#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)
+#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;
typedef unsigned long ull;
+typedef unsigned short intDist;
struct IntNode {
int lvalue;
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 {
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 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
};
//**********************************************************************************************************************
-
template<typename T>
-inline 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);
+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>
-inline 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;
+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>
-inline bool convertTest(const string& s, T& x, bool failIfLeftoverChars = true){
- istringstream i(s);
- char c;
- if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
- {
- cout << "unable to be converted into an integer.\n" << endl;
- return false;
- }
- return true;
+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();
+
+ stringstream output;
+ output << x;
+ return output.str();
+
}
//**********************************************************************************************************************
template<typename T>
string toHex(const T&x){
- stringstream output;
- output << hex << x;
+ stringstream output;
+
+ output << hex << x;
- return output.str();
+ return output.str();
+
}
//**********************************************************************************************************************
template<typename T>
string toString(const T&x, int i){
- stringstream output;
-
- output.precision(i);
- output << fixed << x;
-
- return output.str();
-}
-/***********************************************************************/
-
-inline int openOutputFileAppend(string fileName, ofstream& fileHandle){
-
- fileHandle.open(fileName.c_str(), ios::app);
- if(!fileHandle) {
- cout << "Error: Could not open " << fileName << endl;
- return 1;
- }
- else {
- return 0;
- }
-
-}
-/***********************************************************************/
-
-inline void gobble(istream& f){
-
- char d;
- while(isspace(d=f.get())) {;}
- f.putback(d);
-
-}
-
-/***********************************************************************/
-
-inline string getline(ifstream& fileHandle) {
- try {
- string line = "";
-
- while (!fileHandle.eof()) {
- //get next character
- char c = fileHandle.get();
-
- //are you at the end of the line
- if ((c == '\n') || (c == '\r') || (c == '\f')){ break; }
- else { line += c; }
- }
-
- return line;
-
- }
- catch(exception& e) {
- cout << "Error in mothur function getline" << endl;
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-
-inline void mothurOut(string message) {
- try{
- ofstream out;
- string logFileName = "mothur.logFile";
- openOutputFileAppend(logFileName, out);
+ stringstream output;
- cout << message;
- out << message;
+ output.precision(i);
+ output << fixed << x;
- out.close();
- }
- catch(exception& e) {
- cout << "Error in mothur class mothurOut" << endl;
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-inline void mothurOut(string message, string precision) {
- try{
- ofstream out;
- string logFileName = "mothur.logFile";
- openOutputFileAppend(logFileName, out);
-
- cout << precision << message;
- out << precision << message;
-
- out.close();
- }
- catch(exception& e) {
- cout << "Error in mothur class mothurOut" << endl;
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-
-inline void mothurOutEndLine() {
- try {
- ofstream out;
- string logFileName = "mothur.logFile";
- openOutputFileAppend(logFileName, out);
-
- cout << endl;
- out << endl;
-
- out.close();
- }
- catch(exception& e) {
- cout << "error in mothur mothurOutEndLine" << endl;
- exit(1);
- }
-}
-
-
-/**************************************************************************************************/
-
-inline void errorOut(exception& e, string object, string function) {
-
- mothurOut("Error: ");
- mothurOut(toString(e.what()));
- mothurOut(" has occurred in the " + object + " class function " + function + ". Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.");
- mothurOutEndLine();
+ return output.str();
}
+//**********************************************************************************************************************
-
-
-
-/***********************************************************************/
-
-inline bool isTrue(string f){
-
- if ((f == "TRUE") || (f == "T") || (f == "true") || (f == "t")) { return true; }
- else { return false; }
-}
-
-/***********************************************************************/
-
-inline float roundDist(float dist, int precision){
-
- return int(dist * precision + 0.5)/float(precision);
-
-}
-
-/***********************************************************************/
-
-inline int getNumNames(string names){
-
- int count = 0;
-
- if(names != ""){
- count = 1;
- for(int i=0;i<names.size();i++){
- if(names[i] == ','){
- count++;
- }
- }
- }
-
- return count;
-
-}
-
-/**************************************************************************************************/
-
-inline vector<vector<double> > binomial(int maxOrder){
-
- vector<vector<double> > binomial(maxOrder+1);
-
- for(int i=0;i<=maxOrder;i++){
- binomial[i].resize(maxOrder+1);
- binomial[i][0]=1;
- binomial[0][i]=0;
- }
- binomial[0][0]=1;
-
- binomial[1][0]=1;
- binomial[1][1]=1;
-
- for(int i=2;i<=maxOrder;i++){
- binomial[1][i]=0;
- }
-
- for(int i=2;i<=maxOrder;i++){
- for(int j=1;j<=maxOrder;j++){
- if(i==j){ binomial[i][j]=1; }
- if(j>i) { binomial[i][j]=0; }
- else { binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j]; }
- }
- }
-
- return binomial;
-}
-
-/***********************************************************************/
-
-inline string getRootName(string longName){
-
- string rootName = longName;
-
- if(longName.find_last_of(".") != longName.npos){
- int pos = longName.find_last_of('.')+1;
