short clipQualLeft;
unsigned short clipQualRight;
unsigned short clipAdapterLeft;
unsigned short clipAdapterRight;
string name; //length depends on nameLength
string timestamp;
string region;
string xy;
Header() { headerLength=0; nameLength=0; numBases=0; clipQualLeft=0; clipQualRight=0; clipAdapterLeft=0; clipAdapterRight=0; }
~Header() { }
};
/**********************************************************/
struct seqRead {
vector<unsigned short> flowgram;
vector<unsigned int> flowIndex;
string bases;
vector<unsigned int> qualScores;
seqRead() { }
~seqRead() { }
};
/**********************************************************/
struct linePair {
unsigned long long start;
unsigned long long end;
linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
linePair(){ start=0; end=0; }
~linePair(){}
};
/***********************************************************************/
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 listCt{
string bin;
int binSize;
listCt() : bin(""), binSize(0) {};
listCt(string b, int a) : bin(b), binSize(a) {}
};
/***********************************************************************/
struct consTax2{
string taxonomy;
int abundance;
string otuName;
consTax2() : otuName("OTUxxx"), taxonomy("unknown"), abundance(0) {};
consTax2(string n, string t, int a) : otuName(n), 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 oligosPair {
string forward;
string reverse;
oligosPair() { forward = ""; reverse = ""; }
oligosPair(string f, string r) : forward(f), reverse(r) {}
~oligosPair() {}
};
/************************************************************/
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);
}
//********************************************************************************************************************
inline double max(double left, double right){
if (left > right) { return left; }
else { return right; }
}
//********************************************************************************************************************
inline double max(int left, double right){
double value = left;
if (left > right) { return value; }
else { return right; }
}
//********************************************************************************************************************
inline double max(double left, int right){
double value = right;
if (left > value) { return left; }
else { return value; }
}
//********************************************************************************************************************
//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