+++ /dev/null
-/*
- * bayesian.cpp
- * Mothur
- *
- * Created by westcott on 11/3/09.
- * Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
-
-#include "bayesian.h"
-#include "kmer.hpp"
-#include "phylosummary.h"
-#include "referencedb.h"
-/**************************************************************************************************/
-Bayesian::Bayesian(string tfile, string tempFile, string method, int ksize, int cutoff, int i, int tid, bool f) :
-Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
- try {
- ReferenceDB* rdb = ReferenceDB::getInstance();
-
- threadID = tid;
- flip = f;
- string baseName = tempFile;
-
- if (baseName == "saved") { baseName = rdb->getSavedReference(); }
-
- string baseTName = tfile;
- if (baseTName == "saved") { baseTName = rdb->getSavedTaxonomy(); }
-
- /************calculate the probablity that each word will be in a specific taxonomy*************/
- string tfileroot = m->getFullPathName(baseTName.substr(0,baseTName.find_last_of(".")+1));
- string tempfileroot = m->getRootName(m->getSimpleName(baseName));
- string phyloTreeName = tfileroot + "tree.train";
- string phyloTreeSumName = tfileroot + "tree.sum";
- string probFileName = tfileroot + tempfileroot + char('0'+ kmerSize) + "mer.prob";
- string probFileName2 = tfileroot + tempfileroot + char('0'+ kmerSize) + "mer.numNonZero";
-
- ofstream out;
- ofstream out2;
-
- ifstream phyloTreeTest(phyloTreeName.c_str());
- ifstream probFileTest2(probFileName2.c_str());
- ifstream probFileTest(probFileName.c_str());
- ifstream probFileTest3(phyloTreeSumName.c_str());
-
- int start = time(NULL);
-
- //if they are there make sure they were created after this release date
- bool FilesGood = false;
- if(probFileTest && probFileTest2 && phyloTreeTest && probFileTest3){
- FilesGood = checkReleaseDate(probFileTest, probFileTest2, phyloTreeTest, probFileTest3);
- }
-
- //if you want to save, but you dont need to calculate then just read
- if (rdb->save && probFileTest && probFileTest2 && phyloTreeTest && probFileTest3 && FilesGood && (tempFile != "saved")) {
- ifstream saveIn;
- m->openInputFile(tempFile, saveIn);
-
- while (!saveIn.eof()) {
- Sequence temp(saveIn);
- m->gobble(saveIn);
-
- rdb->referenceSeqs.push_back(temp);
- }
- saveIn.close();
- }
-
- if(probFileTest && probFileTest2 && phyloTreeTest && probFileTest3 && FilesGood){
- if (tempFile == "saved") { m->mothurOutEndLine(); m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory."); m->mothurOutEndLine(); }
-
- m->mothurOut("Reading template taxonomy... "); cout.flush();
-
- phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
-
- m->mothurOut("DONE."); m->mothurOutEndLine();
-
- genusNodes = phyloTree->getGenusNodes();
- genusTotals = phyloTree->getGenusTotals();
-
- if (tfile == "saved") {
- m->mothurOutEndLine(); m->mothurOut("Using probabilties from " + rdb->getSavedTaxonomy() + " that are saved in memory... "); cout.flush();;
- wordGenusProb = rdb->wordGenusProb;
- WordPairDiffArr = rdb->WordPairDiffArr;
- }else {
- m->mothurOut("Reading template probabilities... "); cout.flush();
- readProbFile(probFileTest, probFileTest2, probFileName, probFileName2);
- }
-
- //save probabilities
- if (rdb->save) { rdb->wordGenusProb = wordGenusProb; rdb->WordPairDiffArr = WordPairDiffArr; }
- }else{
-
- //create search database and names vector
- generateDatabaseAndNames(tfile, tempFile, method, ksize, 0.0, 0.0, 0.0, 0.0);
-
- //prevents errors caused by creating shortcut files if you had an error in the sanity check.
