+int MothurOut::renameFile(string oldName, string newName){
+ try {
+
+ if (oldName == newName) { return 0; }
+
+ ifstream inTest;
+ int exist = openInputFile(newName, inTest, "");
+ inTest.close();
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ if (exist == 0) { //you could open it so you want to delete it
+ string command = "rm " + newName;
+ system(command.c_str());
+ }
+
+ string command = "mv " + oldName + " " + newName;
+ system(command.c_str());
+ #else
+ mothurRemove(newName);
+ int renameOk = rename(oldName.c_str(), newName.c_str());
+ #endif
+ return 0;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "renameFile");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
+ try {
+
+ string completeFileName = getFullPathName(fileName);
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#ifdef USE_COMPRESSION
+ // check for gzipped file
+ if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
+ string tempName = string(tmpnam(0));
+ mkfifo(tempName.c_str(), 0666);
+ cerr << "Compressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
+ int fork_result = fork();
+ if (fork_result < 0) {
+ cerr << "Error forking.\n";
+ exit(1);
+ } else if (fork_result == 0) {
+ string command = string(endsWith(completeFileName, ".gz") ? "gzip" : "bzip2") + " -v > " + completeFileName + string(" < ") + tempName;
+ system(command.c_str());
+ exit(0);
+ } else {
+ completeFileName = tempName;
+ }
+ }
+#endif
+#endif
+ fileHandle.open(completeFileName.c_str(), ios::trunc);
+ if(!fileHandle) {
+ mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
+ return 1;
+ }
+ else {
+ return 0;
+ }
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "openOutputFile");
+ exit(1);
+ }
+
+}
+
+/**************************************************************************************************/
+int MothurOut::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");
+ //int ableToOpen = openInputFile(temp, input);
+
+ int numLines = 0;
+ if (ableToOpen == 0) { //you opened it
+
+ char buffer[4096];
+ while (!input.eof()) {
+ input.read(buffer, 4096);
+ output.write(buffer, input.gcount());
+ //count number of lines
+ for (int i = 0; i < input.gcount(); i++) { if (buffer[i] == '\n') {numLines++;} }
+ }
+ input.close();
+ }
+
+ output.close();
+
+ return numLines;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "appendFiles");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+string MothurOut::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) || (__linux__) || (__unix__) || (__unix)
+ 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.eof()) {
+ 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;
+ ofstream output2;
+ openInputFile(tempOutfile, input2);
+ openOutputFile(outfile, output2);
+
+ while (!input2.eof()) {
+ input2 >> dist >> firstName >> secondName;
+ output2 << firstName << '\t' << secondName << '\t' << dist << endl;
+ gobble(input2);
+ }
+ input2.close();
+ output2.close();
+
+ //remove temp files
+ mothurRemove(tempDistFile);
+ mothurRemove(tempOutfile);
+ #endif
+
+ return outfile;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "sortFile");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num) {
+ try {
+ vector<unsigned long long> positions;
+ ifstream inFASTA;
+ //openInputFile(filename, inFASTA);
+ inFASTA.open(filename.c_str(), ios::binary);
+
+ string input;
+ unsigned long long count = 0;
+ while(!inFASTA.eof()){
+ //input = getline(inFASTA);
+ //cout << input << '\t' << inFASTA.tellg() << endl;
+ //if (input.length() != 0) {
+ // if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); cout << (pos - input.length() - 1) << endl; }
+ //}
+ //gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
+ char c = inFASTA.get(); count++;
+ if (c == '>') {
+ positions.push_back(count-1);
+ //cout << count << endl;
+ }
+ }
+ 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);
+ }*/
+
+ unsigned long long size = positions[(positions.size()-1)];
+ ifstream in;
+ openInputFile(filename, in);
+
+ in.seekg(size);
+
+ while(in.get()){
+ if(in.eof()) { break; }
+ else { size++; }
+ }
+ in.close();
+
+ positions.push_back(size);
+ positions[0] = 0;
+
+ return positions;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "setFilePosFasta");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+vector<unsigned long long> MothurOut::setFilePosEachLine(string filename, int& num) {
+ try {
+ filename = getFullPathName(filename);
+
+ vector<unsigned long long> positions;
+ ifstream in;
+ //openInputFile(filename, in);
+ in.open(filename.c_str(), ios::binary);
+
+ string input;
+ unsigned long long count = 0;
+ positions.push_back(0);
+
+ while(!in.eof()){
+ //getline counting reads
+ char d = in.get(); count++;
+ while ((d != '\n') && (d != '\r') && (d != '\f') && (d != in.eof())) {
+ //get next character
+ d = in.get();
+ count++;
+ }
+
+ if (!in.eof()) {
+ d=in.get(); count++;
+ while(isspace(d) && (d != in.eof())) { d=in.get(); count++;}
+ }
+ positions.push_back(count-1);
+ //cout << count-1 << endl;
+ }
+ in.close();
+
+ num = positions.size()-1;
+
+ FILE * pFile;
+ unsigned long 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[(positions.size()-1)] = size;
+
+ return positions;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "setFilePosEachLine");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
+ try{
+ vector<unsigned long long> filePos;
+ filePos.push_back(0);
+
+ FILE * pFile;
+ unsigned long long size;
+
+ filename = getFullPathName(filename);
+
+ //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);
+ }
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
+ //estimate file breaks
+ unsigned long long chunkSize = 0;
+ chunkSize = size / proc;
+
+ //file to small to divide by processors
+ if (chunkSize == 0) { proc = 1; filePos.push_back(size); return filePos; }
+
+ //for each process seekg to closest file break and search for next '>' char. make that the filebreak
+ for (int i = 0; i < proc; i++) {
+ unsigned long long spot = (i+1) * chunkSize;
+
+ ifstream in;
+ openInputFile(filename, in);
+ in.seekg(spot);
+
+ //look for next '>'
+ unsigned long long newSpot = spot;
+ while (!in.eof()) {
+ char c = in.get();
+
+ if (c == '>') { in.putback(c); newSpot = in.tellg(); break; }
+ else if (int(c) == -1) { break; }
+
+ }
+
+ //there was not another sequence before the end of the file
