X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clustercommand.cpp;h=94129654e1d2b11275e82d3a5da0382b1448efa9;hp=4db95b45d00e3857513606383f05810f31a30ecd;hb=615301e57c25e241356a9c2380648d117709458d;hpb=753dc84cf289b1d5dc0ca5b0c043640927aa951a diff --git a/clustercommand.cpp b/clustercommand.cpp index 4db95b4..9412965 100644 --- a/clustercommand.cpp +++ b/clustercommand.cpp @@ -8,142 +8,399 @@ */ #include "clustercommand.h" +#include "readphylip.h" +#include "readcolumn.h" +#include "readmatrix.hpp" +#include "clusterdoturcommand.h" + +//********************************************************************************************************************** +vector ClusterCommand::setParameters(){ + try { + CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","list",false,false,true); parameters.push_back(pphylip); + CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","rabund-sabund",false,false,true); parameters.push_back(pname); + CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pcount); + CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName","list",false,false,true); parameters.push_back(pcolumn); + CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pcutoff); + CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision); + CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "","",false,false,true); parameters.push_back(pmethod); + CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshowabund); + CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming); + CommandParameter psim("sim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psim); + CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + //CommandParameter padjust("adjust", "String", "", "F", "", "", "","",false,false); parameters.push_back(padjust); + 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); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ClusterCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string ClusterCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The cluster command parameter options are phylip, column, name, count, method, cuttoff, hard, precision, sim, showabund and timing. Phylip or column and name are required, unless you have a valid current file.\n"; + //helpString += "The adjust parameter is used to handle missing distances. If you set a cutoff, adjust=f by default. If not, adjust=t by default. Adjust=f, means ignore missing distances and adjust cutoff as needed with the average neighbor method. Adjust=t, will treat missing distances as 1.0. You can also set the value the missing distances should be set to, adjust=0.5 would give missing distances a value of 0.5.\n"; + helpString += "The cluster command should be in the following format: \n"; + helpString += "cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n"; + helpString += "The acceptable cluster methods are furthest, nearest, average and weighted. If no method is provided then average is assumed.\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "ClusterCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +string ClusterCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "list") { pattern = "[filename],[clustertag],list-[filename],[clustertag],[tag2],list"; } + else if (type == "rabund") { pattern = "[filename],[clustertag],rabund"; } + else if (type == "sabund") { pattern = "[filename],[clustertag],sabund"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "ClusterCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** +ClusterCommand::ClusterCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["list"] = tempOutNames; + outputTypes["rabund"] = tempOutNames; + outputTypes["sabund"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ClusterCommand", "ClusterCommand"); + exit(1); + } +} //********************************************************************************************************************** //This function checks to make sure the cluster command has no errors and then clusters based on the method chosen. -ClusterCommand::ClusterCommand(string option){ +ClusterCommand::ClusterCommand(string option) { try{ - globaldata = GlobalData::getInstance(); - abort = false; + abort = false; calledHelp = false; //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string Array[] = {"cutoff","precision","method"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); + map::iterator it; ValidParameters validParameter; //check to make sure all parameters are valid for command - for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { - if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + for (it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { + abort = true; + } } - //error checking to make sure they read a distance file - if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) { - cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl; abort = true; - } + //initialize outputTypes + vector tempOutNames; + outputTypes["list"] = tempOutNames; + outputTypes["rabund"] = tempOutNames; + outputTypes["sabund"] = tempOutNames; + //if the user changes the output directory command factory will send this info to us in the output parameter + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; } + + string inputDir = validParameter.validFile(parameters, "inputdir", false); + if (inputDir == "not found"){ inputDir = ""; } + else { + string path; + it = parameters.find("phylip"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["phylip"] = inputDir + it->second; } + } + + it = parameters.find("column"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["column"] = inputDir + it->second; } + } + + it = parameters.find("name"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["name"] = inputDir + it->second; } + } + + it = parameters.find("count"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["count"] = inputDir + it->second; } + } + } + + //check for required parameters + phylipfile = validParameter.validFile(parameters, "phylip", true); + if (phylipfile == "not open") { phylipfile = ""; abort = true; } + else if (phylipfile == "not found") { phylipfile = ""; } + else { distfile = phylipfile; format = "phylip"; m->setPhylipFile(phylipfile); } + + columnfile = validParameter.validFile(parameters, "column", true); + if (columnfile == "not open") { columnfile = ""; abort = true; } + else if (columnfile == "not found") { columnfile = ""; } + else { distfile = columnfile; format = "column"; m->setColumnFile(columnfile); } + + namefile = validParameter.validFile(parameters, "name", true); + if (namefile == "not open") { abort = true; } + else if (namefile == "not found") { namefile = ""; } + else { m->setNameFile(namefile); } + + countfile = validParameter.validFile(parameters, "count", true); + if (countfile == "not open") { abort = true; countfile = ""; } + else if (countfile == "not found") { countfile = ""; } + else { m->setCountTableFile(countfile); } + + if ((phylipfile == "") && (columnfile == "")) { + //is there are current file available for either of these? + //give priority to column, then phylip + columnfile = m->getColumnFile(); + if (columnfile != "") { distfile = columnfile; format = "column"; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); } + else { + phylipfile = m->getPhylipFile(); + if (phylipfile != "") { distfile = phylipfile; format = "phylip"; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("No valid current files. You must provide a phylip or column file before you can use the cluster command."); m->mothurOutEndLine(); + abort = true; + } + } + } + else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a cluster command you must enter ONLY ONE of the following: phylip or column."); m->mothurOutEndLine(); abort = true; } + + if (columnfile != "") { + if ((namefile == "") && (countfile == "")){ + namefile = m->getNameFile(); + if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); } + else { + countfile = m->getCountTableFile(); + if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("You need to provide a namefile or countfile if you are going to use the column format."); m->mothurOutEndLine(); + abort = true; + } + } + } + } + + if ((countfile != "") && (namefile != "")) { m->mothurOut("When executing a cluster command you must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; } + //check for optional parameter and set defaults // ...at some point should added some additional type checking... //get user cutoff and precision or use defaults string temp; - temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; } + temp = validParameter.validFile(parameters, "precision", false); + if (temp == "not found") { temp = "100"; } //saves precision legnth for formatting below length = temp.length(); - convert(temp, precision); - - temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; } - convert(temp, cutoff); - cutoff += (5 / (precision * 10.0)); - - method = validParameter.validFile(parameters, "method", false); if (method == "not found") { method = "furthest"; } - + m->mothurConvert(temp, precision); - if ((method == "furthest") || (method == "nearest") || (method == "average")) { } - else {cout << "Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average." << endl; abort = true; } - + temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "T"; } + hard = m->isTrue(temp); - if (abort == false) { + temp = validParameter.validFile(parameters, "sim", false); if (temp == "not found") { temp = "F"; } + sim = m->isTrue(temp); - //get matrix, list and rabund for execute - if(globaldata->gSparseMatrix != NULL) { matrix = globaldata->gSparseMatrix; } + //bool cutoffSet = false; + temp = validParameter.validFile(parameters, "cutoff", false); + if (temp == "not found") { temp = "10"; } + //else { cutoffSet = true; } + m->mothurConvert(temp, cutoff); + cutoff += (5 / (precision * 10.0)); + + //temp = validParameter.validFile(parameters, "adjust", false); if (temp == "not found") { temp = "F"; } + //if (m->isNumeric1(temp)) { m->mothurConvert(temp, adjust); } + //else if (m->isTrue(temp)) { adjust = 1.0; } + //else { adjust = -1.0; } + adjust=-1.0; - if(globaldata->gListVector != NULL){ - list = globaldata->gListVector; - rabund = new RAbundVector(list->getRAbundVector()); - } - - //create cluster - if(method == "furthest") { cluster = new CompleteLinkage(rabund, list, matrix); tag = "fn"; } - else if(method == "nearest"){ cluster = new SingleLinkage(rabund, list, matrix); tag = "nn"; } - else if(method == "average"){ cluster = new AverageLinkage(rabund, list, matrix); tag = "an"; } - else { cout << "error - not recognized method" << endl; abort = true; } - - fileroot = getRootName(globaldata->inputFileName); + method = validParameter.validFile(parameters, "method", false); + if (method == "not found") { method = "average"; } - openOutputFile(fileroot+ tag + ".sabund", sabundFile); - openOutputFile(fileroot+ tag + ".rabund", rabundFile); - openOutputFile(fileroot+ tag + ".list", listFile); - - - } + if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) { } + else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest, average, and weighted."); m->mothurOutEndLine(); abort = true; } - } - - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ClusterCommand class Function ClusterCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ClusterCommand