-/***********************************************************************/
-
-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) {