+ unsigned long long sanityPos = in.tellg();
+
+ if (sanityPos == -1) { break; }
+ else { filePos.push_back(newSpot); }
+
+ in.close();
+ }
+
+ //save end pos
+ filePos.push_back(size);
+
+ //sanity check filePos
+ for (int i = 0; i < (filePos.size()-1); i++) {
+ if (filePos[(i+1)] <= filePos[i]) { filePos.erase(filePos.begin()+(i+1)); i--; }
+ }
+
+ proc = (filePos.size() - 1);
+#else
+ mothurOut("[ERROR]: Windows version should not be calling the divideFile function."); mothurOutEndLine();
+ proc=1;
+ filePos.push_back(size);
+#endif
+ return filePos;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "divideFile");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+vector<unsigned long long> MothurOut::divideFilePerLine(string filename, int& proc) {
+ try{
+ vector<unsigned long long> filePos;
+ filePos.push_back(0);
+
+ FILE * pFile;
+ unsigned long long size;
+
+ filename = getFullPathName(filename);
+
+ //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);
+ }
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
+ //estimate file breaks
+ unsigned long long chunkSize = 0;
+ chunkSize = size / proc;
+
+ //file to small to divide by processors
+ if (chunkSize == 0) { proc = 1; filePos.push_back(size); return filePos; }
+
+ //for each process seekg to closest file break and search for next '>' char. make that the filebreak
+ for (int i = 0; i < proc; i++) {
+ unsigned long long spot = (i+1) * chunkSize;
+
+ ifstream in;
+ openInputFile(filename, in);
+ in.seekg(spot);
+
+ //look for next line break
+ unsigned long long newSpot = spot;
+ while (!in.eof()) {
+ char c = in.get();
+
+ if ((c == '\n') || (c == '\r') || (c == '\f')) { gobble(in); newSpot = in.tellg(); break; }
+ else if (int(c) == -1) { break; }
+ }
+
+ //there was not another line before the end of the file
+ unsigned long long sanityPos = in.tellg();
+
+ if (sanityPos == -1) { break; }
+ else { filePos.push_back(newSpot); }
+
+ in.close();
+ }
+
+ //save end pos
+ filePos.push_back(size);
+
+ //sanity check filePos
+ for (int i = 0; i < (filePos.size()-1); i++) {
+ if (filePos[(i+1)] <= filePos[i]) { filePos.erase(filePos.begin()+(i+1)); i--; }
+ }
+
+ proc = (filePos.size() - 1);
+#else
+ mothurOut("[ERROR]: Windows version should not be calling the divideFile function."); mothurOutEndLine();
+ proc=1;
+ filePos.push_back(size);
+#endif
+ return filePos;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "divideFile");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int MothurOut::divideFile(string filename, int& proc, vector<string>& files) {
+ try{
+
+ vector<unsigned long long> filePos = divideFile(filename, proc);
+
+ for (int i = 0; i < (filePos.size()-1); i++) {
+
+ //read file chunk
+ ifstream in;
+ openInputFile(filename, in);
+ in.seekg(filePos[i]);
+ unsigned long long size = filePos[(i+1)] - filePos[i];
+ char* chunk = new char[size];
+ in.read(chunk, size);
+ in.close();
+
+ //open new file
+ string fileChunkName = filename + "." + toString(i) + ".tmp";
+ ofstream out;
+ openOutputFile(fileChunkName, out);
+
+ out << chunk << endl;
+ out.close();
+ delete[] chunk;
+
+ //save name
+ files.push_back(fileChunkName);
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "divideFile");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+bool MothurOut::isTrue(string f){
+ try {
+
+ for (int i = 0; i < f.length(); i++) { f[i] = toupper(f[i]); }
+
+ if ((f == "TRUE") || (f == "T")) { return true; }
+ else { return false; }
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "isTrue");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+float MothurOut::roundDist(float dist, int precision){
+ try {
+ return int(dist * precision + 0.5)/float(precision);
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "roundDist");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+float MothurOut::ceilDist(float dist, int precision){
+ try {
+ return int(ceil(dist * precision))/float(precision);
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "ceilDist");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+vector<string> MothurOut::splitWhiteSpace(string& rest, char buffer[], int size){
+ try {
+ vector<string> pieces;
+
+ for (int i = 0; i < size; i++) {
+ if (!isspace(buffer[i])) { rest += buffer[i]; }
+ else {
+ if (rest != "") { pieces.push_back(rest); rest = ""; }
+ while (i < size) { //gobble white space
+ if (isspace(buffer[i])) { i++; }
+ else { rest = buffer[i]; break; } //cout << "next piece buffer = " << nextPiece << endl;
+ }
+ }
+ }
+
+ return pieces;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "splitWhiteSpace");
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<string> MothurOut::splitWhiteSpace(string input){
+ try {
+ vector<string> pieces;
+ string rest = "";
+
+ for (int i = 0; i < input.length(); i++) {
+ if (!isspace(input[i])) { rest += input[i]; }
+ else {
+ if (rest != "") { pieces.push_back(rest); rest = ""; }
+ while (i < input.length()) { //gobble white space
+ if (isspace(input[i])) { i++; }
+ else { rest = input[i]; break; } //cout << "next piece buffer = " << nextPiece << endl;
+ }
+ }
+ }
+
+ if (rest != "") { pieces.push_back(rest); }
+
+ return pieces;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "splitWhiteSpace");
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<string> MothurOut::splitWhiteSpaceWithQuotes(string input){
+ try {
+ vector<string> pieces;
+ string rest = "";
+
+ int pos = input.find('\'');
+ int pos2 = input.find('\"');
+
+ if ((pos == string::npos) && (pos2 == string::npos)) { return splitWhiteSpace(input); } //no quotes to worry about
+ else {
+ for (int i = 0; i < input.length(); i++) {
+ if ((input[i] == '\'') || (input[i] == '\"') || (rest == "\'") || (rest == "\"")) { //grab everything til end or next ' or "
+ rest += input[i];
+ for (int j = i+1; j < input.length(); j++) {
+ if ((input[j] == '\'') || (input[j] == '\"')) { //then quit
+ rest += input[j];
+ i = j+1;
+ j+=input.length();
+ }else { rest += input[j]; }
+ }
+ }else if (!isspace(input[i])) { rest += input[i]; }
+ else {
+ if (rest != "") { pieces.push_back(rest); rest = ""; }
+ while (i < input.length()) { //gobble white space
+ if (isspace(input[i])) { i++; }
+ else { rest = input[i]; break; } //cout << "next piece buffer = " << nextPiece << endl;
+ }
+ }
+ }
+
+ if (rest != "") { pieces.push_back(rest); }