class function ClusterCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } -} + showabund = validParameter.validFile(parameters, "showabund", false); + if (showabund == "not found") { showabund = "T"; } -//********************************************************************************************************************** - -void ClusterCommand::help(){ - try { - cout << "The cluster command can only be executed after a successful read.dist command." << "\n"; - cout << "The cluster command parameter options are method, cuttoff and precision. No parameters are required." << "\n"; - cout << "The cluster command should be in the following format: " << "\n"; - cout << "cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) " << "\n"; - cout << "The acceptable cluster methods are furthest, nearest and average. If no method is provided then furthest is assumed." << "\n" << "\n"; + timing = validParameter.validFile(parameters, "timing", false); + if (timing == "not found") { timing = "F"; } + + } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ClusterCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ClusterCommand", "ClusterCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the ClusterCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } - //********************************************************************************************************************** - -ClusterCommand::~ClusterCommand(){ - delete cluster; - delete rabund; -} - +ClusterCommand::~ClusterCommand(){} //********************************************************************************************************************** int ClusterCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + //phylip file given and cutoff not given - use cluster.classic because it uses less memory and is faster + if ((format == "phylip") && (cutoff > 10.0)) { + m->mothurOutEndLine(); m->mothurOut("You are using a phylip file and no cutoff. I will run cluster.classic to save memory and time."); m->mothurOutEndLine(); + + //run unique.seqs for deconvolute results + string inputString = "phylip=" + distfile; + if (namefile != "") { inputString += ", name=" + namefile; } + else if (countfile != "") { inputString += ", count=" + countfile; } + inputString += ", precision=" + toString(precision); + inputString += ", method=" + method; + if (hard) { inputString += ", hard=T"; } + else { inputString += ", hard=F"; } + if (sim) { inputString += ", sim=T"; } + else { inputString += ", sim=F"; } + + + m->mothurOutEndLine(); + m->mothurOut("/------------------------------------------------------------/"); m->mothurOutEndLine(); + m->mothurOut("Running command: cluster.classic(" + inputString + ")"); m->mothurOutEndLine(); + + Command* clusterClassicCommand = new ClusterDoturCommand(inputString); + clusterClassicCommand->execute(); + delete clusterClassicCommand; + + m->mothurOut("/------------------------------------------------------------/"); m->mothurOutEndLine(); + + return 0; + } + + ReadMatrix* read; + if (format == "column") { read = new ReadColumnMatrix(columnfile, sim); } //sim indicates whether its a similarity matrix + else if (format == "phylip") { read = new ReadPhylipMatrix(phylipfile, sim); } + + read->setCutoff(cutoff); + + NameAssignment* nameMap = NULL; + CountTable* ct = NULL; + if(namefile != ""){ + nameMap = new NameAssignment(namefile); + nameMap->readMap(); + read->read(nameMap); + }else if (countfile != "") { + ct = new CountTable(); + ct->readTable(countfile, false); + read->read(ct); + }else { read->read(nameMap); } + + list = read->getListVector(); + matrix = read->getDMatrix(); + + if(countfile != "") { + rabund = new RAbundVector(); + createRabund(ct, list, rabund); //creates an rabund that includes the counts for the unique list + delete ct; + }else { rabund = new RAbundVector(list->getRAbundVector()); } + delete read; + + if (m->control_pressed) { //clean up + delete list; delete matrix; delete rabund; if(countfile == ""){rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } + listFile.close(); m->mothurRemove((fileroot+ tag + ".list")); outputTypes.clear(); return 0; + } + //create cluster + if (method == "furthest") { cluster = new CompleteLinkage(rabund, list, matrix, cutoff, method, adjust); } + else if(method == "nearest"){ cluster = new SingleLinkage(rabund, list, matrix, cutoff, method, adjust); } + else if(method == "average"){ cluster = new AverageLinkage(rabund, list, matrix, cutoff, method, adjust); } + else if(method == "weighted"){ cluster = new WeightedLinkage(rabund, list, matrix, cutoff, method, adjust); } + tag = cluster->getTag(); + + if (outputDir == "") { outputDir += m->hasPath(distfile); } + fileroot = outputDir + m->getRootName(m->getSimpleName(distfile)); + + map variables; + variables["[filename]"] = fileroot; + variables["[clustertag]"] = tag; + string sabundFileName = getOutputFileName("sabund", variables); + string rabundFileName = getOutputFileName("rabund", variables); + if (countfile != "") { variables["[tag2]"] = "unique_list"; } + string listFileName = getOutputFileName("list", variables); + + if (countfile == "") { + m->openOutputFile(sabundFileName, sabundFile); + m->openOutputFile(rabundFileName, rabundFile); + outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName); + outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName); + + } + m->openOutputFile(listFileName, listFile); + outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName); + + + time_t estart = time(NULL); float previousDist = 0.00000; float rndPreviousDist = 0.00000; oldRAbund = *rabund; oldList = *list; + + print_start = true; + start = time(NULL); + loops = 0; + double saveCutoff = cutoff; - float x; - x=0.1; - toString(x, 2); - - while(matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){ - cluster->update(); - float dist = matrix->getSmallDist(); - float rndDist = roundDist(dist, precision); + while (matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){ + + if (m->control_pressed) { //clean up + delete list; delete matrix; delete rabund; delete cluster; + if(countfile == "") {rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } + listFile.close(); m->mothurRemove((fileroot+ tag + ".list")); outputTypes.clear(); return 0; + } + + if (print_start && m->isTrue(timing)) { + m->mothurOut("Clustering (" + tag + ") dist " + toString(matrix->getSmallDist()) + "/" + + toString(m->roundDist(matrix->getSmallDist(), precision)) + + "\t(precision: " + toString(precision) + ", Nodes: " + toString(matrix->getNNodes()) + ")"); + cout.flush(); + print_start = false; + } + + loops++; + + cluster->update(cutoff); + + float dist = matrix->getSmallDist(); + float rndDist; + if (hard) { + rndDist = m->ceilDist(dist, precision); + }else{ + rndDist = m->roundDist(dist, precision); + } if(previousDist <= 0.0000 && dist != previousDist){ printData("unique"); @@ -157,7 +414,14 @@ int ClusterCommand::execute(){ oldRAbund = *rabund; oldList = *list; } - + + if (print_start && m->isTrue(timing)) { + m->mothurOut("Clustering (" + tag + ") for distance " + toString(previousDist) + "/" + toString(rndPreviousDist) + + "\t(precision: " + toString(precision) + ", Nodes: " + toString(matrix->getNNodes()) + ")"); + cout.flush(); + print_start = false; + } + if(previousDist <= 0.0000){ printData("unique"); } @@ -165,51 +429,113 @@ int ClusterCommand::execute(){ printData(toString(rndPreviousDist, length-1)); } - //delete globaldata's copy of the sparsematrix and listvector to free up memory - delete globaldata->gSparseMatrix; globaldata->gSparseMatrix = NULL; - delete globaldata->gListVector; globaldata->gListVector = NULL; + delete matrix; + delete list; + delete rabund; + delete cluster; + if (countfile == "") { + sabundFile.close(); + rabundFile.close(); + } + listFile.close(); + + if (saveCutoff != cutoff) { + if (hard) { saveCutoff = m->ceilDist(saveCutoff, precision); } + else { saveCutoff = m->roundDist(saveCutoff, precision); } + + m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine(); + } + + //set list file as new current listfile + string current = ""; + itTypes = outputTypes.find("list"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); } + } + + //set rabund file as new current rabundfile + itTypes = outputTypes.find("rabund"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); } + } + + //set sabund file as new current sabundfile + itTypes = outputTypes.find("sabund"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); } + } + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + m->mothurOutEndLine(); + - //saves .list file so you can do the collect, rarefaction and summary commands without doing a read.list - if (globaldata->getFormat() == "phylip") { globaldata->setPhylipFile(""); } - else if (globaldata->getFormat() == "column") { globaldata->setColumnFile(""); } + //if (m->isTrue(timing)) { + m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster"); m->mothurOutEndLine(); + //} - globaldata->setListFile(fileroot+ tag + ".list"); - globaldata->setNameFile(""); - globaldata->setFormat("list"); return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ClusterCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ClusterCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ClusterCommand", "execute"); exit(1); } - } //********************************************************************************************************************** void ClusterCommand::printData(string label){ try { - oldRAbund.setLabel(label); - oldRAbund.getSAbundVector().print(cout); - oldRAbund.print(rabundFile); - oldRAbund.getSAbundVector().print(sabundFile); - + if (m->isTrue(timing)) { + m->mothurOut("\tTime: " + toString(time(NULL) - start) + "\tsecs for " + toString(oldRAbund.getNumBins()) + + "\tclusters. Updates: " + toString(loops)); m->mothurOutEndLine(); + } + print_start = true; + loops = 0; + start = time(NULL); + + oldRAbund.setLabel(label); + if (countfile == "") { + oldRAbund.print(rabundFile); + oldRAbund.getSAbundVector().print(sabundFile); + } + + if (m->isTrue(showabund)) { + oldRAbund.getSAbundVector().print(cout); + } + oldList.setLabel(label); oldList.print(listFile); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ClusterCommand class Function printData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ClusterCommand", "printData"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the ClusterCommand class function printData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + + +} +//********************************************************************************************************************** + +int ClusterCommand::createRabund(CountTable*& ct, ListVector*& list, RAbundVector*& rabund){ + try { + rabund->setLabel(list->getLabel()); + for(int i = 0; i < list->getNumBins(); i++) { + if (m->control_pressed) { break; } + vector binNames; + string bin = list->get(i); + m->splitAtComma(bin, binNames); + int total = 0; + for (int j = 0; j < binNames.size(); j++) { total += ct->getNumSeqs(binNames[j]); } + rabund->push_back(total); + } + return 0; + } + catch(exception& e) { + m->errorOut(e, "ClusterCommand", "createRabund"); exit(1); } - + } //**********************************************************************************************************************