#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 <math.h>
#include <algorithm>
+//misc
+#include <cerrno>
+#include <ctime>
+#include <limits>
+
+#ifdef USE_MPI
+ #include "mpi.h"
+#endif
+/***********************************************************************/
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #include <sys/wait.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
+#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 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;
+ float dist;
+ seqDist() {}
+ seqDist(int s1, int s2, float d) : seq1(s1), seq2(s2), dist(d) {}
+ ~seqDist() {}
+};
+//********************************************************************************************************************
+//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>
+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);
+}
+
+//**********************************************************************************************************************
+
+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;
+}
+
+//**********************************************************************************************************************
+
+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;
+}
+
+//**********************************************************************************************************************
+
+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();
+}
+/***********************************************************************/
+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 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;
+
+ size_t found;
+ found=longName.find_last_of("/\\");
+
+ if(found != longName.npos){
+ simpleName = longName.substr(found+1);
+ }
+
+ //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 hasPath(string longName){
+
+ string path = "";
+
+ size_t found;
+ found=longName.find_last_of("/\\");
+
+ if(found != longName.npos){
+ path = longName.substr(0, found+1);
+ }
+
+ return path;
+}
+
+/***********************************************************************/
+
+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 bool isBlank(string fileName){
+
+ ifstream fileHandle;
+ fileHandle.open(fileName.c_str());
+ if(!fileHandle) {
+ cout << "Error: Could not open " << fileName << endl;
+ return false;
+ }else {
+ //check for blank file
+ gobble(fileHandle);
+ if (fileHandle.eof()) { fileHandle.close(); return true; }
+ }
+ return false;
+}
+/***********************************************************************/
+
+inline string getFullPathName(string fileName){
+ try{
+
+ string path = hasPath(fileName);
+ string newFileName;
+ int pos;
+
+ if (path == "") { return fileName; } //its a simple name
+ else { //we need to complete the pathname
+ // ex. ../../../filename
+ // cwd = /user/work/desktop
+
+ string cwd;
+ //get current working directory
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if (path.rfind("./") == -1) { return fileName; } //already complete name
+ else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
+
+ char* cwdpath = new char[1024];
+
+ size_t size;
+ cwdpath=getcwd(cwdpath,size);
+
+ cwd = cwdpath;
+
+ //rip off first '/'
+ string simpleCWD;
+ if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
+
+ //break apart the current working directory
+ vector<string> dirs;
+ while (simpleCWD.find_first_of('/') != -1) {
+ string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
+ simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
+ dirs.push_back(dir);
+ }
+ //get last one // ex. ../../../filename = /user/work/desktop/filename
+ dirs.push_back(simpleCWD); //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
+
+
+ int index = dirs.size()-1;
+
+ while((pos = path.rfind("./")) != -1) { //while you don't have a complete path
+ if (pos == 0) { break; //you are at the end
+ }else if (path[(pos-1)] == '.') { //you want your parent directory ../
+ path = path.substr(0, pos-1);
+ index--;
+ if (index == 0) { break; }
+ }else if (path[(pos-1)] == '/') { //you want the current working dir ./
+ path = path.substr(0, pos);
+ }else if (pos == 1) { break; //you are at the end
+ }else { cout << "cannot resolve path for " << fileName << endl; return fileName; }
+ }
+
+ for (int i = index; i >= 0; i--) {
+ newFileName = dirs[i] + "/" + newFileName;
+ }
+
+ newFileName = "/" + newFileName;
+ return newFileName;
+
+ #else
+ if (path.rfind(".\\") == -1) { return fileName; } //already complete name
+ else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
+
+ char *cwdpath = NULL;
+ cwdpath = getcwd(NULL, 0); // or _getcwd
+ if ( cwdpath != NULL) { cwd = cwdpath; }
+ else { cwd = ""; }
+
+ //break apart the current working directory
+ vector<string> dirs;
+ while (cwd.find_first_of('\\') != -1) {
+ string dir = cwd.substr(0,cwd.find_first_of('\\'));
+ cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
+ dirs.push_back(dir);
+
+ }
+ //get last one
+ dirs.push_back(cwd); //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
+
+ int index = dirs.size()-1;
+
+ while((pos = path.rfind(".\\")) != -1) { //while you don't have a complete path
+ if (pos == 0) { break; //you are at the end
+ }else if (path[(pos-1)] == '.') { //you want your parent directory ../
+ path = path.substr(0, pos-1);
+ index--;
+ if (index == 0) { break; }
+ }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
+ path = path.substr(0, pos);
+ }else if (pos == 1) { break; //you are at the end
+ }else { cout << "cannot resolve path for " << fileName << endl; return fileName; }
+ }
+
+ for (int i = index; i >= 0; i--) {
+ newFileName = dirs[i] + "\\" + newFileName;
+ }
+
+ return newFileName;
+
+ #endif
