X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.cpp;h=e2ca937ed971e87194fd3623c48aec343d2f3ca5;hb=4f4070ac3fbb5da75f834b48062e9123364b006e;hp=7d1f6a0308b5358b2ef39ef70579d866fafca6da;hpb=526a868606faa50caf86e7399f7554c0335b39e5;p=mothur.git diff --git a/distancecommand.cpp b/distancecommand.cpp index 7d1f6a0..e2ca937 100644 --- a/distancecommand.cpp +++ b/distancecommand.cpp @@ -20,12 +20,17 @@ DistanceCommand::DistanceCommand(){ try { globaldata = GlobalData::getInstance(); validCalculator = new ValidCalculators(); - ends = globaldata->getEnds(); + countends = globaldata->getCountEnds(); convert(globaldata->getProcessors(), processors); convert(globaldata->getCutOff(), cutoff); + //open file + string filename = globaldata->getFastaFile(); + openInputFile(filename, in); + + int i; - if (ends != "T") { + if (isTrue(countends) == true) { for (i=0; iEstimators.size(); i++) { if (validCalculator->isValidCalculator("distance", globaldata->Estimators[i]) == true) { if (globaldata->Estimators[i] == "nogaps") { @@ -33,7 +38,7 @@ DistanceCommand::DistanceCommand(){ }else if (globaldata->Estimators[i] == "eachgap") { distCalculator = new eachGapDist(); }else if (globaldata->Estimators[i] == "onegap") { - distCalculator = new oneGapDist(); } + distCalculator = new oneGapDist(); } } } }else { @@ -49,7 +54,7 @@ DistanceCommand::DistanceCommand(){ } } } - + //reset calc for next command globaldata->setCalc(""); } @@ -67,116 +72,235 @@ DistanceCommand::DistanceCommand(){ int DistanceCommand::execute(){ try { - //read file - string filename = globaldata->inputFileName; - - if(globaldata->getFastaFile() != "") { - readSeqs = new ReadFasta(filename); } - else if(globaldata->getNexusFile() != "") { - readSeqs = new ReadNexus(filename); } - else if(globaldata->getClustalFile() != "") { - readSeqs = new ReadClustal(filename); } - else if(globaldata->getPhylipFile() != "") { - readSeqs = new ReadPhylip(filename); } - - readSeqs->read(); - seqDB = readSeqs->getDB(); - + //reads fasta file and fills sequenceDB + if(globaldata->getFastaFile() != "") { seqDB = new SequenceDB(in); } + else { cout << "Error no fasta file." << endl; return 0; } + int numSeqs = seqDB->getNumSeqs(); + cutoff += 0.005; string distFile = getRootName(globaldata->getFastaFile()) + "dist"; + string phylipFile = getRootName(globaldata->getFastaFile()) + "phylip.dist"; + remove(phylipFile.c_str()); remove(distFile.c_str()); + //output numSeqs to phylip formatted dist file + openOutputFile(phylipFile, phylipOut); + phylipOut << numSeqs << endl; + phylipOut.close(); + //# if defined (_WIN32) - //figure out how to implement the fork and wait commands in windows - // driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff); + //figure out how to implement the fork and wait commands in windows + // driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile, cutoff); //# endif - # if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - if(processors == 1){ - driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff); - } - else if(processors == 2){ - - int pid = fork(); - if(pid > 0){ - driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", cutoff); - appendFiles((distFile+"tempa"), distFile); - remove((distFile + "tempa").c_str()); +#if defined (__APPLE__) || (__MACH__) + if(processors == 1){ + driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile + "tempPhylipA", cutoff); + appendFiles((phylipFile + "tempPhylipA"), phylipFile); + remove((phylipFile + "tempPhylipA").c_str()); + } + else if(processors == 2){ + + int pid = fork(); + if(pid > 0){ + driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", phylipFile + "tempPhylipA", cutoff); + appendFiles((distFile+"tempa"), distFile); + remove((distFile + "tempa").c_str()); + appendFiles((phylipFile + "tempPhylipA"), phylipFile); + remove((phylipFile + "tempPhylipA").c_str()); + } + else{ + driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", phylipFile + "tempPhylipB", cutoff); + appendFiles((distFile+"tempb"), distFile); + remove((distFile + "tempb").c_str()); + appendFiles((phylipFile + "tempPhylipB"), phylipFile); + remove((phylipFile + "tempPhylipB").c_str()); + } + wait(NULL); + + } + else if(processors == 3){ + int pid1 = fork(); + if(pid1 > 0){ + int pid2 = fork(); + if(pid2 > 0){ + driver(distCalculator, seqDB, 0, sqrt(3) * numSeqs / 3, distFile + "tempa", phylipFile + "tempPhylipA", cutoff); + appendFiles(distFile+"tempa", distFile); + appendFiles((phylipFile + "tempPhylipA"), phylipFile); + remove((distFile + "tempa").c_str()); + remove((phylipFile + "tempPhylipA").c_str()); } else{ - driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", cutoff); - appendFiles((distFile+"tempb"), distFile); + driver(distCalculator, seqDB, sqrt(3) * numSeqs / 3, sqrt(6) * numSeqs / 3, distFile + "tempb", phylipFile + "tempPhylipB", cutoff); + appendFiles(distFile+"tempb", distFile); + appendFiles((phylipFile + "tempPhylipB"), phylipFile); remove((distFile + "tempb").c_str()); + remove((phylipFile + "tempPhylipB").c_str()); } wait(NULL); - } - else if(processors == 3){ - int pid1 = fork(); - if(pid1 > 0){ - int pid2 = fork(); - if(pid2 > 0){ - driver(distCalculator, seqDB, 0, sqrt(3) * numSeqs / 3, distFile + "tempa", cutoff); - appendFiles(distFile+"tempa", distFile); - remove((distFile + "tempa").c_str()); - } - else{ - driver(distCalculator, seqDB, sqrt(3) * numSeqs / 3, sqrt(6) * numSeqs / 3, distFile + "tempb", cutoff); - appendFiles(distFile+"tempb", distFile); - remove((distFile + "tempb").c_str()); - } - wait(NULL); + else{ + driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", phylipFile + "tempPhylipC", cutoff); + appendFiles(distFile+"tempc", distFile); + appendFiles((phylipFile + "tempPhylipC"), phylipFile); + remove((distFile + "tempc").c_str()); + remove((phylipFile + "tempPhylipC").c_str()); + } + wait(NULL); + } + else if(processors == 4){ + int pid1 = fork(); + if(pid1 > 0){ + int pid2 = fork(); + if(pid2 > 0){ + driver(distCalculator, seqDB, 0, numSeqs / 2, distFile + "tempa", phylipFile + "tempPhylipA", cutoff); + appendFiles(distFile+"tempa", distFile); + appendFiles((phylipFile + "tempPhylipA"), phylipFile); + remove((distFile + "tempa").c_str()); + remove((phylipFile + "tempPhylipA").c_str()); } else{ - driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", cutoff); - appendFiles(distFile+"tempc", distFile); - remove((distFile + "tempc").c_str()); + driver(distCalculator, seqDB, numSeqs / 2, (numSeqs/sqrt(2)), distFile + "tempb", phylipFile + "tempPhylipB", cutoff); + appendFiles(distFile+"tempb", distFile); + appendFiles((phylipFile + "tempPhylipB"), phylipFile); + remove((distFile + "tempb").c_str()); + remove((phylipFile + "tempPhylipB").c_str()); } wait(NULL); } - else if(processors == 4){ - int pid1 = fork(); - if(pid1 > 0){ - int pid2 = fork(); - if(pid2 > 0){ - driver(distCalculator, seqDB, 0, numSeqs / 2, distFile + "tempa", cutoff); - appendFiles(distFile+"tempa", distFile); - remove((distFile + "tempa").c_str()); - } - else{ - driver(distCalculator, seqDB, numSeqs / 2, (numSeqs/sqrt(2)), distFile + "tempb", cutoff); - appendFiles(distFile+"tempb", distFile); - remove((distFile + "tempb").c_str()); - } - wait(NULL); + else{ + int pid3 = fork(); + if(pid3 > 0){ + driver(distCalculator, seqDB, (numSeqs/sqrt(2)), (sqrt(3) * numSeqs / 2), distFile + "tempc", phylipFile + "tempPhylipC", cutoff); + appendFiles(distFile+"tempc", distFile); + appendFiles((phylipFile + "tempPhylipC"), phylipFile); + remove((distFile + "tempc").c_str()); + remove((phylipFile + "tempPhylipC").c_str()); + } else{ - int pid3 = fork(); - if(pid3 > 0){ - driver(distCalculator, seqDB, (numSeqs/sqrt(2)), (sqrt(3) * numSeqs / 2), distFile + "tempc", cutoff); - appendFiles(distFile+"tempc", distFile); - remove((distFile + "tempc").c_str()); - } - else{ - driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", cutoff); - appendFiles(distFile+"tempd", distFile); - remove((distFile + "tempd").c_str()); - } - wait(NULL); + driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", phylipFile + "tempPhylipD", cutoff); + appendFiles(distFile+"tempd", distFile); + appendFiles((phylipFile + "tempPhylipD"), phylipFile); + remove((distFile + "tempd").c_str()); + remove((phylipFile + "tempPhylipD").c_str()); } wait(NULL); } wait(NULL); - # else - driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff); - # endif - + } + wait(NULL); +#elif (linux) || (__linux) + if(processors == 1){ + driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile + "tempPhylipA", cutoff); + appendFiles((phylipFile + "tempPhylipA"), phylipFile); + remove((phylipFile + "tempPhylipA").c_str()); + } + else if(processors == 2){ + + int pid = fork(); + if(pid > 0){ + driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", phylipFile + "tempPhylipA", cutoff); + appendFiles((distFile+"tempa"), distFile); + appendFiles((phylipFile + "tempPhylipA"), phylipFile); + remove((distFile + "tempa").c_str()); + remove((phylipFile + "tempPhylipA").c_str()); + + } + else{ + driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", phylipFile + "tempPhylipB", cutoff); + appendFiles((distFile+"tempb"), distFile); + appendFiles((phylipFile + "tempPhylipB"), phylipFile); + remove((distFile + "tempb").c_str()); + remove((phylipFile + "tempPhylipB").c_str()); + } + wait(); + + } + else if(processors == 3){ + int pid1 = fork(); + if(pid1 > 0){ + int pid2 = fork(); + if(pid2 > 0){ + driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", phylipFile + "tempPhylipA", cutoff); + appendFiles((distFile+"tempa"), distFile); + appendFiles((phylipFile + "tempPhylipA"), phylipFile); + remove((distFile + "tempa").c_str()); + remove((phylipFile + "tempPhylipA").c_str()); + + } + else{ + driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", phylipFile + "tempPhylipB", cutoff); + appendFiles((distFile+"tempb"), distFile); + appendFiles((phylipFile + "tempPhylipB"), phylipFile); + remove((distFile + "tempb").c_str()); + remove((phylipFile + "tempPhylipB").c_str()); + } + wait(); + } + else{ + driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", phylipFile + "tempPhylipC", cutoff); + appendFiles(distFile+"tempc", distFile); + appendFiles((phylipFile + "tempPhylipC"), phylipFile); + remove((distFile + "tempc").c_str()); + remove((phylipFile + "tempPhylipC").c_str()); + } + wait(); + } + else if(processors == 4){ + int pid1 = fork(); + if(pid1 > 0){ + int pid2 = fork(); + if(pid2 > 0){ + driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", phylipFile + "tempPhylipA", cutoff); + appendFiles((distFile+"tempa"), distFile); + appendFiles((phylipFile + "tempPhylipA"), phylipFile); + remove((distFile + "tempa").c_str()); + remove((phylipFile + "tempPhylipA").c_str()); + } + else{ + driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", phylipFile + "tempPhylipB", cutoff); + appendFiles((distFile+"tempb"), distFile); + appendFiles((phylipFile + "tempPhylipB"), phylipFile); + remove((distFile + "tempb").c_str()); + remove((phylipFile + "tempPhylipB").c_str()); + } + wait(); + } + else{ + int pid3 = fork(); + if(pid3 > 0){ + driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", phylipFile + "tempPhylipC", cutoff); + appendFiles(distFile+"tempc", distFile); + appendFiles((phylipFile + "tempPhylipC"), phylipFile); + remove((distFile + "tempc").c_str()); + remove((phylipFile + "tempPhylipC").c_str()); + } + else{ + driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", phylipFile + "tempPhylipD", cutoff); + appendFiles(distFile+"tempd", distFile); + appendFiles((phylipFile + "tempPhylipD"), phylipFile); + remove((distFile + "tempd").c_str()); + remove((phylipFile + "tempPhylipD").c_str()); + } + wait(); + } + wait(); + } + wait(); + +#else + driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile + "tempPhylipA", cutoff); + appendFiles((phylipFile + "tempPhylipA"), phylipFile); + remove((phylipFile + "tempPhylipA").c_str()); +#endif + delete distCalculator; - + return 0; - + } catch(exception& e) { cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; @@ -190,36 +314,44 @@ int DistanceCommand::execute(){ /**************************************************************************************************/ /////// need to fix to work with calcs and sequencedb -int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLine, int endLine, string dFileName, float cutoff){ +int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLine, int endLine, string dFileName, string pFilename, float cutoff){ try { int startTime = time(NULL); - + + //column file ofstream distFile(dFileName.c_str(), ios::trunc); distFile.setf(ios::fixed, ios::showpoint); distFile << setprecision(4); - - for(int i=startLine;iget(i).getUnaligned() << " " << align->get(j).getUnaligned() << endl; -//cout << "aligned" << endl; -//cout << align->get(i).getAligned() << " " << align->get(j).getAligned() << endl; - distCalculator->calcDist(align->get(i), align->get(j)); + distCalculator->calcDist(*(align->get(i)), *(align->get(j))); double dist = distCalculator->getDist(); - + if(dist <= cutoff){ - distFile << align->get(i).getName() << ' ' << align->get(j).getName() << ' ' << dist << endl; + distFile << align->get(i)->getName() << ' ' << align->get(j)->getName() << ' ' << dist << endl; } - + philFile << dist << '\t'; } + + philFile << endl; + if(i % 100 == 0){ cout << i << '\t' << time(NULL) - startTime << endl; } - + } cout << endLine-1 << '\t' << time(NULL) - startTime << endl; - + + //philFile.close(); + //distFile.close(); + return 1; } catch(exception& e) { @@ -230,7 +362,7 @@ int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLi cout << "An unknown error has occurred in the DistanceCommand class function driver. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; exit(1); } - + } /**************************************************************************************************/ @@ -253,7 +385,7 @@ void DistanceCommand::appendFiles(string temp, string filename) { output << line << endl; // Appending back newline char } } - + input.close(); output.close(); }