- if (m->control_pressed) { m->mothurRemove(phyloTreeName); m->mothurRemove(probFileName); m->mothurRemove(probFileName2); }
- else{
- genusNodes = phyloTree->getGenusNodes();
- genusTotals = phyloTree->getGenusTotals();
-
- m->mothurOut("Calculating template taxonomy tree... "); cout.flush();
-
- phyloTree->printTreeNodes(phyloTreeName);
-
- m->mothurOut("DONE."); m->mothurOutEndLine();
-
- m->mothurOut("Calculating template probabilities... "); cout.flush();
-
- numKmers = database->getMaxKmer() + 1;
-
- //initialze probabilities
- wordGenusProb.resize(numKmers);
- WordPairDiffArr.resize(numKmers);
-
- for (int j = 0; j < wordGenusProb.size(); j++) { wordGenusProb[j].resize(genusNodes.size()); }
- ofstream out;
- ofstream out2;
-
- #ifdef USE_MPI
- int pid;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
- if (pid == 0) {
- #endif
-
-
- m->openOutputFile(probFileName, out);
-
- //output mothur version
- out << "#" << m->getVersion() << endl;
-
- out << numKmers << endl;
-
- m->openOutputFile(probFileName2, out2);
-
- //output mothur version
- out2 << "#" << m->getVersion() << endl;
-
- #ifdef USE_MPI
- }
- #endif
-
-
- //for each word
- for (int i = 0; i < numKmers; i++) {
- if (m->control_pressed) { break; }
-
- #ifdef USE_MPI
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
- if (pid == 0) {
- #endif
-
- out << i << '\t';
-
- #ifdef USE_MPI
- }
- #endif
-
- vector<int> seqsWithWordi = database->getSequencesWithKmer(i);
-
- map<int, int> count;
- for (int k = 0; k < genusNodes.size(); k++) { count[genusNodes[k]] = 0; }
-
- //for each sequence with that word
- for (int j = 0; j < seqsWithWordi.size(); j++) {
- int temp = phyloTree->getIndex(names[seqsWithWordi[j]]);
- count[temp]++; //increment count of seq in this genus who have this word
- }
-
- //probabilityInTemplate = (# of seqs with that word in template + 0.50) / (total number of seqs in template + 1);
- float probabilityInTemplate = (seqsWithWordi.size() + 0.50) / (float) (names.size() + 1);
- diffPair tempProb(log(probabilityInTemplate), 0.0);
- WordPairDiffArr[i] = tempProb;
-
- int numNotZero = 0;
- for (int k = 0; k < genusNodes.size(); k++) {
- //probabilityInThisTaxonomy = (# of seqs with that word in this taxonomy + probabilityInTemplate) / (total number of seqs in this taxonomy + 1);
-
-
- wordGenusProb[i][k] = log((count[genusNodes[k]] + probabilityInTemplate) / (float) (genusTotals[k] + 1));
-
- if (count[genusNodes[k]] != 0) {
- #ifdef USE_MPI
- int pid;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
- if (pid == 0) {
- #endif
-
- out << k << '\t' << wordGenusProb[i][k] << '\t' ;
-
- #ifdef USE_MPI
- }
- #endif
-
- numNotZero++;
- }
- }
-
- #ifdef USE_MPI
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
- if (pid == 0) {
- #endif
-
- out << endl;
- out2 << probabilityInTemplate << '\t' << numNotZero << '\t' << log(probabilityInTemplate) << endl;
-
- #ifdef USE_MPI
- }
- #endif
- }
-
- #ifdef USE_MPI
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
- if (pid == 0) {
- #endif
-
- out.close();
- out2.close();
-
- #ifdef USE_MPI
- }
- #endif
-
- //read in new phylotree with less info. - its faster
- ifstream phyloTreeTest(phyloTreeName.c_str());
- delete phyloTree;
-
- phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
-
- //save probabilities
- if (rdb->save) { rdb->wordGenusProb = wordGenusProb; rdb->WordPairDiffArr = WordPairDiffArr; }
- }
- }
-
- generateWordPairDiffArr();
-
- //save probabilities
- if (rdb->save) { rdb->wordGenusProb = wordGenusProb; rdb->WordPairDiffArr = WordPairDiffArr; }
-
- m->mothurOut("DONE."); m->mothurOutEndLine();
