X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=124fbb876b38def3d61f1bf425ef15f36237fa5f;hb=9b53f130ac9af5e95444ce2e817fce25ed19ff03;hp=9704464bf80326c87d4afa556e3353b95fcbf37e;hpb=5a4ac4f954c4b4445bcee272f1f8220ddcc9c1e4;p=mothur.git diff --git a/mothurout.cpp b/mothurout.cpp index 9704464..124fbb8 100644 --- a/mothurout.cpp +++ b/mothurout.cpp @@ -939,7 +939,7 @@ string MothurOut::getFullPathName(string fileName){ } for (int i = index; i >= 0; i--) { - newFileName = dirs[i] + "\\" + newFileName; + newFileName = dirs[i] + "\\\\" + newFileName; } return newFileName; @@ -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); @@ -1541,10 +1542,49 @@ 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 { - //open input file ifstream in; openInputFile(namefile, in); @@ -1575,6 +1615,23 @@ int MothurOut::readTax(string namefile, map& taxMap) { } } 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(); @@ -1587,7 +1644,6 @@ int MothurOut::readTax(string namefile, map& taxMap) { /**********************************************************************************************************************/ int MothurOut::readNames(string namefile, map& nameMap, bool redund) { try { - //open input file ifstream in; openInputFile(namefile, in); @@ -1618,6 +1674,23 @@ int MothurOut::readNames(string namefile, map& nameMap, bool red } } 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(); @@ -1630,7 +1703,6 @@ int MothurOut::readNames(string namefile, map& nameMap, bool red /**********************************************************************************************************************/ int MothurOut::readNames(string namefile, map& nameMap, int flip) { try { - //open input file ifstream in; openInputFile(namefile, in); @@ -1658,6 +1730,20 @@ int MothurOut::readNames(string namefile, map& nameMap, int flip } } 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(); @@ -1670,7 +1756,7 @@ int MothurOut::readNames(string namefile, map& nameMap, int flip /**********************************************************************************************************************/ int MothurOut::readNames(string namefile, map& nameMap, map& nameCount) { try { - nameMap.clear(); nameCount.clear(); + nameMap.clear(); nameCount.clear(); //open input file ifstream in; openInputFile(namefile, in); @@ -1703,6 +1789,24 @@ int MothurOut::readNames(string namefile, map& nameMap, map 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(); } @@ -1714,7 +1818,6 @@ int MothurOut::readNames(string namefile, map& nameMap, map& nameMap) { try { - //open input file ifstream in; openInputFile(namefile, in); @@ -1739,6 +1842,17 @@ int MothurOut::readNames(string namefile, map& nameMap) { } } 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(); @@ -1750,8 +1864,7 @@ int MothurOut::readNames(string namefile, map& nameMap) { } /**********************************************************************************************************************/ int MothurOut::readNames(string namefile, map >& nameMap) { - try { - + try { //open input file ifstream in; openInputFile(namefile, in); @@ -1782,6 +1895,22 @@ int MothurOut::readNames(string namefile, map >& nameMap) } 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) { @@ -1792,7 +1921,6 @@ int MothurOut::readNames(string namefile, map >& nameMap) /**********************************************************************************************************************/ map MothurOut::readNames(string namefile) { try { - map nameMap; //open input file @@ -1823,6 +1951,20 @@ map MothurOut::readNames(string namefile) { } } 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; @@ -1875,6 +2017,29 @@ int MothurOut::readNames(string namefile, vector& nameVector, m } 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) { @@ -1885,7 +2050,7 @@ int MothurOut::readNames(string namefile, vector& nameVector, m //********************************************************************************************************************** set MothurOut::readAccnos(string accnosfile){ try { - set names; + set names; ifstream in; openInputFile(accnosfile, in); string name; @@ -1903,6 +2068,10 @@ set MothurOut::readAccnos(string accnosfile){ } 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) { @@ -1930,6 +2099,11 @@ int MothurOut::readAccnos(string accnosfile, vector& names){ 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; } @@ -1981,6 +2155,32 @@ 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 { @@ -2271,6 +2471,9 @@ 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& 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 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) { @@ -2719,8 +2963,53 @@ 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); + } +} +/**************************************************************************************************/