X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=468c063cb5c7e74a8d5901a1a38203f47409e2d5;hb=8159f34321e2c771638059b59a986caca9f3ab60;hp=d9df5a078b425b773611d25b2616e3f66a58bddf;hpb=5b72d1cf3fa48730e5bb70d59cced1e43e1fe424;p=mothur.git diff --git a/mothurout.cpp b/mothurout.cpp index d9df5a0..468c063 100644 --- a/mothurout.cpp +++ b/mothurout.cpp @@ -1183,7 +1183,7 @@ string MothurOut::sortFile(string distFile, string outputDir){ string firstName, secondName; float dist; - while (input) { + while (!input.eof()) { input >> firstName >> secondName >> dist; output << dist << '\t' << firstName << '\t' << secondName << endl; gobble(input); @@ -1199,16 +1199,17 @@ string MothurOut::sortFile(string distFile, string outputDir){ //read in sorted file and put distance at end again ifstream input2; + ofstream output2; openInputFile(tempOutfile, input2); - openOutputFile(outfile, output); + openOutputFile(outfile, output2); - while (input2) { + while (!input2.eof()) { input2 >> dist >> firstName >> secondName; - output << firstName << '\t' << secondName << '\t' << dist << endl; + output2 << firstName << '\t' << secondName << '\t' << dist << endl; gobble(input2); } input2.close(); - output.close(); + output2.close(); //remove temp files mothurRemove(tempDistFile); @@ -1541,6 +1542,46 @@ vector MothurOut::splitWhiteSpace(string input){ exit(1); } } +/***********************************************************************/ +vector MothurOut::splitWhiteSpaceWithQuotes(string input){ + try { + vector 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& taxMap) { try { @@ -1567,8 +1608,17 @@ int MothurOut::readTax(string namefile, map& taxMap) { 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"); } + map::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; } } @@ -1585,8 +1635,18 @@ int MothurOut::readTax(string namefile, map& taxMap) { 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"); } + map::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; } } @@ -2430,6 +2490,9 @@ void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){ //This function parses the estimator options and puts them in a vector void MothurOut::splitAtChar(string& estim, vector& container, char symbol) { try { + + if (symbol == '-') { splitAtDash(estim, container); return; } + string individual = ""; int estimLength = estim.size(); for(int i=0;i Groups) { exit(1); } } +/**************************************************************************************************/ + +bool MothurOut::inUsersGroups(vector set, vector< vector > 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 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 groupnames, vector Groups) { @@ -2890,8 +2982,53 @@ 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); + } +} +/**************************************************************************************************/ +// function for calculating standard deviation +double MothurOut::getStandardDeviation(vector& 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); + } +} +/**************************************************************************************************/