+ }
+ return pieces;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "splitWhiteSpace");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int MothurOut::readTax(string namefile, map<string, string>& taxMap) {
+ try {
+ //open input file
+ ifstream in;
+ openInputFile(namefile, in);
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ checkName(firstCol);
+ //are there confidence scores, if so remove them
+ if (secondCol.find_first_of('(') != -1) { removeConfidences(secondCol); }
+ map<string, string>::iterator itTax = taxMap.find(firstCol);
+
+ if(itTax == taxMap.end()) {
+ bool ignore = false;
+ if (secondCol != "") { if (secondCol[secondCol.length()-1] != ';') { mothurOut("[ERROR]: " + firstCol + " is missing the final ';', ignoring.\n"); ignore=true; }
+ }
+ if (!ignore) { taxMap[firstCol] = secondCol; }
+ if (debug) { mothurOut("[DEBUG]: name = '" + firstCol + "' tax = '" + secondCol + "'\n"); }
+ }else {
+ mothurOut("[ERROR]: " + firstCol + " is already in your taxonomy file, names must be unique./n"); control_pressed = true;
+ }
+ pairDone = false;
+ }
+ }
+ }
+ in.close();
+
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ checkName(firstCol);
+ //are there confidence scores, if so remove them
+ if (secondCol.find_first_of('(') != -1) { removeConfidences(secondCol); }
+ map<string, string>::iterator itTax = taxMap.find(firstCol);
+
+ if(itTax == taxMap.end()) {
+ bool ignore = false;
+ if (secondCol != "") { if (secondCol[secondCol.length()-1] != ';') { mothurOut("[ERROR]: " + firstCol + " is missing the final ';', ignoring.\n"); ignore=true; }
+ }
+ if (!ignore) { taxMap[firstCol] = secondCol; }
+ if (debug) { mothurOut("[DEBUG]: name = '" + firstCol + "' tax = '" + secondCol + "'\n"); }
+ }else {
+ mothurOut("[ERROR]: " + firstCol + " is already in your taxonomy file, names must be unique./n"); control_pressed = true;
+ }
+
+ pairDone = false;
+ }
+ }
+ }
+
+ return taxMap.size();
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readTax");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, map<string, string>& nameMap, bool redund) {
+ try {
+ //open input file
+ ifstream in;
+ openInputFile(namefile, in);
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ checkName(firstCol);
+ checkName(secondCol);
+
+ //parse names into vector
+ vector<string> theseNames;
+ splitAtComma(secondCol, theseNames);
+ for (int i = 0; i < theseNames.size(); i++) { nameMap[theseNames[i]] = firstCol; }
+ pairDone = false;
+ }
+ }
+ }
+ in.close();
+
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ checkName(firstCol);
+ checkName(secondCol);
+
+ //parse names into vector
+ vector<string> theseNames;
+ splitAtComma(secondCol, theseNames);
+ for (int i = 0; i < theseNames.size(); i++) { nameMap[theseNames[i]] = firstCol; }
+ pairDone = false;
+ }
+ }
+ }
+
+ return nameMap.size();
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, map<string, string>& nameMap, int flip) {
+ try {
+ //open input file
+ ifstream in;
+ openInputFile(namefile, in);
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ checkName(firstCol);
+ checkName(secondCol);
+ nameMap[secondCol] = firstCol;
+ pairDone = false;
+ }
+ }
+ }
+ in.close();
+
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ checkName(firstCol);
+ checkName(secondCol);
+ nameMap[secondCol] = firstCol;
+ pairDone = false;
+ }
+ }
+ }
+
+ return nameMap.size();
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, map<string, string>& nameMap, map<string, int>& nameCount) {
+ try {
+ nameMap.clear(); nameCount.clear();
+ //open input file
+ ifstream in;
+ openInputFile(namefile, in);
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ checkName(firstCol);
+ checkName(secondCol);
+ //parse names into vector
+ vector<string> theseNames;
+ splitAtComma(secondCol, theseNames);
+ for (int i = 0; i < theseNames.size(); i++) { nameMap[theseNames[i]] = firstCol; }
+ nameCount[firstCol] = theseNames.size();
+ pairDone = false;
+ }
+ }
+ }
+ in.close();
+
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ checkName(firstCol);
+ checkName(secondCol);
+ //parse names into vector
+ vector<string> theseNames;
+ splitAtComma(secondCol, theseNames);
+ for (int i = 0; i < theseNames.size(); i++) { nameMap[theseNames[i]] = firstCol; }
+ nameCount[firstCol] = theseNames.size();
+ pairDone = false;
+ }
+ }
+
+ }
+ return nameMap.size();
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, map<string, string>& nameMap) {
+ try {
+ //open input file
+ ifstream in;
+ openInputFile(namefile, in);
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ checkName(firstCol);
+ checkName(secondCol);
+ nameMap[firstCol] = secondCol; pairDone = false; }
+ }
+ }
+ in.close();
+
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ checkName(firstCol);
+ checkName(secondCol);
+ nameMap[firstCol] = secondCol; pairDone = false; }
+ }
+ }
+
+ return nameMap.size();
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, map<string, vector<string> >& nameMap) {
+ try {
+ //open input file
+ ifstream in;
+ openInputFile(namefile, in);
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ checkName(firstCol);
+ checkName(secondCol);
+ vector<string> temp;
+ splitAtComma(secondCol, temp);
+ nameMap[firstCol] = temp;
+ pairDone = false;
+ }
+ }
+ }
+ in.close();
+
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ checkName(firstCol);
+ checkName(secondCol);
+ vector<string> temp;
+ splitAtComma(secondCol, temp);
+ nameMap[firstCol] = temp;
+ pairDone = false;
+ }
+ }
+ }
+
+ return nameMap.size();
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+map<string, int> MothurOut::readNames(string namefile) {
+ try {
+ map<string, int> nameMap;
+
+ //open input file
+ ifstream in;
+ openInputFile(namefile, in);
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ checkName(firstCol);
+ checkName(secondCol);
+ int num = getNumNames(secondCol);
+ nameMap[firstCol] = num;
+ pairDone = false;
+ }
+ }
+ }
+ in.close();
+
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ checkName(firstCol);
+ checkName(secondCol);
+ int num = getNumNames(secondCol);
+ nameMap[firstCol] = num;
+ pairDone = false;
+ }
+ }
+ }
+
+ return nameMap;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+map<string, int> MothurOut::readNames(string namefile, unsigned long int& numSeqs) {
+ try {
