X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=summarysharedcommand.cpp;h=59c12a03dae958f4bb199a6aad94056264c0426a;hp=7116e46e0f9e96045fc3c60a717ae41819949118;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=0ca63a8165baa0afa459e644ebe140ba496d5ba0 diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp index 7116e46..59c12a0 100644 --- a/summarysharedcommand.cpp +++ b/summarysharedcommand.cpp @@ -8,60 +8,23 @@ */ #include "summarysharedcommand.h" -#include "sharedsobscollectsummary.h" -#include "sharedchao1.h" -#include "sharedace.h" -#include "sharednseqs.h" -#include "sharedjabund.h" -#include "sharedsorabund.h" -#include "sharedjclass.h" -#include "sharedsorclass.h" -#include "sharedjest.h" -#include "sharedsorest.h" -#include "sharedthetayc.h" -#include "sharedthetan.h" -#include "sharedkstest.h" -#include "whittaker.h" -#include "sharedochiai.h" -#include "sharedanderbergs.h" -#include "sharedkulczynski.h" -#include "sharedkulczynskicody.h" -#include "sharedlennon.h" -#include "sharedmorisitahorn.h" -#include "sharedbraycurtis.h" -#include "sharedjackknife.h" -#include "whittaker.h" -#include "odum.h" -#include "canberra.h" -#include "structeuclidean.h" -#include "structchord.h" -#include "hellinger.h" -#include "manhattan.h" -#include "structpearson.h" -#include "soergel.h" -#include "spearman.h" -#include "structkulczynski.h" -#include "structchi2.h" -#include "speciesprofile.h" -#include "hamming.h" -#include "gower.h" -#include "memchi2.h" -#include "memchord.h" -#include "memeuclidean.h" -#include "mempearson.h" +#include "subsample.h" //********************************************************************************************************************** vector SummarySharedCommand::setParameters(){ try { - CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared); - CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); - CommandParameter pdistance("distance", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pdistance); - CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "",true,false); parameters.push_back(pcalc); - CommandParameter pall("all", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pall); - CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); - CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pshared); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter psubsample("subsample", "String", "", "", "", "", "","phylip",false,false); parameters.push_back(psubsample); + CommandParameter pdistance("distance", "Boolean", "", "F", "", "", "","phylip",false,false); parameters.push_back(pdistance); + CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson-jsd-rjsd", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "","",true,false,true); parameters.push_back(pcalc); + CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "","",false,false); parameters.push_back(poutput); + CommandParameter pall("all", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pall); + CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); + CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); vector myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -77,11 +40,14 @@ string SummarySharedCommand::getHelpString(){ try { string helpString = ""; ValidCalculators validCalculator; - helpString += "The summary.shared command parameters are shared, label, calc, distance, processors and all. shared is required if there is no current sharedfile.\n"; + helpString += "The summary.shared command parameters are shared, label, calc, distance, processors, subsample, iters and all. shared is required if there is no current sharedfile.\n"; helpString += "The summary.shared command should be in the following format: \n"; helpString += "summary.shared(label=yourLabel, calc=yourEstimators, groups=yourGroups).\n"; helpString += "Example summary.shared(label=unique-.01-.03, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n"; helpString += validCalculator.printCalc("sharedsummary"); + helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n"; + helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group.\n"; + helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n"; helpString += "The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n"; helpString += "The default value for groups is all the groups in your groupfile.