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function getFullPathName. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+inline int openInputFile(string fileName, ifstream& fileHandle, string m){
+
+ //get full path name
+ string completeFileName = getFullPathName(fileName);
+
+ fileHandle.open(completeFileName.c_str());
+ if(!fileHandle) {
+ return 1;
+ }else {
+ //check for blank file
+ gobble(fileHandle);
+ return 0;
+ }
+}
+/***********************************************************************/
+
+inline int openInputFile(string fileName, ifstream& fileHandle){
+
+ //get full path name
+ string completeFileName = getFullPathName(fileName);
+
+ fileHandle.open(completeFileName.c_str());
+ if(!fileHandle) {
+ cout << "Error: Could not open " << completeFileName << endl;
+ return 1;
+ }
+ else {
+ //check for blank file
+ gobble(fileHandle);
+ if (fileHandle.eof()) { cout << completeFileName << " is blank. Please correct." << endl; return 1; }
+
+ return 0;
+ }
+
+}
+/***********************************************************************/
+
+inline int renameFile(string oldName, string newName){
+
+ ifstream inTest;
+ int exist = openInputFile(newName, inTest, "");
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if (exist == 0) { //you could open it so you want to delete it
+ inTest.close();
+ string command = "rm " + newName;
+ system(command.c_str());
+ }
+
+ string command = "mv " + oldName + " " + newName;
+ system(command.c_str());
+#else
+ remove(newName.c_str());
+ int renameOk = rename(oldName.c_str(), newName.c_str());
+#endif
+ return 0;
+}
+
+/***********************************************************************/
+
+inline int openOutputFile(string fileName, ofstream& fileHandle){
+
+ string completeFileName = getFullPathName(fileName);
+
+ fileHandle.open(completeFileName.c_str(), ios::trunc);
+ if(!fileHandle) {
+ cout << "Error: Could not open " << completeFileName << endl;
+ 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;
+
+}
+/***********************************************************************/
+
+inline bool inVector(string member, vector<string> group){
+
+ for (int i = 0; i < group.size(); i++) {
+ if (group[i] == member) { return true; }
+ }
+
+ return false;
+}
+/***********************************************************************/
+
+//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) {
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtDash. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
+ 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) {
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtDash. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
+ 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) {
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtDash. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
+ 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) {
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtComma. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
+ 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) {
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtComma. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
+ 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) {
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtEquals. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
+ 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) {
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function inUsersGroups. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+//returns true if any of the strings in first vector are in second vector
+inline bool inUsersGroups(vector<string> groupnames, vector<string> Groups) {
+ try {
+
+ for (int i = 0; i < groupnames.size(); i++) {
+ if (inUsersGroups(groupnames[i], Groups)) { return true; }
+ }
+ return false;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function inUsersGroups. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+//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 == "") { cout << *it << " is not a valid label." << endl; }
+ 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 == "") { cout << "Your file does not include the label unique." << endl; }
+ userLabels.erase("unique");
+ }
+ else {
+ if (errorOff == "") { cout << "Your file does not include the label " << endl; }
+ 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 == "") {cout << s << ". I will use the next smallest distance. " << endl; }
+ }
+ //since they are sorted once you find a bigger one stop looking
+ }else { break; }
+ }
+
+ return smaller;
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function anyLabelsToProcess. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+inline void appendFiles(string temp, string filename) {
+ try{
+ ofstream output;
+ ifstream input;
+
+ //open output file in append mode
+ openOutputFileAppend(filename, output);
+ int ableToOpen = openInputFile(temp, input, "no error");
+
+ if (ableToOpen == 0) { //you opened it
+ while(char c = input.get()){
+ if(input.eof()) { break; }
+ else { output << c; }
+ }
+ input.close();
+ }
+
+ output.close();
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function appendFiles. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+inline string sortFile(string distFile, string outputDir){
+ try {
+
+ //if (outputDir == "") { outputDir += hasPath(distFile); }
+ string outfile = getRootName(distFile) + "sorted.dist";
+
+
+ //if you can, use the unix sort since its been optimized for years
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ string command = "sort -n -k +3 " + distFile + " -o " + outfile;
+ system(command.c_str());
+ #else //you are stuck with my best attempt...