+ map<string, int> nameMap;
+ numSeqs = 0;
+
+ //open input file
+ ifstream in;
+ openInputFile(namefile, in);
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ checkName(firstCol);
+ checkName(secondCol);
+ int num = getNumNames(secondCol);
+ nameMap[firstCol] = num;
+ pairDone = false;
+ numSeqs += num;
+ }
+ }
+ }
+ in.close();
+
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ checkName(firstCol);
+ checkName(secondCol);
+ int num = getNumNames(secondCol);
+ nameMap[firstCol] = num;
+ pairDone = false;
+ numSeqs += num;
+ }
+ }
+ }
+
+ return nameMap;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ exit(1);
+ }
+}
+/************************************************************/
+int MothurOut::checkName(string& name) {
+ try {
+ for (int i = 0; i < name.length(); i++) {
+ if (name[i] == ':') { name[i] = '_'; changedSeqNames = true; }
+ }
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "checkName");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, vector<seqPriorityNode>& nameVector, map<string, string>& fastamap) {
+ try {
+ int error = 0;
+
+ //open input file
+ ifstream in;
+ openInputFile(namefile, in);
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ checkName(firstCol);
+ checkName(secondCol);
+ int num = getNumNames(secondCol);
+
+ map<string, string>::iterator it = fastamap.find(firstCol);
+ if (it == fastamap.end()) {
+ error = 1;
+ mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
+ }else {
+ seqPriorityNode temp(num, it->second, firstCol);
+ nameVector.push_back(temp);
+ }
+
+ pairDone = false;
+ }
+ }
+ }
+ in.close();
+
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ checkName(firstCol);
+ checkName(secondCol);
+ int num = getNumNames(secondCol);
+
+ map<string, string>::iterator it = fastamap.find(firstCol);
+ if (it == fastamap.end()) {
+ error = 1;
+ mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
+ }else {
+ seqPriorityNode temp(num, it->second, firstCol);
+ nameVector.push_back(temp);
+ }
+
+ pairDone = false;
+ }
+ }
+ }
+ return error;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readNames");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+set<string> MothurOut::readAccnos(string accnosfile){
+ try {
+ set<string> names;
+ ifstream in;
+ openInputFile(accnosfile, in);
+ string name;
+
+ string rest = "";
+ char buffer[4096];
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) { checkName(pieces[i]); names.insert(pieces[i]); }
+ }
+ in.close();
+
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+ for (int i = 0; i < pieces.size(); i++) { checkName(pieces[i]); names.insert(pieces[i]); }
+ }
+ return names;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readAccnos");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int MothurOut::readAccnos(string accnosfile, vector<string>& names){
+ try {
+ names.clear();
+ ifstream in;
+ openInputFile(accnosfile, in);
+ string name;
+
+ string rest = "";
+ char buffer[4096];
+
+ while (!in.eof()) {
+ if (control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+
+ for (int i = 0; i < pieces.size(); i++) { checkName(pieces[i]); names.push_back(pieces[i]); }
+ }
+ in.close();
+
+ if (rest != "") {
+ vector<string> pieces = splitWhiteSpace(rest);
+ for (int i = 0; i < pieces.size(); i++) { checkName(pieces[i]); names.push_back(pieces[i]); }
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "readAccnos");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+int MothurOut::getNumNames(string names){
+ try {
+ int count = 0;
+
+ if(names != ""){
+ count = 1;
+ for(int i=0;i<names.size();i++){
+ if(names[i] == ','){
+ count++;
+ }
+ }
+ }
+
+ return count;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "getNumNames");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+int MothurOut::getNumChar(string line, char c){
+ try {
+ int count = 0;
+
+ if(line != ""){
+ for(int i=0;i<line.size();i++){
+ if(line[i] == c){
+ count++;
+ }
+ }
+ }
+
+ return count;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "getNumChar");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+bool MothurOut::isSubset(vector<string> bigset, vector<string> subset) {
+ try {
+
+
+ if (subset.size() > bigset.size()) { return false; }
+
+ //check if each guy in suset is also in bigset
+ for (int i = 0; i < subset.size(); i++) {
+ bool match = false;
+ for (int j = 0; j < bigset.size(); j++) {
+ if (subset[i] == bigset[j]) { match = true; break; }
+ }
+
+ //you have a guy in subset that had no match in bigset
+ if (match == false) { return false; }
+ }
+
+ return true;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "isSubset");
+ exit(1);
+ }
+}
+/***********************************************************************/
+int MothurOut::mothurRemove(string filename){
+ try {
+ filename = getFullPathName(filename);
+ int error = remove(filename.c_str());
+ //if (error != 0) {
+ // if (errno != ENOENT) { //ENOENT == file does not exist
+ // string message = "Error deleting file " + filename;
+ // perror(message.c_str());
+ // }
+ //}
+ return error;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "mothurRemove");
+ exit(1);
+ }
+}
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, int& num){
+ try {
+ bool error = false;
+
+ if (isNumeric1(item)) {
+ convert(item, num);
+ }else {
+ num = 0;
+ error = true;
+ mothurOut("[ERROR]: cannot convert " + item + " to an integer."); mothurOutEndLine();
+ commandInputsConvertError = true;
+ }
+
+ return error;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "mothurConvert");
+ exit(1);
+ }
+}
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, intDist& num){
+ try {
+ bool error = false;
+
+ if (isNumeric1(item)) {
+ convert(item, num);
+ }else {
+ num = 0;
+ error = true;
+ mothurOut("[ERROR]: cannot convert " + item + " to an integer."); mothurOutEndLine();
+ commandInputsConvertError = true;
+ }
+
+ return error;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "mothurConvert");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+bool MothurOut::isNumeric1(string stringToCheck){
+ try {
+ bool numeric = false;
+
+ if(stringToCheck.find_first_not_of("0123456789.-") == string::npos) { numeric = true; }
+
+ return numeric;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "isNumeric1");
+ exit(1);
+ }
+
+}
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, float& num){