\n"; helpString += "The distance parameter allows you to indicate you would like a distance file created for each calculator for each label, default=f.\n"; @@ -98,12 +64,29 @@ string SummarySharedCommand::getHelpString(){ } } //********************************************************************************************************************** +string SummarySharedCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "summary") { pattern = "[filename],summary-[filename],[tag],summary"; } + else if (type == "phylip") { pattern = "[filename],[calc],[distance],[outputtag],[tag2],dist"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "SummarySharedCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** SummarySharedCommand::SummarySharedCommand(){ try { abort = true; calledHelp = true; setParameters(); vector tempOutNames; outputTypes["summary"] = tempOutNames; + outputTypes["phylip"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "SummarySharedCommand", "SummarySharedCommand"); @@ -138,6 +121,7 @@ SummarySharedCommand::SummarySharedCommand(string option) { //initialize outputTypes vector tempOutNames; outputTypes["summary"] = tempOutNames; + outputTypes["phylip"] = tempOutNames; //if the user changes the input directory command factory will send this info to us in the output parameter string inputDir = validParameter.validFile(parameters, "inputdir", false); @@ -200,9 +184,27 @@ SummarySharedCommand::SummarySharedCommand(string option) { string temp = validParameter.validFile(parameters, "all", false); if (temp == "not found") { temp = "false"; } all = m->isTrue(temp); - temp = validParameter.validFile(parameters, "distance", false); if (temp == "not found") { temp = "false"; } + temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } + m->mothurConvert(temp, iters); + + output = validParameter.validFile(parameters, "output", false); + if(output == "not found"){ output = "lt"; } + else { createPhylip = true; } + if ((output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are lt and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; } + + temp = validParameter.validFile(parameters, "subsample", false); if (temp == "not found") { temp = "F"; } + if (m->isNumeric1(temp)) { m->mothurConvert(temp, subsampleSize); subsample = true; } + else { + if (m->isTrue(temp)) { subsample = true; subsampleSize = -1; } //we will set it to smallest group later + else { subsample = false; } + } + + if (subsample == false) { iters = 0; } + + temp = validParameter.validFile(parameters, "distance", false); if (temp == "not found") { temp = "false"; } createPhylip = m->isTrue(temp); - + if (subsample) { createPhylip = true; } + temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } m->setProcessors(temp); m->mothurConvert(temp, processors); @@ -292,6 +294,10 @@ SummarySharedCommand::SummarySharedCommand(string option) { sumCalculators.push_back(new MemEuclidean()); }else if (Estimators[i] == "mempearson") { sumCalculators.push_back(new MemPearson()); + }else if (Estimators[i] == "jsd") { + sumCalculators.push_back(new JSD()); + }else if (Estimators[i] == "rjsd") { + sumCalculators.push_back(new RJSD()); } } } @@ -313,7 +319,9 @@ int SummarySharedCommand::execute(){ if (abort == true) { if (calledHelp) { return 0; } return 2; } ofstream outputFileHandle, outAll; - string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "shared.summary"; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)); + string outputFileName = getOutputFileName("summary",variables); //if the users entered no valid calculators don't execute command if (sumCalculators.size() == 0) { return 0; } @@ -344,7 +352,8 @@ int SummarySharedCommand::execute(){ outputFileHandle.close(); //create file and put column headers for multiple groups file - string outAllFileName = ((m->getRootName(sharedfile)) + "sharedmultiple.summary"); + variables["[tag]"]= "multiple"; + string outAllFileName = getOutputFileName("summary",variables); if (mult == true) { m->openOutputFile(outAllFileName, outAll); outputNames.push_back(outAllFileName); @@ -384,11 +393,38 @@ int SummarySharedCommand::execute(){ return 0; } /******************************************************/ - + if (subsample) { + if (subsampleSize == -1) { //user has not set size, set size = smallest samples size + subsampleSize = lookup[0]->getNumSeqs(); + for (int i = 1; i < lookup.size(); i++) { + int thisSize = lookup[i]->getNumSeqs(); + + if (thisSize < subsampleSize) { subsampleSize = thisSize; } + } + }else { + m->clearGroups(); + Groups.clear(); + vector temp; + for (int i = 0; i < lookup.size(); i++) { + if (lookup[i]->getNumSeqs() < subsampleSize) { + m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine(); + delete lookup[i]; + }else { + Groups.push_back(lookup[i]->getGroup()); + temp.push_back(lookup[i]); + } + } + lookup = temp; + m->setGroups(Groups); + } + + if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; delete input; return 0; } + } + /******************************************************/ //comparison breakup to be used by different processes later - numGroups = m->getNumGroups(); + numGroups = lookup.size(); lines.resize(processors); for (int i = 0; i < processors; i++) { lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups); @@ -504,157 +540,343 @@ int SummarySharedCommand::execute(){ exit(1); } } - /***********************************************************/ -int SummarySharedCommand::process(vector thisLookup, string sumFileName, string sumAllFileName) { +int SummarySharedCommand::printSims(ostream& out, vector< vector >& simMatrix) { try { - vector< vector > calcDists; //vector containing vectors that contains the summary results for each group compare - calcDists.resize(sumCalculators.size()); //one for each calc, this will be used to make .dist files - - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - if(processors == 1){ - driver(thisLookup, 0, numGroups, sumFileName+".temp", sumAllFileName+".temp", calcDists); - m->appendFiles((sumFileName + ".temp"), sumFileName); - m->mothurRemove((sumFileName + ".temp")); - if (mult) { - m->appendFiles((sumAllFileName + ".temp"), sumAllFileName); - m->mothurRemove((sumAllFileName + ".temp")); - } - }else{ - int process = 1; - vector processIDS; - //loop through and create all the processes you want - while (process != processors) { - int pid = fork(); - - if (pid > 0) { - processIDS.push_back(pid); - process++; - }else if (pid == 0){ - driver(thisLookup, lines[process].start, lines[process].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists); - - //only do this if you want a distance file - if (createPhylip) { - string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(getpid()) + ".dist"; - ofstream outtemp; - m->openOutputFile(tempdistFileName, outtemp); - - for (int i = 0; i < calcDists.size(); i++) { - outtemp << calcDists[i].size() << endl; - - for (int j = 0; j < calcDists[i].size(); j++) { - outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl; - } - } - outtemp.close(); - } - - exit(0); - }else { - m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); - for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); } - exit(0); - } - } - - //parent do your part - driver(thisLookup, lines[0].start, lines[0].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists); - m->appendFiles((sumFileName + toString(getpid()) + ".temp"), sumFileName); - m->mothurRemove((sumFileName + toString(getpid()) + ".temp")); - if (mult) { m->appendFiles((sumAllFileName + toString(getpid()) + ".temp"), sumAllFileName); } - - //force parent to wait until all the processes are done - for (int i = 0; i < processIDS.size(); i++) { - int temp = processIDS[i]; - wait(&temp); - } - - for (int i = 0; i < processIDS.size(); i++) { - m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName); - m->mothurRemove((sumFileName + toString(processIDS[i]) + ".temp")); - if (mult) { m->mothurRemove((sumAllFileName + toString(processIDS[i]) + ".temp")); } - - if (createPhylip) { - string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(processIDS[i]) + ".dist"; - ifstream intemp; - m->openInputFile(tempdistFileName, intemp); - - for (int k = 0; k < calcDists.size(); k++) { - int size = 0; - intemp >> size; m->gobble(intemp); - - for (int j = 0; j < size; j++) { - int seq1 = 0; - int seq2 = 0; - float dist = 1.0; - - intemp >> seq1 >> seq2 >> dist; m->gobble(intemp); - - seqDist