- m->mothurOut("It took " + toString(time(NULL) - start) + " seconds get probabilities. "); m->mothurOutEndLine();
- }
- catch(exception& e) {
- m->errorOut(e, "Bayesian", "Bayesian");
- exit(1);
- }
-}
-/**************************************************************************************************/
-Bayesian::~Bayesian() {
- try {
-
- delete phyloTree;
- if (database != NULL) { delete database; }
- }
- catch(exception& e) {
- m->errorOut(e, "Bayesian", "~Bayesian");
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-string Bayesian::getTaxonomy(Sequence* seq) {
- try {
- string tax = "";
- Kmer kmer(kmerSize);
- flipped = false;
-
- //get words contained in query
- //getKmerString returns a string where the index in the string is hte kmer number
- //and the character at that index can be converted to be the number of times that kmer was seen
- string queryKmerString = kmer.getKmerString(seq->getUnaligned());
-
- vector<int> queryKmers;
- for (int i = 0; i < queryKmerString.length()-1; i++) { // the -1 is to ignore any kmer with an N in it
- if (queryKmerString[i] != '!') { //this kmer is in the query
- queryKmers.push_back(i);
- }
- }
-
- //if user wants to test reverse compliment and its reversed use that instead
- if (flip) {
- if (isReversed(queryKmers)) {
- flipped = true;
- seq->reverseComplement();
- queryKmerString = kmer.getKmerString(seq->getUnaligned());
- queryKmers.clear();
- for (int i = 0; i < queryKmerString.length()-1; i++) { // the -1 is to ignore any kmer with an N in it
- if (queryKmerString[i] != '!') { //this kmer is in the query
- queryKmers.push_back(i);
- }
- }
- }
- }
-
- if (queryKmers.size() == 0) { m->mothurOut(seq->getName() + "is bad."); m->mothurOutEndLine(); simpleTax = "unknown;"; return "unknown;"; }
-
-
- int index = getMostProbableTaxonomy(queryKmers);
-
- if (m->control_pressed) { return tax; }
-
- //bootstrap - to set confidenceScore
- int numToSelect = queryKmers.size() / 8;
-
- tax = bootstrapResults(queryKmers, index, numToSelect);
-
- return tax;
- }
- catch(exception& e) {
- m->errorOut(e, "Bayesian", "getTaxonomy");
- exit(1);
- }
-}
-/**************************************************************************************************/
-string Bayesian::bootstrapResults(vector<int> kmers, int tax, int numToSelect) {
- try {
-
- map<int, int> confidenceScores;
-
- //initialize confidences to 0
- int seqIndex = tax;
- TaxNode seq = phyloTree->get(tax);
- confidenceScores[tax] = 0;
-
- while (seq.level != 0) { //while you are not at the root
- seqIndex = seq.parent;
- confidenceScores[seqIndex] = 0;
- seq = phyloTree->get(seq.parent);
- }
-
- map<int, int>::iterator itBoot;
- map<int, int>::iterator itBoot2;
- map<int, int>::iterator itConvert;
-
- for (int i = 0; i < iters; i++) {
- if (m->control_pressed) { return "control"; }
-
- vector<int> temp;
- for (int j = 0; j < numToSelect; j++) {
- int index = int(rand() % kmers.size());
-
- //add word to temp
- temp.push_back(kmers[index]);
- }
-
- //get taxonomy
- int newTax = getMostProbableTaxonomy(temp);
- //int newTax = 1;
- TaxNode taxonomyTemp = phyloTree->get(newTax);
-
- //add to confidence results
- while (taxonomyTemp.level != 0) { //while you are not at the root
- itBoot2 = confidenceScores.find(newTax); //is this a classification we already have a count on
-
- if (itBoot2 != confidenceScores.end()) { //this is a classification we need a confidence for
- (itBoot2->second)++;
- }
-
- newTax = taxonomyTemp.parent;
- taxonomyTemp = phyloTree->get(newTax);
- }
-
- }
-
- string confidenceTax = "";
- simpleTax = "";
-
- int seqTaxIndex = tax;
- TaxNode seqTax = phyloTree->get(tax);