+ try {
+ bool error = false;
+
+ if (isNumeric1(item)) {
+ convert(item, num);
+ }else {
+ num = 0;
+ error = true;
+ mothurOut("[ERROR]: cannot convert " + item + " to a float."); mothurOutEndLine();
+ commandInputsConvertError = true;
+ }
+
+ return error;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "mothurConvert");
+ exit(1);
+ }
+}
+/***********************************************************************/
+bool MothurOut::mothurConvert(string item, double& num){
+ try {
+ bool error = false;
+
+ if (isNumeric1(item)) {
+ convert(item, num);
+ }else {
+ num = 0;
+ error = true;
+ mothurOut("[ERROR]: cannot convert " + item + " to a double."); mothurOutEndLine();
+ commandInputsConvertError = true;
+ }
+
+ return error;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "mothurConvert");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+vector<vector<double> > MothurOut::binomial(int maxOrder){
+ try {
+ 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;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "binomial");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+unsigned int MothurOut::fromBase36(string base36){
+ try {
+ unsigned int num = 0;
+
+ map<char, int> converts;
+ converts['A'] = 0;
+ converts['a'] = 0;
+ converts['B'] = 1;
+ converts['b'] = 1;
+ converts['C'] = 2;
+ converts['c'] = 2;
+ converts['D'] = 3;
+ converts['d'] = 3;
+ converts['E'] = 4;
+ converts['e'] = 4;
+ converts['F'] = 5;
+ converts['f'] = 5;
+ converts['G'] = 6;
+ converts['g'] = 6;
+ converts['H'] = 7;
+ converts['h'] = 7;
+ converts['I'] = 8;
+ converts['i'] = 8;
+ converts['J'] = 9;
+ converts['j'] = 9;
+ converts['K'] = 10;
+ converts['k'] = 10;
+ converts['L'] = 11;
+ converts['l'] = 11;
+ converts['M'] = 12;
+ converts['m'] = 12;
+ converts['N'] = 13;
+ converts['n'] = 13;
+ converts['O'] = 14;
+ converts['o'] = 14;
+ converts['P'] = 15;
+ converts['p'] = 15;
+ converts['Q'] = 16;
+ converts['q'] = 16;
+ converts['R'] = 17;
+ converts['r'] = 17;
+ converts['S'] = 18;
+ converts['s'] = 18;
+ converts['T'] = 19;
+ converts['t'] = 19;
+ converts['U'] = 20;
+ converts['u'] = 20;
+ converts['V'] = 21;
+ converts['v'] = 21;
+ converts['W'] = 22;
+ converts['w'] = 22;
+ converts['X'] = 23;
+ converts['x'] = 23;
+ converts['Y'] = 24;
+ converts['y'] = 24;
+ converts['Z'] = 25;
+ converts['z'] = 25;
+ converts['0'] = 26;
+ converts['1'] = 27;
+ converts['2'] = 28;
+ converts['3'] = 29;
+ converts['4'] = 30;
+ converts['5'] = 31;
+ converts['6'] = 32;
+ converts['7'] = 33;
+ converts['8'] = 34;
+ converts['9'] = 35;
+
+ int i = 0;
+ while (i < base36.length()) {
+ char c = base36[i];
+ num = 36 * num + converts[c];
+ i++;
+ }
+
+ return num;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "fromBase36");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+int MothurOut::factorial(int num){
+ try {
+ int total = 1;
+
+ for (int i = 1; i <= num; i++) {
+ total *= i;
+ }
+
+ return total;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "factorial");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+int MothurOut::getNumSeqs(ifstream& file){
+ try {
+ int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
+ file.seekg(0);
+ return numSeqs;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "getNumSeqs");
+ exit(1);
+ }
+}
+/***********************************************************************/
+void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
+ try {
+ string input;
+ numSeqs = 0;
+ while(!file.eof()){
+ input = getline(file);
+ if (input.length() != 0) {
+ if(input[0] == '>'){ numSeqs++; }
+ }
+ }
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "getNumSeqs");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+//This function parses the estimator options and puts them in a vector
+void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
+ try {
+
+ if (symbol == '-') { splitAtDash(estim, container); return; }
+
+ string individual = "";
+ int estimLength = estim.size();
+ for(int i=0;i<estimLength;i++){
+ if(estim[i] == symbol){
+ container.push_back(individual);
+ individual = "";
+ }
+ else{
+ individual += estim[i];
+ }
+ }
+ container.push_back(individual);
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "splitAtChar");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+//This function parses the estimator options and puts them in a vector
+void MothurOut::splitAtDash(string& estim, vector<string>& container) {
+ try {
+ string individual = "";
+ int estimLength = estim.size();
+ bool prevEscape = false;
+ /*for(int i=0;i<estimLength;i++){
+ if(prevEscape){
+ individual += estim[i];
+ prevEscape = false;
+ }
+ else{
+ if(estim[i] == '\\'){
+ prevEscape = true;
+ }
+ else if(estim[i] == '-'){
+ container.push_back(individual);
+ individual = "";
+ prevEscape = false;
+ }
+ else{
+ individual += estim[i];
+ prevEscape = false;
+ }
+ }
+ }*/
+
+
+ for(int i=0;i<estimLength;i++){
+ if(estim[i] == '-'){
+ if (prevEscape) { individual += estim[i]; prevEscape = false; } //add in dash because it was escaped.
+ else {
+ container.push_back(individual);
+ individual = "";
+ }
+ }else if(estim[i] == '\\'){
+ if (i < estimLength-1) {
+ if (estim[i+1] == '-') { prevEscape=true; } //are you a backslash before a dash, if yes ignore
+ else { individual += estim[i]; prevEscape = false; } //if no, add in
+ }else { individual += estim[i]; }
+ }else {
+ individual += estim[i];
+ }
+ }
+
+
+
+ container.push_back(individual);
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "splitAtDash");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+//This function parses the label options and puts them in a set
+void MothurOut::splitAtDash(string& estim, set<string>& container) {
+ try {
+ string individual = "";
+ int estimLength = estim.size();
+ bool prevEscape = false;
+ /*
+ for(int i=0;i<estimLength;i++){
+ if(prevEscape){
+ individual += estim[i];
+ prevEscape = false;
+ }
+ else{
+ if(estim[i] == '\\'){
+ prevEscape = true;
+ }
+ else if(estim[i] == '-'){
+ container.insert(individual);
+ individual = "";
+ prevEscape = false;
+ }
+ else{
+ individual += estim[i];
+ prevEscape = false;
+ }
+ }
+ }
+ */
+
+ for(int i=0;i<estimLength;i++){
+ if(estim[i] == '-'){
+ if (prevEscape) { individual += estim[i]; prevEscape = false; } //add in dash because it was escaped.