tempDist(seq1, seq2, dist); - calcDists[k].push_back(tempDist); - } - } - intemp.close(); - m->mothurRemove(tempdistFileName); - } - } - - } - #else - driver(thisLookup, 0, numGroups, (sumFileName + ".temp"), (sumAllFileName + ".temp"), calcDists); - m->appendFiles((sumFileName + ".temp"), sumFileName); - m->mothurRemove((sumFileName + ".temp")); - if (mult) { - m->appendFiles((sumAllFileName + ".temp"), sumAllFileName); - m->mothurRemove((sumAllFileName + ".temp")); + out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); + + //output num seqs + out << simMatrix.size() << endl; + + if (output == "lt") { + for (int b = 0; b < simMatrix.size(); b++) { + out << lookup[b]->getGroup() << '\t'; + for (int n = 0; n < b; n++) { + if (m->control_pressed) { return 0; } + out << simMatrix[b][n] << '\t'; } - #endif - - if (createPhylip) { - for (int i = 0; i < calcDists.size(); i++) { - if (m->control_pressed) { break; } - - string distFileName = outputDir + m->getRootName(m->getSimpleName(sumFileName)) + sumCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist"; - outputNames.push_back(distFileName); - ofstream outDist; - m->openOutputFile(distFileName, outDist); - outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint); - - //initialize matrix - vector< vector > matrix; //square matrix to represent the distance - matrix.resize(thisLookup.size()); - for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); } - - - for (int j = 0; j < calcDists[i].size(); j++) { - int row = calcDists[i][j].seq1; - int column = calcDists[i][j].seq2; - float dist = calcDists[i][j].dist; - - matrix[row][column] = dist; - matrix[column][row] = dist; - } - - //output to file - outDist << thisLookup.size() << endl; - for (int r=0; rgetGroup(); - if (name.length() < 10) { //pad with spaces to make compatible - while (name.length() < 10) { name += " "; } - } - outDist << name << '\t'; - - //output distances - for (int l = 0; l < r; l++) { outDist << matrix[r][l] << '\t'; } - outDist << endl; - } - - outDist.close(); + out << endl; + } + }else{ + for (int b = 0; b < simMatrix.size(); m++) { + out << lookup[b]->getGroup() << '\t'; + for (int n = 0; n < simMatrix[b].size(); n++) { + if (m->control_pressed) { return 0; } + out << simMatrix[b][n] << '\t'; } + out << endl; } - return 0; + } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "SummarySharedCommand", "printSims"); + exit(1); + } +} +/***********************************************************/ +int SummarySharedCommand::process(vector thisLookup, string sumFileName, string sumAllFileName) { + try { + vector< vector< vector > > calcDistsTotals; //each iter, one for each calc, then each groupCombos dists. this will be used to make .dist files + vector< vector > calcDists; calcDists.resize(sumCalculators.size()); + + for (int thisIter = 0; thisIter < iters+1; thisIter++) { + + vector thisItersLookup = thisLookup; + + if (subsample && (thisIter != 0)) { //we want the summary results for the whole dataset, then the subsampling + SubSample sample; + vector tempLabels; //dont need since we arent printing the sampled sharedRabunds + + //make copy of lookup so we don't get access violations + vector newLookup; + for (int k = 0; k < thisItersLookup.size(); k++) { + SharedRAbundVector* temp = new SharedRAbundVector(); + temp->setLabel(thisItersLookup[k]->getLabel()); + temp->setGroup(thisItersLookup[k]->getGroup()); + newLookup.push_back(temp); + } + + //for each bin + for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) { + if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; } + for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); } + } + + tempLabels = sample.getSample(newLookup, subsampleSize); + thisItersLookup = newLookup; + } + + + if(processors == 1){ + driver(thisLookup, 0, numGroups, sumFileName+".temp", sumAllFileName+".temp", calcDists); + m->appendFiles((sumFileName + ".temp"), sumFileName); + m->mothurRemove((sumFileName + ".temp")); + if (mult) { + m->appendFiles((sumAllFileName + ".temp"), sumAllFileName); + m->mothurRemove((sumAllFileName + ".temp")); + } + }else{ + + int process = 1; + vector processIDS; + +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + //loop through and create all the processes you want + while (process != processors) { + int pid = fork(); + + if (pid > 0) { + processIDS.push_back(pid); + process++; + }else if (pid == 0){ + driver(thisLookup, lines[process].start, lines[process].