-
- while (seqTax.level != 0) { //while you are not at the root
-
- itBoot2 = confidenceScores.find(seqTaxIndex); //is this a classification we already have a count on
-
- int confidence = 0;
- if (itBoot2 != confidenceScores.end()) { //already in confidence scores
- confidence = itBoot2->second;
- }
-
- if (((confidence/(float)iters) * 100) >= confidenceThreshold) {
- confidenceTax = seqTax.name + "(" + toString(((confidence/(float)iters) * 100)) + ");" + confidenceTax;
- simpleTax = seqTax.name + ";" + simpleTax;
- }
-
- seqTaxIndex = seqTax.parent;
- seqTax = phyloTree->get(seqTax.parent);
- }
-
- if (confidenceTax == "") { confidenceTax = "unknown;"; simpleTax = "unknown;"; }
-
- return confidenceTax;
-
- }
- catch(exception& e) {
- m->errorOut(e, "Bayesian", "bootstrapResults");
- exit(1);
- }
-}
-/**************************************************************************************************/
-int Bayesian::getMostProbableTaxonomy(vector<int> queryKmer) {
- try {
- int indexofGenus = 0;
-
- double maxProbability = -1000000.0;
- //find taxonomy with highest probability that this sequence is from it
-
-
-// cout << genusNodes.size() << endl;
-
-
- for (int k = 0; k < genusNodes.size(); k++) {
- //for each taxonomy calc its probability
-
- double prob = 0.0000;
- for (int i = 0; i < queryKmer.size(); i++) {
- prob += wordGenusProb[queryKmer[i]][k];
- }
-
-// cout << phyloTree->get(genusNodes[k]).name << '\t' << prob << endl;
-
- //is this the taxonomy with the greatest probability?
- if (prob > maxProbability) {
- indexofGenus = genusNodes[k];
- maxProbability = prob;
- }
- }
-
-
- return indexofGenus;
- }
- catch(exception& e) {
- m->errorOut(e, "Bayesian", "getMostProbableTaxonomy");
- exit(1);
- }
-}
-//********************************************************************************************************************
-//if it is more probable that the reverse compliment kmers are in the template, then we assume the sequence is reversed.
-bool Bayesian::isReversed(vector<int>& queryKmers){
- try{
- bool reversed = false;
- float prob = 0;
- float reverseProb = 0;
-
- for (int i = 0; i < queryKmers.size(); i++){
- int kmer = queryKmers[i];
- if (kmer >= 0){
- prob += WordPairDiffArr[kmer].prob;
- reverseProb += WordPairDiffArr[kmer].reverseProb;
- }
- }
-
- if (reverseProb > prob){ reversed = true; }
-
- return reversed;
- }
- catch(exception& e) {
- m->errorOut(e, "Bayesian", "isReversed");
- exit(1);
- }
-}
-//********************************************************************************************************************
-int Bayesian::generateWordPairDiffArr(){
- try{
- Kmer kmer(kmerSize);
- for (int i = 0; i < WordPairDiffArr.size(); i++) {
- int reversedWord = kmer.getReverseKmerNumber(i);
- WordPairDiffArr[i].reverseProb = WordPairDiffArr[reversedWord].prob;
- }
-
- return 0;
- }catch(exception& e) {
- m->errorOut(e, "Bayesian", "generateWordPairDiffArr");
- exit(1);
- }
-}
-/*************************************************************************************************
-map<string, int> Bayesian::parseTaxMap(string newTax) {
- try{
-
- map<string, int> parsed;
-
- newTax = newTax.substr(0, newTax.length()-1); //get rid of last ';'
-
- //parse taxonomy
- string individual;
- while (newTax.find_first_of(';') != -1) {
- individual = newTax.substr(0,newTax.find_first_of(';'));
- newTax = newTax.substr(newTax.find_first_of(';')+1, newTax.length());
- parsed[individual] = 1;
- }
-
- //get last one
- parsed[newTax] = 1;
-
- return parsed;
-
- }
- catch(exception& e) {
- m->errorOut(e, "Bayesian", "parseTax");
- exit(1);
- }
-}