+ else {
+ container.insert(individual);
+ individual = "";
+ }
+ }else if(estim[i] == '\\'){
+ if (i < estimLength-1) {
+ if (estim[i+1] == '-') { prevEscape=true; } //are you a backslash before a dash, if yes ignore
+ else { individual += estim[i]; prevEscape = false; } //if no, add in
+ }else { individual += estim[i]; }
+ }else {
+ individual += estim[i];
+ }
+ }
+ container.insert(individual);
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "splitAtDash");
+ exit(1);
+ }
+}
+/***********************************************************************/
+//This function parses the line options and puts them in a set
+void MothurOut::splitAtDash(string& estim, set<int>& container) {
+ try {
+ string individual = "";
+ int lineNum;
+ int estimLength = estim.size();
+ bool prevEscape = false;
+ /*
+ for(int i=0;i<estimLength;i++){
+ if(prevEscape){
+ individual += estim[i];
+ prevEscape = false;
+ }
+ else{
+ if(estim[i] == '\\'){
+ prevEscape = true;
+ }
+ else if(estim[i] == '-'){
+ convert(individual, lineNum); //convert the string to int
+ container.insert(lineNum);
+ individual = "";
+ prevEscape = false;
+ }
+ else{
+ individual += estim[i];
+ prevEscape = false;
+ }
+ }
+ }*/
+
+ for(int i=0;i<estimLength;i++){
+ if(estim[i] == '-'){
+ if (prevEscape) { individual += estim[i]; prevEscape = false; } //add in dash because it was escaped.
+ else {
+ convert(individual, lineNum); //convert the string to int
+ container.insert(lineNum);
+ individual = "";
+ }
+ }else if(estim[i] == '\\'){
+ if (i < estimLength-1) {
+ if (estim[i+1] == '-') { prevEscape=true; } //are you a backslash before a dash, if yes ignore
+ else { individual += estim[i]; prevEscape = false; } //if no, add in
+ }else { individual += estim[i]; }
+ }else {
+ individual += estim[i];
+ }
+ }
+
+ convert(individual, lineNum); //convert the string to int
+ container.insert(lineNum);
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "splitAtDash");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+string MothurOut::makeList(vector<string>& names) {
+ try {
+ string list = "";
+
+ if (names.size() == 0) { return list; }
+
+ for (int i = 0; i < names.size()-1; i++) { list += names[i] + ","; }
+
+ //get last name
+ list += names[names.size()-1];
+
+ return list;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "makeList");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+//This function parses the a string and puts peices in a vector
+void MothurOut::splitAtComma(string& estim, vector<string>& container) {
+ try {
+ string individual = "";
+ int estimLength = estim.size();
+ for(int i=0;i<estimLength;i++){
+ if(estim[i] == ','){
+ container.push_back(individual);
+ individual = "";
+ }
+ else{
+ individual += estim[i];
+ }
+ }
+ container.push_back(individual);
+
+
+
+
+// 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, "MothurOut", "splitAtComma");
+ exit(1);
+ }
+}
+/***********************************************************************/
+//This function splits up the various option parameters
+void MothurOut::splitAtChar(string& prefix, string& suffix, char c){
+ try {
+ prefix = suffix.substr(0,suffix.find_first_of(c));
+ if ((suffix.find_first_of(c)+2) <= suffix.length()) { //checks to make sure you don't have comma at end of string
+ suffix = suffix.substr(suffix.find_first_of(c)+1, suffix.length());
+ string space = " ";
+ while(suffix.at(0) == ' ')
+ suffix = suffix.substr(1, suffix.length());
+ }else { suffix = ""; }
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "splitAtChar");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+//This function splits up the various option parameters
+void MothurOut::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());
+ }else { suffix = ""; }
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "splitAtComma");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+//This function separates the key value from the option value i.e. dist=96_...
+void MothurOut::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, "MothurOut", "splitAtEquals");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+bool MothurOut::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, "MothurOut", "inUsersGroups");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+bool MothurOut::inUsersGroups(vector<int> set, vector< vector<int> > sets) {
+ try {
+ for (int i = 0; i < sets.size(); i++) {
+ if (set == sets[i]) { return true; }
+ }
+ return false;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "inUsersGroups");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+bool MothurOut::inUsersGroups(int groupname, vector<int> Groups) {
+ try {
+ for (int i = 0; i < Groups.size(); i++) {
+ if (groupname == Groups[i]) { return true; }
+ }
+ return false;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "inUsersGroups");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+//returns true if any of the strings in first vector are in second vector
+bool MothurOut::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) {
+ errorOut(e, "MothurOut", "inUsersGroups");
+ 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.
+bool MothurOut::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 {
+ if (convertTestFloat(label, labelFloat)) {
+ convert(label, labelFloat);
+ }else { //cant convert
+ return false;
+ }
+ }
+
+ //go through users set and make them floats
+ for(it = userLabels.begin(); it != userLabels.end();) {
+
+ float temp;
+ if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
+ convert(*it, temp);
+ orderFloat.push_back(temp);
+ userMap[*it] = temp;
+ it++;
+ }else if (*it == "unique") {
+ orderFloat.push_back(-1.0);
+ userMap["unique"] = -1.0;
+ it++;
+ }else {
+ if (errorOff == "") { mothurOut(*it + " is not a valid label."); mothurOutEndLine(); }
+ userLabels.erase(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, "MothurOut", "anyLabelsToProcess");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
+ try {
+
+ bool good = true;
+
+ string line = getline(file);
+
+ //before we added this check
+ if (line[0] != '#') { good = false; }
+ else {
+ //rip off #
+ line = line.substr(1);
+
+ vector<string> versionVector;
+ splitAtChar(version, versionVector, '.');
+
+ //check file version
+ vector<string> linesVector;
+ splitAtChar(line, linesVector, '.');
+
+ if (versionVector.size() != linesVector.size()) { good = false; }
+ else {
+ for (int j = 0; j < versionVector.size(); j++) {
+ int num1, num2;
+ convert(versionVector[j], num1);
+ convert(linesVector[j], num2);
+
+ //if mothurs version is newer than this files version, then we want to remake it
+ if (num1 > num2) { good = false; break; }
+ }
+ }
+
+ }
+
+ if (!good) { file.close(); }
+ else { file.seekg(0); }
+
+ return good;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "checkReleaseVersion");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+vector<double> MothurOut::getAverages(vector< vector<double> >& dists) {
+ try{
+ vector<double> averages; //averages.resize(numComp, 0.0);
+ for (int i = 0; i < dists[0].size(); i++) { averages.push_back(0.0); }
+
+ for (int thisIter = 0; thisIter < dists.size(); thisIter++) {
+ for (int i = 0; i < dists[thisIter].size(); i++) {
+ averages[i] += dists[thisIter][i];
+ }
+ }
+
+ //finds average.