- rootName = longName.substr(0, pos);
- }
-
- return rootName;
-}
-/***********************************************************************/
-
-inline string getSimpleName(string longName){
-
- string simpleName = longName;
-
- if(longName.find_last_of("/") != longName.npos){
- int pos = longName.find_last_of('/')+1;
- simpleName = longName.substr(pos, longName.length());
- }
-
- return simpleName;
-}
-
-/***********************************************************************/
-
-inline int factorial(int num){
- int total = 1;
-
- for (int i = 1; i <= num; i++) {
- total *= i;
- }
-
- return total;
-}
-/**************************************************************************************************
-
-double min(double x, double y)
-{
- if(x<y){ return x; }
- else { return y; }
-}
-
-/***********************************************************************/
-
-inline string getPathName(string longName){
-
- string rootPathName = longName;
-
- if(longName.find_last_of('/') != longName.npos){
- int pos = longName.find_last_of('/')+1;
- rootPathName = longName.substr(0, pos);
- }
-
- return rootPathName;
-}
-
-/***********************************************************************/
-
-inline string getExtension(string longName){
-
- string extension = longName;
-
- if(longName.find_last_of('.') != longName.npos){
- int pos = longName.find_last_of('.');
- extension = longName.substr(pos, longName.length());
- }
-
- return extension;
-}
-
-/***********************************************************************/
-
-inline int openInputFile(string fileName, ifstream& fileHandle){
-
- fileHandle.open(fileName.c_str());
- if(!fileHandle) {
- mothurOut("Error: Could not open " + fileName); mothurOutEndLine();
- return 1;
- }
- else {
- //check for blank file
- gobble(fileHandle);
- if (fileHandle.eof()) { mothurOut(fileName + " is blank. Please correct."); mothurOutEndLine(); return 1; }
-
- return 0;
- }
-
-}
-
-/***********************************************************************/
-
-inline int openOutputFile(string fileName, ofstream& fileHandle){
-
- fileHandle.open(fileName.c_str(), ios::trunc);
- if(!fileHandle) {
- mothurOut("Error: Could not open " + fileName); mothurOutEndLine();
- return 1;
- }
- else {
- return 0;
- }
-
-}
-
-/***********************************************************************/
-
-inline int getNumSeqs(ifstream& file){
-
- int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
- file.seekg(0);
- return numSeqs;
-
-}
-
-/***********************************************************************/
-
-//This function parses the estimator options and puts them in a vector
-inline void splitAtDash(string& estim, vector<string>& container) {
- try {
- string individual;
-
- while (estim.find_first_of('-') != -1) {
- individual = estim.substr(0,estim.find_first_of('-'));
- if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
- estim = estim.substr(estim.find_first_of('-')+1, estim.length());
- container.push_back(individual);
- }
- }
- //get last one
- container.push_back(estim);
- }
- catch(exception& e) {
- errorOut(e, "mothur", "splitAtDash");
- exit(1);
- }
-}
-
-/***********************************************************************/
-//This function parses the label options and puts them in a set
-inline void splitAtDash(string& estim, set<string>& container) {
- try {
- string individual;
-
- while (estim.find_first_of('-') != -1) {
- individual = estim.substr(0,estim.find_first_of('-'));
- if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
- estim = estim.substr(estim.find_first_of('-')+1, estim.length());
- container.insert(individual);
- }
- }
- //get last one
- container.insert(estim);
- }
- catch(exception& e) {
- errorOut(e, "mothur", "splitAtDash");
- exit(1);
- }
-}
-/***********************************************************************/
-//This function parses the line options and puts them in a set
-inline void splitAtDash(string& estim, set<int>& container) {
- try {
- string individual;
- int lineNum;
-
- while (estim.find_first_of('-') != -1) {
- individual = estim.substr(0,estim.find_first_of('-'));
- if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
- estim = estim.substr(estim.find_first_of('-')+1, estim.length());
- convert(individual, lineNum); //convert the string to int
- container.insert(lineNum);
- }
- }
- //get last one
- convert(estim, lineNum); //convert the string to int
- container.insert(lineNum);
- }
- catch(exception& e) {
- errorOut(e, "mothur", "splitAtDash");
- exit(1);
- }
-}
-/***********************************************************************/
-//This function parses the a string and puts peices in a vector
-inline void splitAtComma(string& estim, vector<string>& container) {
- try {
- string individual;
-
- while (estim.find_first_of(',') != -1) {
- individual = estim.substr(0,estim.find_first_of(','));
- if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
- estim = estim.substr(estim.find_first_of(',')+1, estim.length());
- container.push_back(individual);
- }
- }
- //get last one
- container.push_back(estim);
- }
- catch(exception& e) {
- errorOut(e, "mothur", "splitAtComma");
- exit(1);
- }
-}
-/***********************************************************************/
-
-//This function splits up the various option parameters
-inline void splitAtComma(string& prefix, string& suffix){
- try {
- prefix = suffix.substr(0,suffix.find_first_of(','));
- if ((suffix.find_first_of(',')+2) <= suffix.length()) { //checks to make sure you don't have comma at end of string
- suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
- string space = " ";
- while(suffix.at(0) == ' ')
- suffix = suffix.substr(1, suffix.length());
- }
-
- }
- catch(exception& e) {
- errorOut(e, "mothur", "splitAtComma");
- exit(1);
- }
-}
-/***********************************************************************/
-
-//This function separates the key value from the option value i.e. dist=96_...