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists); + + //only do this if you want a distance file + if (createPhylip) { + string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(getpid()) + ".dist"; + ofstream outtemp; + m->openOutputFile(tempdistFileName, outtemp); + + for (int i = 0; i < calcDists.size(); i++) { + outtemp << calcDists[i].size() << endl; + + for (int j = 0; j < calcDists[i].size(); j++) { + outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl; + } + } + outtemp.close(); + } + + exit(0); + }else { + m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); + for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); } + exit(0); + } + } + + //parent do your part + driver(thisLookup, lines[0].start, lines[0].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists); + m->appendFiles((sumFileName + toString(getpid()) + ".temp"), sumFileName); + m->mothurRemove((sumFileName + toString(getpid()) + ".temp")); + if (mult) { m->appendFiles((sumAllFileName + toString(getpid()) + ".temp"), sumAllFileName); } + + //force parent to wait until all the processes are done + for (int i = 0; i < processIDS.size(); i++) { + int temp = processIDS[i]; + wait(&temp); + } + + for (int i = 0; i < processIDS.size(); i++) { + m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName); + m->mothurRemove((sumFileName + toString(processIDS[i]) + ".temp")); + if (mult) { m->mothurRemove((sumAllFileName + toString(processIDS[i]) + ".temp")); } + + if (createPhylip) { + string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(processIDS[i]) + ".dist"; + ifstream intemp; + m->openInputFile(tempdistFileName, intemp); + + for (int k = 0; k < calcDists.size(); k++) { + int size = 0; + intemp >> size; m->gobble(intemp); + + for (int j = 0; j < size; j++) { + int seq1 = 0; + int seq2 = 0; + float dist = 1.0; + + intemp >> seq1 >> seq2 >> dist; m->gobble(intemp); + + seqDist tempDist(seq1, seq2, dist); + calcDists[k].push_back(tempDist); + } + } + intemp.close(); + m->mothurRemove(tempdistFileName); + } + } +#else + ////////////////////////////////////////////////////////////////////////////////////////////////////// + //Windows version shared memory, so be careful when passing variables through the summarySharedData struct. + //Above fork() will clone, so memory is separate, but that's not the case with windows, + //Taking advantage of shared memory to pass results vectors. + ////////////////////////////////////////////////////////////////////////////////////////////////////// + + vector pDataArray; + DWORD dwThreadIdArray[processors-1]; + HANDLE hThreadArray[processors-1]; + + //Create processor worker threads. + for( int i=1; i newLookup; + for (int k = 0; k < thisLookup.size(); k++) { + SharedRAbundVector* temp = new SharedRAbundVector(); + temp->setLabel(thisLookup[k]->getLabel()); + temp->setGroup(thisLookup[k]->getGroup()); + newLookup.push_back(temp); + } + + + //for each bin + for (int k = 0; k < thisLookup[0]->getNumBins(); k++) { + if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; } + for (int j = 0; j < thisLookup.size(); j++) { newLookup[j]->push_back(thisLookup[j]->getAbundance(k), thisLookup[j]->getGroup()); } + } + + // Allocate memory for thread data. + summarySharedData* tempSum = new summarySharedData((sumFileName+toString(i)+".temp"), m, lines[i].start, lines[i].end, Estimators, newLookup); + pDataArray.push_back(tempSum); + processIDS.push_back(i); + + hThreadArray[i-1] = CreateThread(NULL, 0, MySummarySharedThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]); + } + + //parent do your part + driver(thisLookup, lines[0].start, lines[0].end, sumFileName +"0.temp", sumAllFileName + "0.temp", calcDists); + m->appendFiles((sumFileName + "0.temp"), sumFileName); + m->mothurRemove((sumFileName + "0.temp")); + if (mult) { m->appendFiles((sumAllFileName + "0.temp"), sumAllFileName); } + + //Wait until all threads have terminated. + WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE); + + //Close all thread handles and free memory allocations. + for(int i=0; i < pDataArray.size(); i++){ + if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) { + m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " groups assigned to it, quitting. \n"); m->control_pressed = true; + } + m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName); + m->mothurRemove((sumFileName + toString(processIDS[i]) + ".temp")); + + for (int j = 0; j < pDataArray[i]->thisLookup.size(); j++) { delete pDataArray[i]->thisLookup[j]; } + + if (createPhylip) { + for (int k = 0; k < calcDists.size(); k++) { + int size = pDataArray[i]->calcDists[k].size(); + for (int j = 0; j < size; j++) { calcDists[k].push_back(pDataArray[i]->calcDists[k][j]); } + } + } + + CloseHandle(hThreadArray[i]); + delete pDataArray[i]; + } + +#endif + } + + if (subsample && (thisIter != 0)) { //we want the summary results for the whole dataset, then the subsampling + + calcDistsTotals.push_back(calcDists); + //clean up memory + for (int i = 0; i < thisItersLookup.size(); i++) { delete thisItersLookup[i]; } + thisItersLookup.clear(); + }else { + if (createPhylip) { + for (int i = 0; i < calcDists.size(); i++) { + if (m->control_pressed) { break; } + + //initialize matrix + vector< vector > matrix; //square matrix to represent the distance + matrix.resize(thisLookup.size()); + for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); } + + for (int j = 0; j < calcDists[i].size(); j++) { + int row = calcDists[i][j].seq1; + int column = calcDists[i][j].seq2; + double dist = calcDists[i][j].dist; + + matrix[row][column] = dist; + matrix[column][row] = dist; + } + + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)); + variables["[calc]"] = sumCalculators[i]->getName(); + variables["[distance]"] = thisLookup[0]->getLabel(); + variables["[outputtag]"] = output; + variables["[tag2]"] = ""; + string distFileName = getOutputFileName("phylip",variables); + outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName); + ofstream outDist; + m->openOutputFile(distFileName, outDist); + outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint); + + printSims(outDist, matrix); + + outDist.close(); + } + } + } + for (int i = 0; i < calcDists.size(); i++) { calcDists[i].clear(); } + } + + if (iters != 0) { + //we need to find the average distance and standard deviation for each groups distance + vector< vector > calcAverages = m->getAverages(calcDistsTotals); + + //find standard deviation + vector< vector > stdDev = m->getStandardDeviation(calcDistsTotals, calcAverages); + + //print results + for (int i = 0; i < calcDists.size(); i++) { + vector< vector > matrix; //square matrix to represent the distance + matrix.resize(thisLookup.size()); + for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); } + + vector< vector > stdmatrix; //square matrix to represent the stdDev + stdmatrix.resize(thisLookup.size()); + for (int k = 0; k < thisLookup.size(); k++) { stdmatrix[k].resize(thisLookup.size(), 0.0); } + + + for (int j = 0; j < calcAverages[i].size(); j++) { + int row = calcAverages[i][j].seq1; + int column = calcAverages[i][j].seq2; + float dist = calcAverages[i][j].dist; + float stdDist = stdDev[i][j].dist; + + matrix[row][column] = dist; + matrix[column][row] = dist; + stdmatrix[row][column] = stdDist; + stdmatrix[column][row] = stdDist; + } + + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)); + variables["[calc]"] = sumCalculators[i]->getName(); + variables["[distance]"] = thisLookup[0]->getLabel(); + variables["[outputtag]"] = output; + variables["[tag2]"] = "ave"; + string distFileName = getOutputFileName("phylip",variables); + outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName); + ofstream outAve; + m->openOutputFile(distFileName, outAve); + outAve.setf(ios::fixed, ios::floatfield); outAve.setf(ios::showpoint); + + printSims(outAve, matrix); + + outAve.close(); + + variables["[tag2]"] = "std"; + distFileName = getOutputFileName("phylip",variables); + outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName); + ofstream outSTD; + m->openOutputFile(distFileName, outSTD); + outSTD.setf(ios::fixed, ios::floatfield); outSTD.setf(ios::showpoint); + + printSims(outSTD, stdmatrix); + + outSTD.close(); + + } + } + + return 0; } catch(exception& e) { m->errorOut(e, "SummarySharedCommand", "process");