+ for (int i = 0; i < averages.size(); i++) { averages[i] /= (double) dists.size(); }
+
+ return averages;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "getAverages");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+vector<double> MothurOut::getStandardDeviation(vector< vector<double> >& dists) {
+ try{
+
+ vector<double> averages = getAverages(dists);
+
+ //find standard deviation
+ vector<double> stdDev; //stdDev.resize(numComp, 0.0);
+ for (int i = 0; i < dists[0].size(); i++) { stdDev.push_back(0.0); }
+
+ for (int thisIter = 0; thisIter < dists.size(); thisIter++) { //compute the difference of each dist from the mean, and square the result of each
+ for (int j = 0; j < dists[thisIter].size(); j++) {
+ stdDev[j] += ((dists[thisIter][j] - averages[j]) * (dists[thisIter][j] - averages[j]));
+ }
+ }
+ for (int i = 0; i < stdDev.size(); i++) {
+ stdDev[i] /= (double) dists.size();
+ stdDev[i] = sqrt(stdDev[i]);
+ }
+
+ return stdDev;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "getAverages");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+vector<double> MothurOut::getStandardDeviation(vector< vector<double> >& dists, vector<double>& averages) {
+ try{
+ //find standard deviation
+ vector<double> stdDev; //stdDev.resize(numComp, 0.0);
+ for (int i = 0; i < dists[0].size(); i++) { stdDev.push_back(0.0); }
+
+ for (int thisIter = 0; thisIter < dists.size(); thisIter++) { //compute the difference of each dist from the mean, and square the result of each
+ for (int j = 0; j < dists[thisIter].size(); j++) {
+ stdDev[j] += ((dists[thisIter][j] - averages[j]) * (dists[thisIter][j] - averages[j]));
+ }
+ }
+ for (int i = 0; i < stdDev.size(); i++) {
+ stdDev[i] /= (double) dists.size();
+ stdDev[i] = sqrt(stdDev[i]);
+ }
+
+ return stdDev;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "getAverages");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+vector< vector<seqDist> > MothurOut::getAverages(vector< vector< vector<seqDist> > >& calcDistsTotals, string mode) {
+ try{
+
+ vector< vector<seqDist> > calcAverages; //calcAverages.resize(calcDistsTotals[0].size());
+ for (int i = 0; i < calcDistsTotals[0].size(); i++) { //initialize sums to zero.
+ //calcAverages[i].resize(calcDistsTotals[0][i].size());
+ vector<seqDist> temp;
+ for (int j = 0; j < calcDistsTotals[0][i].size(); j++) {
+ seqDist tempDist;
+ tempDist.seq1 = calcDistsTotals[0][i][j].seq1;
+ tempDist.seq2 = calcDistsTotals[0][i][j].seq2;
+ tempDist.dist = 0.0;
+ temp.push_back(tempDist);
+ }
+ calcAverages.push_back(temp);
+ }
+
+ if (mode == "average") {
+ for (int thisIter = 0; thisIter < calcDistsTotals.size(); thisIter++) { //sum all groups dists for each calculator
+ for (int i = 0; i < calcAverages.size(); i++) { //initialize sums to zero.
+ for (int j = 0; j < calcAverages[i].size(); j++) {
+ calcAverages[i][j].dist += calcDistsTotals[thisIter][i][j].dist;
+ }
+ }
+ }
+
+ for (int i = 0; i < calcAverages.size(); i++) { //finds average.
+ for (int j = 0; j < calcAverages[i].size(); j++) {
+ calcAverages[i][j].dist /= (float) calcDistsTotals.size();
+ }
+ }
+ }else { //find median
+ for (int i = 0; i < calcAverages.size(); i++) { //for each calc
+ for (int j = 0; j < calcAverages[i].size(); j++) { //for each comparison
+ vector<double> dists;
+ for (int thisIter = 0; thisIter < calcDistsTotals.size(); thisIter++) { //for each subsample
+ dists.push_back(calcDistsTotals[thisIter][i][j].dist);
+ }
+ sort(dists.begin(), dists.end());
+ calcAverages[i][j].dist = dists[(calcDistsTotals.size()/2)];
+ }
+ }
+ }
+
+ return calcAverages;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "getAverages");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+vector< vector<seqDist> > MothurOut::getAverages(vector< vector< vector<seqDist> > >& calcDistsTotals) {
+ try{
+
+ vector< vector<seqDist> > calcAverages; //calcAverages.resize(calcDistsTotals[0].size());
+ for (int i = 0; i < calcDistsTotals[0].size(); i++) { //initialize sums to zero.
+ //calcAverages[i].resize(calcDistsTotals[0][i].size());
+ vector<seqDist> temp;
+ for (int j = 0; j < calcDistsTotals[0][i].size(); j++) {
+ seqDist tempDist;
+ tempDist.seq1 = calcDistsTotals[0][i][j].seq1;
+ tempDist.seq2 = calcDistsTotals[0][i][j].seq2;
+ tempDist.dist = 0.0;
+ temp.push_back(tempDist);
+ }
+ calcAverages.push_back(temp);
+ }
+
+
+ for (int thisIter = 0; thisIter < calcDistsTotals.size(); thisIter++) { //sum all groups dists for each calculator
+ for (int i = 0; i < calcAverages.size(); i++) { //initialize sums to zero.
