X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=c5eb0dca828a47023973f1684986ba05d45bb0fb;hb=96dbe925073caefaed6e6db85659c144a806aeb1;hp=ae4cb524cba877f5a9ec843e1686569032c6528d;hpb=7dab6ac3ae5a5f1ce37dca8cfacaa719881fd5b2;p=mothur.git diff --git a/mothurout.cpp b/mothurout.cpp index ae4cb52..c5eb0dc 100644 --- a/mothurout.cpp +++ b/mothurout.cpp @@ -18,8 +18,46 @@ MothurOut* MothurOut::getInstance() { return _uniqueInstance; } /*********************************************************************************************/ +set MothurOut::getCurrentTypes() { + try { + + set types; + types.insert("fasta"); + types.insert("accnos"); + types.insert("column"); + types.insert("design"); + types.insert("group"); + types.insert("list"); + types.insert("name"); + types.insert("oligos"); + types.insert("order"); + types.insert("ordergroup"); + types.insert("phylip"); + types.insert("qfile"); + types.insert("relabund"); + types.insert("sabund"); + types.insert("rabund"); + types.insert("sff"); + types.insert("shared"); + types.insert("taxonomy"); + types.insert("tree"); + types.insert("flow"); + types.insert("biom"); + types.insert("count"); + types.insert("processors"); + + return types; + } + catch(exception& e) { + errorOut(e, "MothurOut", "getCurrentTypes"); + exit(1); + } +} +/*********************************************************************************************/ void MothurOut::printCurrentFiles() { try { + + if (accnosfile != "") { mothurOut("accnos=" + accnosfile); mothurOutEndLine(); } if (columnfile != "") { mothurOut("column=" + columnfile); mothurOutEndLine(); } if (designfile != "") { mothurOut("design=" + designfile); mothurOutEndLine(); } @@ -41,6 +79,7 @@ void MothurOut::printCurrentFiles() { if (treefile != "") { mothurOut("tree=" + treefile); mothurOutEndLine(); } if (flowfile != "") { mothurOut("flow=" + flowfile); mothurOutEndLine(); } if (biomfile != "") { mothurOut("biom=" + biomfile); mothurOutEndLine(); } + if (counttablefile != "") { mothurOut("count=" + counttablefile); mothurOutEndLine(); } if (processors != "1") { mothurOut("processors=" + processors); mothurOutEndLine(); } } @@ -75,6 +114,7 @@ bool MothurOut::hasCurrentFiles() { if (treefile != "") { return true; } if (flowfile != "") { return true; } if (biomfile != "") { return true; } + if (counttablefile != "") { return true; } if (processors != "1") { return true; } return hasCurrent; @@ -110,6 +150,7 @@ void MothurOut::clearCurrentFiles() { taxonomyfile = ""; flowfile = ""; biomfile = ""; + counttablefile = ""; processors = "1"; } catch(exception& e) { @@ -117,6 +158,81 @@ void MothurOut::clearCurrentFiles() { exit(1); } } +/***********************************************************************/ +string MothurOut::findProgramPath(string programName){ + try { + + string envPath = getenv("PATH"); + string pPath = ""; + + //delimiting path char + char delim; +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + delim = ':'; +#else + delim = ';'; +#endif + + //break apart path variable by ':' + vector dirs; + splitAtChar(envPath, dirs, delim); + + if (debug) { mothurOut("[DEBUG]: dir's in path: \n"); } + + //get path related to mothur + for (int i = 0; i < dirs.size(); i++) { + + if (debug) { mothurOut("[DEBUG]: " + dirs[i] + "\n"); } + + //to lower so we can find it + string tempLower = ""; + for (int j = 0; j < dirs[i].length(); j++) { tempLower += tolower(dirs[i][j]); } + + //is this mothurs path? + if (tempLower.find(programName) != -1) { pPath = dirs[i]; break; } + } + + if (debug) { mothurOut("[DEBUG]: programPath = " + pPath + "\n"); } + + if (pPath != "") { + //add programName so it looks like what argv would look like +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + pPath += "/" + programName; +#else + pPath += "\\" + programName; +#endif + }else { + //okay programName is not in the path, so the folder programName is in must be in the path + //lets find out which one + + //get path related to the program + for (int i = 0; i < dirs.size(); i++) { + + if (debug) { mothurOut("[DEBUG]: looking in " + dirs[i] + " for " + programName + " \n"); } + + //is this the programs path? + ifstream in; + string tempIn = dirs[i]; +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + tempIn += "/" + programName; +#else + tempIn += "\\" + programName; +#endif + openInputFile(tempIn, in, ""); + + //if this file exists + if (in) { in.close(); pPath = tempIn; if (debug) { mothurOut("[DEBUG]: found it, programPath = " + pPath + "\n"); } break; } + } + } + + return pPath; + + } + catch(exception& e) { + errorOut(e, "MothurOut", "findProgramPath"); + exit(1); + } +} /*********************************************************************************************/ void MothurOut::setFileName(string filename) { try { @@ -823,7 +939,7 @@ string MothurOut::getFullPathName(string fileName){ } for (int i = index; i >= 0; i--) { - newFileName = dirs[i] + "\\" + newFileName; + newFileName = dirs[i] + "\\\\" + newFileName; } return newFileName; @@ -936,6 +1052,9 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle){ int MothurOut::renameFile(string oldName, string newName){ try { + + if (oldName == newName) { return 0; } + ifstream inTest; int exist = openInputFile(newName, inTest, ""); inTest.close(); @@ -1017,11 +1136,14 @@ int MothurOut::appendFiles(string temp, string filename) { int numLines = 0; if (ableToOpen == 0) { //you opened it - while(!input.eof()){ - char c = input.get(); - if(input.eof()) { break; } - else { output << c; if (c == '\n') {numLines++;} } - } + + 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(); } @@ -1176,16 +1298,6 @@ vector MothurOut::setFilePosEachLine(string filename, int& n positions.push_back(0); while(!in.eof()){ - //unsigned long long lastpos = in.tellg(); - //input = getline(in); - //if (input.length() != 0) { - //unsigned long long pos = in.tellg(); - //if (pos != -1) { positions.push_back(pos - input.length() - 1); } - //else { positions.push_back(lastpos); } - //} - //gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions - - //getline counting reads char d = in.get(); count++; while ((d != '\n') && (d != '\r') && (d != '\f') && (d != in.eof())) { @@ -1379,23 +1491,165 @@ float MothurOut::ceilDist(float dist, int precision){ exit(1); } } -/**********************************************************************************************************************/ -int MothurOut::readNames(string namefile, map& nameMap) { +/***********************************************************************/ + +vector MothurOut::splitWhiteSpace(string& rest, char buffer[], int size){ try { + vector 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 MothurOut::splitWhiteSpace(string input){ + try { + vector 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); + } +} +//********************************************************************************************************************** +int MothurOut::readTax(string namefile, map& 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 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) { + //are there confidence scores, if so remove them + if (secondCol.find_first_of('(') != -1) { removeConfidences(secondCol); } + taxMap[firstCol] = secondCol; + if (debug) { mothurOut("[DEBUG]: name = '" + firstCol + "' tax = '" + secondCol + "'\n"); } + pairDone = false; + } + } + } + in.close(); + + if (rest != "") { + vector 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) { + //are there confidence scores, if so remove them + if (secondCol.find_first_of('(') != -1) { removeConfidences(secondCol); } + taxMap[firstCol] = secondCol; + if (debug) { mothurOut("[DEBUG]: name = '" + firstCol + "' tax = '" + secondCol + "'\n"); } + pairDone = false; + } + } + } + return taxMap.size(); + + } + catch(exception& e) { + errorOut(e, "MothurOut", "readTax"); + exit(1); + } +} +/**********************************************************************************************************************/ +int MothurOut::readNames(string namefile, map& 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; } - string firstCol, secondCol; - in >> firstCol >> secondCol; gobble(in); - - nameMap[firstCol] = secondCol; + in.read(buffer, 4096); + vector 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) { + //parse names into vector + vector theseNames; + splitAtComma(secondCol, theseNames); + for (int i = 0; i < theseNames.size(); i++) { nameMap[theseNames[i]] = firstCol; } + pairDone = false; + } + } } in.close(); + + if (rest != "") { + vector 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) { + //parse names into vector + vector theseNames; + splitAtComma(secondCol, theseNames); + for (int i = 0; i < theseNames.size(); i++) { nameMap[theseNames[i]] = firstCol; } + pairDone = false; + } + } + } return nameMap.size(); @@ -1406,25 +1660,158 @@ int MothurOut::readNames(string namefile, map& nameMap) { } } /**********************************************************************************************************************/ -int MothurOut::readNames(string namefile, map >& nameMap) { +int MothurOut::readNames(string namefile, map& 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; } - string firstCol, secondCol; - in >> firstCol >> secondCol; gobble(in); + in.read(buffer, 4096); + vector 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) { + nameMap[secondCol] = firstCol; + pairDone = false; + } + } + } + in.close(); + + if (rest != "") { + vector 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) { + nameMap[secondCol] = firstCol; + pairDone = false; + } + } + } + + return nameMap.size(); + + } + catch(exception& e) { + errorOut(e, "MothurOut", "readNames"); + exit(1); + } +} +/**********************************************************************************************************************/ +int MothurOut::readNames(string namefile, map& nameMap, map& 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; } - vector temp; - splitAtComma(secondCol, temp); + in.read(buffer, 4096); + vector 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) { + //parse names into vector + vector 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 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) { + //parse names into vector + vector 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& 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; } - nameMap[firstCol] = temp; + in.read(buffer, 4096); + vector 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) { nameMap[firstCol] = secondCol; pairDone = false; } + } } in.close(); + + if (rest != "") { + vector 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) { nameMap[firstCol] = secondCol; pairDone = false; } + } + } return nameMap.size(); @@ -1435,26 +1822,108 @@ int MothurOut::readNames(string namefile, map >& nameMap) } } /**********************************************************************************************************************/ +int MothurOut::readNames(string namefile, map >& 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 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) { + vector temp; + splitAtComma(secondCol, temp); + nameMap[firstCol] = temp; + pairDone = false; + } + } + } + in.close(); + + if (rest != "") { + vector 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) { + vector temp; + splitAtComma(secondCol, temp); + nameMap[firstCol] = temp; + pairDone = false; + } + } + } + + return nameMap.size(); + } + catch(exception& e) { + errorOut(e, "MothurOut", "readNames"); + exit(1); + } +} +/**********************************************************************************************************************/ map MothurOut::readNames(string namefile) { try { - map 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; } - string firstCol, secondCol; - in >> firstCol >> secondCol; gobble(in); - - int num = getNumNames(secondCol); - - nameMap[firstCol] = num; + in.read(buffer, 4096); + vector 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) { + int num = getNumNames(secondCol); + nameMap[firstCol] = num; + pairDone = false; + } + } } - in.close(); + in.close(); + + if (rest != "") { + vector 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) { + int num = getNumNames(secondCol); + nameMap[firstCol] = num; + pairDone = false; + } + } + } return nameMap; @@ -1473,34 +1942,135 @@ int MothurOut::readNames(string namefile, vector& nameVector, m 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; } - string firstCol, secondCol; - in >> firstCol >> secondCol; gobble(in); - - int num = getNumNames(secondCol); - - map::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); - } + in.read(buffer, 4096); + vector 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) { + int num = getNumNames(secondCol); + + map::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(); - + in.close(); + + if (rest != "") { + vector 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) { + int num = getNumNames(secondCol); + + map::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 MothurOut::readAccnos(string accnosfile){ + try { + set 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 pieces = splitWhiteSpace(rest, buffer, in.gcount()); + + for (int i = 0; i < pieces.size(); i++) { names.insert(pieces[i]); } + } + in.close(); + + if (rest != "") { + vector pieces = splitWhiteSpace(rest); + for (int i = 0; i < pieces.size(); i++) { names.insert(pieces[i]); } + } + return names; + } + catch(exception& e) { + errorOut(e, "MothurOut", "readAccnos"); + exit(1); + } +} +//********************************************************************************************************************** +int MothurOut::readAccnos(string accnosfile, vector& 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 pieces = splitWhiteSpace(rest, buffer, in.gcount()); + + for (int i = 0; i < pieces.size(); i++) { names.push_back(pieces[i]); } + } + in.close(); + + if (rest != "") { + vector pieces = splitWhiteSpace(rest); + for (int i = 0; i < pieces.size(); i++) { names.push_back(pieces[i]); } + } + + return 0; + } + catch(exception& e) { + errorOut(e, "MothurOut", "readAccnos"); + exit(1); + } +} /***********************************************************************/ int MothurOut::getNumNames(string names){ @@ -1544,6 +2114,32 @@ int MothurOut::getNumChar(string line, char c){ exit(1); } } +//********************************************************************************************************************** +bool MothurOut::isSubset(vector bigset, vector 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 { @@ -1583,6 +2179,28 @@ bool MothurOut::mothurConvert(string item, int& num){ 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 { @@ -1839,30 +2457,29 @@ void MothurOut::splitAtDash(string& estim, vector& container) { try { string individual = ""; int estimLength = estim.size(); + bool prevEscape = false; for(int i=0;i& container) { try { string individual = ""; int estimLength = estim.size(); + bool prevEscape = false; for(int i=0;i& container) { //This function parses the line options and puts them in a set void MothurOut::splitAtDash(string& estim, set& container) { try { - string individual; + 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); + int estimLength = estim.size(); + bool prevEscape = false; + for(int i=0;i& container) { exit(1); } } +/***********************************************************************/ +string MothurOut::makeList(vector& 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& container) { @@ -2240,6 +2890,28 @@ int MothurOut::removeConfidences(string& tax) { } } /**************************************************************************************************/ +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); + } +} +/**************************************************************************************************/