+ //windows sort does not have a way to specify a column, only a character in the line
+ //since we cannot assume that the distance will always be at the the same character location on each line
+ //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back.
+
+ //read in file line by file and put distance first
+ string tempDistFile = distFile + ".temp";
+ ifstream input;
+ ofstream output;
+ openInputFile(distFile, input);
+ openOutputFile(tempDistFile, output);
+
+ string firstName, secondName;
+ float dist;
+ while (input) {
+ input >> firstName >> secondName >> dist;
+ output << dist << '\t' << firstName << '\t' << secondName << endl;
+ gobble(input);
+ }
+ input.close();
+ output.close();
+
+
+ //sort using windows sort
+ string tempOutfile = outfile + ".temp";
+ string command = "sort " + tempDistFile + " /O " + tempOutfile;
+ system(command.c_str());
+
+ //read in sorted file and put distance at end again
+ ifstream input2;
+ openInputFile(tempOutfile, input2);
+ openOutputFile(outfile, output);
+
+ while (input2) {
+ input2 >> dist >> firstName >> secondName;
+ output << firstName << '\t' << secondName << '\t' << dist << endl;
+ gobble(input2);
+ }
+ input2.close();
+ output.close();
+
+ //remove temp files
+ remove(tempDistFile.c_str());
+ remove(tempOutfile.c_str());
+ #endif
+
+ return outfile;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function sortfile. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+inline vector<long> setFilePosFasta(string filename, int& num) {
+
+ vector<long> positions;
+ ifstream inFASTA;
+ openInputFile(filename, inFASTA);
+
+ string input;
+ while(!inFASTA.eof()){
+ input = getline(inFASTA); gobble(inFASTA);
+ if (input.length() != 0) {
+ if(input[0] == '>'){ long pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
+ }
+ }
+ inFASTA.close();
+
+ num = positions.size();
+
+ /*FILE * pFile;
+ long size;
+
+ //get num bytes in file
+ pFile = fopen (filename.c_str(),"rb");
+ if (pFile==NULL) perror ("Error opening file");
+ else{
+ fseek (pFile, 0, SEEK_END);
+ size=ftell (pFile);
+ fclose (pFile);
+ }*/
+
+ long size = positions[(positions.size()-1)];
+ ifstream in;
+ openInputFile(filename, in);
+
+ in.seekg(size);
+
+ while(char c = in.get()){
+ if(in.eof()) { break; }
+ else { size++; }
+ }
+ in.close();
+
+ positions.push_back(size);
+
+ return positions;
+}
+/**************************************************************************************************/
+inline vector<long> setFilePosEachLine(string filename, int& num) {
+
+ vector<long> positions;
+ ifstream in;
+ openInputFile(filename, in);
+
+ string input;
+ while(!in.eof()){
+ long lastpos = in.tellg();
+ input = getline(in); gobble(in);
+ if (input.length() != 0) {
+ long pos = in.tellg();
+ if (pos != -1) { positions.push_back(pos - input.length() - 1); }
+ else { positions.push_back(lastpos); }
+ }
+ }
+ in.close();
+
+ num = positions.size();
+
+ FILE * pFile;
+ long size;
+
+ //get num bytes in file
+ pFile = fopen (filename.c_str(),"rb");
+ if (pFile==NULL) perror ("Error opening file");
+ else{
+ fseek (pFile, 0, SEEK_END);
+ size=ftell (pFile);
+ fclose (pFile);
+ }
+
+ positions.push_back(size);
+
+ return positions;
+}
+
+/**************************************************************************************************/
#endif
projects / mothur.git / blobdiff