-**************************************************************************************************/
-void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string inNumName) {
- try{
-
- #ifdef USE_MPI
-
- int pid, num, num2, processors;
- vector<unsigned long long> positions;
- vector<unsigned long long> positions2;
-
- MPI_Status status;
- MPI_File inMPI;
- MPI_File inMPI2;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
- MPI_Comm_size(MPI_COMM_WORLD, &processors);
- int tag = 2001;
-
- char inFileName[1024];
- strcpy(inFileName, inNumName.c_str());
-
- char inFileName2[1024];
- strcpy(inFileName2, inName.c_str());
-
- MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
- MPI_File_open(MPI_COMM_WORLD, inFileName2, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI2); //comm, filename, mode, info, filepointer
-
- if (pid == 0) {
- positions = m->setFilePosEachLine(inNumName, num);
- positions2 = m->setFilePosEachLine(inName, num2);
-
- for(int i = 1; i < processors; i++) {
- MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
- MPI_Send(&positions[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
-
- MPI_Send(&num2, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
- MPI_Send(&positions2[0], (num2+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
- }
-
- }else{
- MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
- positions.resize(num+1);
- MPI_Recv(&positions[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
-
- MPI_Recv(&num2, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
- positions2.resize(num2+1);
- MPI_Recv(&positions2[0], (num2+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
- }
-
- //read version
- int length = positions2[1] - positions2[0];
- char* buf5 = new char[length];
-
- MPI_File_read_at(inMPI2, positions2[0], buf5, length, MPI_CHAR, &status);
- delete buf5;
-
- //read numKmers
- length = positions2[2] - positions2[1];
- char* buf = new char[length];
-
- MPI_File_read_at(inMPI2, positions2[1], buf, length, MPI_CHAR, &status);
-
- string tempBuf = buf;
- if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
- delete buf;
-
- istringstream iss (tempBuf,istringstream::in);
- iss >> numKmers;
-
- //initialze probabilities
- wordGenusProb.resize(numKmers);
-
- for (int j = 0; j < wordGenusProb.size(); j++) { wordGenusProb[j].resize(genusNodes.size()); }
-
- int kmer, name;
- vector<int> numbers; numbers.resize(numKmers);
- float prob;
- vector<float> zeroCountProb; zeroCountProb.resize(numKmers);
- WordPairDiffArr.resize(numKmers);
-
- //read version
- length = positions[1] - positions[0];
- char* buf6 = new char[length];
-
- MPI_File_read_at(inMPI2, positions[0], buf6, length, MPI_CHAR, &status);
- delete buf6;
-
- //read file
- for(int i=1;i<num;i++){
- //read next sequence
- length = positions[i+1] - positions[i];
- char* buf4 = new char[length];
-
- MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status);
-
- tempBuf = buf4;
- if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
- delete buf4;
-
- istringstream iss (tempBuf,istringstream::in);
- float probTemp;
- iss >> zeroCountProb[i] >> numbers[i] >> probTemp;
- WordPairDiffArr[i].prob = probTemp;
-
- }
-
- MPI_File_close(&inMPI);
-
- for(int i=2;i<num2;i++){
- //read next sequence
- length = positions2[i+1] - positions2[i];
- char* buf4 = new char[length];
-
- MPI_File_read_at(inMPI2, positions2[i], buf4, length, MPI_CHAR, &status);
-
- tempBuf = buf4;
- if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
- delete buf4;
-
- istringstream iss (tempBuf,istringstream::in);
-
- iss >> kmer;
-
- //set them all to zero value
- for (int i = 0; i < genusNodes.size(); i++) {