+ for (int j = 0; j < calcAverages[i].size(); j++) {
+ calcAverages[i][j].dist += calcDistsTotals[thisIter][i][j].dist;
+ }
+ }
+ }
+
+ for (int i = 0; i < calcAverages.size(); i++) { //finds average.
+ for (int j = 0; j < calcAverages[i].size(); j++) {
+ calcAverages[i][j].dist /= (float) calcDistsTotals.size();
+ }
+ }
+
+ return calcAverages;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "getAverages");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+vector< vector<seqDist> > MothurOut::getStandardDeviation(vector< vector< vector<seqDist> > >& calcDistsTotals) {
+ try{
+
+ vector< vector<seqDist> > calcAverages = getAverages(calcDistsTotals);
+
+ //find standard deviation
+ vector< vector<seqDist> > stdDev;
+ for (int i = 0; i < calcDistsTotals[0].size(); i++) { //initialize sums to zero.
+ vector<seqDist> temp;
+ for (int j = 0; j < calcDistsTotals[0][i].size(); j++) {
+ seqDist tempDist;
+ tempDist.seq1 = calcDistsTotals[0][i][j].seq1;
+ tempDist.seq2 = calcDistsTotals[0][i][j].seq2;
+ tempDist.dist = 0.0;
+ temp.push_back(tempDist);
+ }
+ stdDev.push_back(temp);
+ }
+
+ for (int thisIter = 0; thisIter < calcDistsTotals.size(); thisIter++) { //compute the difference of each dist from the mean, and square the result of each
+ for (int i = 0; i < stdDev.size(); i++) {
+ for (int j = 0; j < stdDev[i].size(); j++) {
+ stdDev[i][j].dist += ((calcDistsTotals[thisIter][i][j].dist - calcAverages[i][j].dist) * (calcDistsTotals[thisIter][i][j].dist - calcAverages[i][j].dist));
+ }
+ }
+ }
+
+ for (int i = 0; i < stdDev.size(); i++) { //finds average.
+ for (int j = 0; j < stdDev[i].size(); j++) {
+ stdDev[i][j].dist /= (float) calcDistsTotals.size();
+ stdDev[i][j].dist = sqrt(stdDev[i][j].dist);
+ }
+ }
+
+ return stdDev;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "getAverages");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+vector< vector<seqDist> > MothurOut::getStandardDeviation(vector< vector< vector<seqDist> > >& calcDistsTotals, vector< vector<seqDist> >& calcAverages) {
+ try{
+ //find standard deviation
+ vector< vector<seqDist> > stdDev;
+ for (int i = 0; i < calcDistsTotals[0].size(); i++) { //initialize sums to zero.
+ vector<seqDist> temp;
+ for (int j = 0; j < calcDistsTotals[0][i].size(); j++) {
+ seqDist tempDist;
+ tempDist.seq1 = calcDistsTotals[0][i][j].seq1;
+ tempDist.seq2 = calcDistsTotals[0][i][j].seq2;
+ tempDist.dist = 0.0;
+ temp.push_back(tempDist);
+ }
+ stdDev.push_back(temp);
+ }
+
+ for (int thisIter = 0; thisIter < calcDistsTotals.size(); thisIter++) { //compute the difference of each dist from the mean, and square the result of each
+ for (int i = 0; i < stdDev.size(); i++) {
+ for (int j = 0; j < stdDev[i].size(); j++) {
+ stdDev[i][j].dist += ((calcDistsTotals[thisIter][i][j].dist - calcAverages[i][j].dist) * (calcDistsTotals[thisIter][i][j].dist - calcAverages[i][j].dist));
+ }
+ }
+ }
+
+ for (int i = 0; i < stdDev.size(); i++) { //finds average.
+ for (int j = 0; j < stdDev[i].size(); j++) {
+ stdDev[i][j].dist /= (float) calcDistsTotals.size();
+ stdDev[i][j].dist = sqrt(stdDev[i][j].dist);
+ }
+ }
+
+ return stdDev;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "getAverages");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+bool MothurOut::isContainingOnlyDigits(string input) {
+ try{
+
+ //are you a digit in ascii code
+ for (int i = 0;i < input.length(); i++){
+ if( input[i]>47 && input[i]<58){}
+ else { return false; }
+ }
+
+ return true;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "isContainingOnlyDigits");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int MothurOut::removeConfidences(string& tax) {
+ try {
+
+ string taxon;
+ string newTax = "";
+
+ while (tax.find_first_of(';') != -1) {
+
+ if (control_pressed) { return 0; }
+
+ //get taxon
+ taxon = tax.substr(0,tax.find_first_of(';'));
+
+ int pos = taxon.find_last_of('(');
+ if (pos != -1) {
+ //is it a number?
+ int pos2 = taxon.find_last_of(')');
+ if (pos2 != -1) {
+ string confidenceScore = taxon.substr(pos+1, (pos2-(pos+1)));
+ if (isNumeric1(confidenceScore)) {
+ taxon = taxon.substr(0, pos); //rip off confidence
+ }
+ }
+ }
+ taxon += ";";
+
+ tax = tax.substr(tax.find_first_of(';')+1, tax.length());
+ newTax += taxon;
+ }
+
+ tax = newTax;
+
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "removeConfidences");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+string MothurOut::removeQuotes(string tax) {
+ try {
+
+ string taxon;
+ string newTax = "";
+
+ for (int i = 0; i < tax.length(); i++) {
+
+ if (control_pressed) { return newTax; }
+
+ if ((tax[i] != '\'') && (tax[i] != '\"')) { newTax += tax[i]; }
+
+ }
+
+ return newTax;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "removeQuotes");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+// function for calculating standard deviation
+double MothurOut::getStandardDeviation(vector<int>& featureVector){
+ try {
+ //finds sum
+ double average = 0;
+ for (int i = 0; i < featureVector.size(); i++) { average += featureVector[i]; }
+ average /= (double) featureVector.size();
+
+ //find standard deviation
+ double stdDev = 0;
+ for (int i = 0; i < featureVector.size(); i++) { //compute the difference of each dist from the mean, and square the result of each
+ stdDev += ((featureVector[i] - average) * (featureVector[i] - average));
+ }
+
+ stdDev /= (double) featureVector.size();
+ stdDev = sqrt(stdDev);
+
+ return stdDev;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "getStandardDeviation");
+ exit(1);
+ }
+}
+/**************************************************************************************************/