-inline void splitAtEquals(string& key, string& value){
- try {
- if(value.find_first_of('=') != -1){
- key = value.substr(0,value.find_first_of('='));
- if ((value.find_first_of('=')+1) <= value.length()) {
- value = value.substr(value.find_first_of('=')+1, value.length());
- }
- }else{
- key = value;
- value = 1;
- }
- }
- catch(exception& e) {
- errorOut(e, "mothur", "splitAtEquals");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-inline bool inUsersGroups(string groupname, vector<string> Groups) {
- try {
- for (int i = 0; i < Groups.size(); i++) {
- if (groupname == Groups[i]) { return true; }
- }
- return false;
- }
- catch(exception& e) {
- errorOut(e, "mothur", "inUsersGroups");
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-
-inline void mothurOutJustToLog(string message) {
- try {
- ofstream out;
- string logFileName = "mothur.logFile";
- openOutputFileAppend(logFileName, out);
-
- out << message;
-
- out.close();
- }
- catch(exception& e) {
- errorOut(e, "mothur", "mothurOutJustToLog");
- exit(1);
- }
-}
-
-
-/**************************************************************************************************/
-
-inline void mothurOut(float num) {
- try {
- ofstream out;
- string logFileName = "mothur.logFile";
- openOutputFileAppend(logFileName, out);
-
- cout << num;
- out << num;
-
- out.close();
- }
- catch(exception& e) {
- cout << "Error in mothur class mothurOut float" << endl;
- exit(1);
- }
-}
-/***********************************************************************/
-inline void mothurOut(double value) {
- try {
- ofstream out;
- string logFileName = "mothur.logFile";
- openOutputFileAppend(logFileName, out);
-
- cout << value;
- out << value;
-
- out.close();
- }
- catch(exception& e) {
- cout << "Error in mothur class mothurOut double" << endl;
- exit(1);
- }
+template<class T>
+T fromString(const string& s){
+ istringstream stream (s);
+ T t;
+ stream >> t;
+ return t;
}
-/***********************************************************************/
-//this function determines if the user has given us labels that are smaller than the given label.
-//if so then it returns true so that the calling function can run the previous valid distance.
-//it's a "smart" distance function. It also checks for invalid labels.
-inline bool anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
- try {
- set<string>::iterator it;
- vector<float> orderFloat;
- map<string, float> userMap; //the conversion process removes trailing 0's which we need to put back
- map<string, float>::iterator it2;
- float labelFloat;
- bool smaller = false;
-
- //unique is the smallest line
- if (label == "unique") { return false; }
- else { convert(label, labelFloat); }
-
- //go through users set and make them floats
- for(it = userLabels.begin(); it != userLabels.end(); ++it) {
-
- float temp;
- if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
- convert(*it, temp);
- orderFloat.push_back(temp);
- userMap[*it] = temp;
- }else if (*it == "unique") {
- orderFloat.push_back(-1.0);
- userMap["unique"] = -1.0;
- }else {
- if (errorOff == "") { mothurOut(*it + " is not a valid label."); mothurOutEndLine(); }
- userLabels.erase(*it);
- it--;
- }
- }
-
- //sort order
- sort(orderFloat.begin(), orderFloat.end());
-
- /*************************************************/
- //is this label bigger than any of the users labels
- /*************************************************/
-
- //loop through order until you find a label greater than label
- for (int i = 0; i < orderFloat.size(); i++) {
- if (orderFloat[i] < labelFloat) {
- smaller = true;
- if (orderFloat[i] == -1) {
- if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); }
- userLabels.erase("unique");
- }
- else {
- if (errorOff == "") { mothurOut("Your file does not include the label "); mothurOutEndLine(); }
- string s = "";
- for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
- if (it2->second == orderFloat[i]) {
- s = it2->first;
- //remove small labels
- userLabels.erase(s);
- break;
- }
- }
- if (errorOff == "") { mothurOut(s + ". I will use the next smallest distance. "); mothurOutEndLine(); }
- }
- //since they are sorted once you find a bigger one stop looking
- }else { break; }
- }
-
- return smaller;
-
- }
- catch(exception& e) {
- errorOut(e, "mothur", "anyLabelsToProcess");
- exit(1);
- }
-}
+//**********************************************************************************************************************
-/**************************************************************************************************/
#endif
projects / mothur.git / blobdiff