- wordGenusProb[kmer][i] = log(zeroCountProb[kmer] / (float) (genusTotals[i]+1));
- }
-
- //get probs for nonzero values
- for (int i = 0; i < numbers[kmer]; i++) {
- iss >> name >> prob;
- wordGenusProb[kmer][name] = prob;
- }
-
- }
- MPI_File_close(&inMPI2);
- MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
- #else
- //read version
- string line = m->getline(in); m->gobble(in);
-
- in >> numKmers; m->gobble(in);
- //cout << threadID << '\t' << line << '\t' << numKmers << &in << '\t' << &inNum << '\t' << genusNodes.size() << endl;
- //initialze probabilities
- wordGenusProb.resize(numKmers);
-
- for (int j = 0; j < wordGenusProb.size(); j++) { wordGenusProb[j].resize(genusNodes.size()); }
-
- int kmer, name, count; count = 0;
- vector<int> num; num.resize(numKmers);
- float prob;
- vector<float> zeroCountProb; zeroCountProb.resize(numKmers);
- WordPairDiffArr.resize(numKmers);
-
- //read version
- string line2 = m->getline(inNum); m->gobble(inNum);
- float probTemp;
- //cout << threadID << '\t' << line2 << '\t' << this << endl;
- while (inNum) {
- inNum >> zeroCountProb[count] >> num[count] >> probTemp;
- WordPairDiffArr[count].prob = probTemp;
- count++;
- m->gobble(inNum);
- //cout << threadID << '\t' << count << endl;
- }
- inNum.close();
- //cout << threadID << '\t' << "here1 " << &wordGenusProb << '\t' << &num << endl; //
- //cout << threadID << '\t' << &genusTotals << '\t' << endl;
- //cout << threadID << '\t' << genusNodes.size() << endl;
- while(in) {
- in >> kmer;
- //cout << threadID << '\t' << kmer << endl;
- //set them all to zero value
- for (int i = 0; i < genusNodes.size(); i++) {
- wordGenusProb[kmer][i] = log(zeroCountProb[kmer] / (float) (genusTotals[i]+1));
- }
- //cout << threadID << '\t' << num[kmer] << "here" << endl;
- //get probs for nonzero values
- for (int i = 0; i < num[kmer]; i++) {
- in >> name >> prob;
- wordGenusProb[kmer][name] = prob;
- }
-
- m->gobble(in);
- }
- in.close();
- //cout << threadID << '\t' << "here" << endl;
- #endif
- }
- catch(exception& e) {
- m->errorOut(e, "Bayesian", "readProbFile");
- exit(1);
- }
-}
-/**************************************************************************************************/
-bool Bayesian::checkReleaseDate(ifstream& file1, ifstream& file2, ifstream& file3, ifstream& file4) {
- try {
-
- bool good = true;
-
- vector<string> lines;
- lines.push_back(m->getline(file1));
- lines.push_back(m->getline(file2));
- lines.push_back(m->getline(file3));
- lines.push_back(m->getline(file4));
-
- //before we added this check
- if ((lines[0][0] != '#') || (lines[1][0] != '#') || (lines[2][0] != '#') || (lines[3][0] != '#')) { good = false; }
- else {
- //rip off #
- for (int i = 0; i < lines.size(); i++) { lines[i] = lines[i].substr(1); }
-
- //get mothurs current version
- string version = m->getVersion();
-
- vector<string> versionVector;
- m->splitAtChar(version, versionVector, '.');
-
- //check each files version
- for (int i = 0; i < lines.size(); i++) {
- vector<string> linesVector;
- m->splitAtChar(lines[i], linesVector, '.');
-
- if (versionVector.size() != linesVector.size()) { good = false; break; }
- 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) { break; }
- }
- }
-
- if (!good) { file1.close(); file2.close(); file3.close(); file4.close(); }
- else { file1.seekg(0); file2.seekg(0); file3.seekg(0); file4.seekg(0); }
-
- return good;
- }
- catch(exception& e) {
- m->errorOut(e, "Bayesian", "checkReleaseDate");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-
-
-
-
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projects / mothur.git / blobdiff