X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustercommand.cpp;h=059f277db6856e2b8c360dbb03b1929d7fa39de5;hb=19fcbbdba99658f5eca244803280f9ee7f9f6607;hp=d14af108d69c36f98617fc2e133c3dcfb537c553;hpb=2397df97b12cd5d21ea10dc4248c18a5803ddd41;p=mothur.git diff --git a/clustercommand.cpp b/clustercommand.cpp index d14af10..059f277 100644 --- a/clustercommand.cpp +++ b/clustercommand.cpp @@ -8,43 +8,172 @@ */ #include "clustercommand.h" +#include "readphylip.h" +#include "readcolumn.h" +#include "readmatrix.hpp" +//********************************************************************************************************************** +vector ClusterCommand::setParameters(){ + try { + CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip); + CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname); + CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn); + CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); 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); 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 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, 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 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); + } +} +//********************************************************************************************************************** +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","showabund","timing","outputdir","inputdir"}; - 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++) { + for (it = parameters.begin(); it != parameters.end(); it++) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { 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 = ""; } - //error checking to make sure they read a distance file - if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) { - mothurOut("Before you use the cluster command, you first need to read in a distance matrix."); mothurOutEndLine(); - abort = true; - } - + 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; } + } + } + + //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); } + + 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 == "") { + namefile = m->getNameFile(); + if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("You need to provide a namefile if you are going to use the column format."); 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 @@ -55,16 +184,22 @@ ClusterCommand::ClusterCommand(string option){ length = temp.length(); convert(temp, precision); + temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "T"; } + hard = m->isTrue(temp); + + temp = validParameter.validFile(parameters, "sim", false); if (temp == "not found") { temp = "F"; } + sim = m->isTrue(temp); + temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; } convert(temp, cutoff); - cutoff += (5 / (precision * 10.0)); + cutoff += (5 / (precision * 10.0)); method = validParameter.validFile(parameters, "method", false); - if (method == "not found") { method = "furthest"; } + if (method == "not found") { method = "average"; } - if ((method == "furthest") || (method == "nearest") || (method == "average")) { } - else { mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average."); mothurOutEndLine(); abort = true; } + 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; } showabund = validParameter.validFile(parameters, "showabund", false); if (showabund == "not found") { showabund = "T"; } @@ -72,72 +207,67 @@ ClusterCommand::ClusterCommand(string option){ timing = validParameter.validFile(parameters, "timing", false); if (timing == "not found") { timing = "F"; } - if (abort == false) { - - - //get matrix, list and rabund for execute - if(globaldata->gSparseMatrix != NULL) { matrix = globaldata->gSparseMatrix; } - - if(globaldata->gListVector != NULL){ - list = globaldata->gListVector; - rabund = new RAbundVector(list->getRAbundVector()); - } - - //create cluster - if (method == "furthest") { cluster = new CompleteLinkage(rabund, list, matrix, cutoff, method); } - else if(method == "nearest"){ cluster = new SingleLinkage(rabund, list, matrix, cutoff, method); } - else if(method == "average"){ cluster = new AverageLinkage(rabund, list, matrix, cutoff, method); } - tag = cluster->getTag(); - - if (outputDir == "") { outputDir += hasPath(globaldata->inputFileName); } - fileroot = outputDir + getRootName(getSimpleName(globaldata->inputFileName)); - - openOutputFile(fileroot+ tag + ".sabund", sabundFile); - openOutputFile(fileroot+ tag + ".rabund", rabundFile); - openOutputFile(fileroot+ tag + ".list", listFile); } - } } catch(exception& e) { - errorOut(e, "ClusterCommand", "ClusterCommand"); + m->errorOut(e, "ClusterCommand", "ClusterCommand"); exit(1); } } - //********************************************************************************************************************** - -void ClusterCommand::help(){ - try { - mothurOut("The cluster command can only be executed after a successful read.dist command.\n"); - mothurOut("The cluster command parameter options are method, cuttoff, precision, showabund and timing. No parameters are required.\n"); - mothurOut("The cluster command should be in the following format: \n"); - mothurOut("cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n"); - mothurOut("The acceptable cluster methods are furthest, nearest and average. If no method is provided then furthest is assumed.\n\n"); - } - catch(exception& e) { - errorOut(e, "ClusterCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - -ClusterCommand::~ClusterCommand(){ - if (abort == false) { - delete cluster; - delete rabund; - } -} - +ClusterCommand::~ClusterCommand(){} //********************************************************************************************************************** int ClusterCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + 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; + if(namefile != ""){ + nameMap = new NameAssignment(namefile); + nameMap->readMap(); + } + + read->read(nameMap); + list = read->getListVector(); + matrix = read->getMatrix(); + rabund = new RAbundVector(list->getRAbundVector()); + delete read; + + if (m->control_pressed) { //clean up + delete list; delete matrix; delete rabund; + sabundFile.close();rabundFile.close();listFile.close(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); + return 0; + } + + //create cluster + if (method == "furthest") { cluster = new CompleteLinkage(rabund, list, matrix, cutoff, method); } + else if(method == "nearest"){ cluster = new SingleLinkage(rabund, list, matrix, cutoff, method); } + else if(method == "average"){ cluster = new AverageLinkage(rabund, list, matrix, cutoff, method); } + else if(method == "weighted"){ cluster = new WeightedLinkage(rabund, list, matrix, cutoff, method); } + tag = cluster->getTag(); + + if (outputDir == "") { outputDir += m->hasPath(distfile); } + fileroot = outputDir + m->getRootName(m->getSimpleName(distfile)); + + m->openOutputFile(fileroot+ tag + ".sabund", sabundFile); + m->openOutputFile(fileroot+ tag + ".rabund", rabundFile); + m->openOutputFile(fileroot+ tag + ".list", listFile); + + outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund"); + outputNames.push_back(fileroot+ tag + ".rabund"); outputTypes["rabund"].push_back(fileroot+ tag + ".rabund"); + outputNames.push_back(fileroot+ tag + ".list"); outputTypes["list"].push_back(fileroot+ tag + ".list"); + time_t estart = time(NULL); - //int ndist = matrix->getNNodes(); float previousDist = 0.00000; float rndPreviousDist = 0.00000; oldRAbund = *rabund; @@ -146,11 +276,20 @@ int ClusterCommand::execute(){ print_start = true; start = time(NULL); loops = 0; + double saveCutoff = cutoff; while (matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){ - if (print_start && isTrue(timing)) { - mothurOut("Clustering (" + tag + ") dist " + toString(matrix->getSmallDist()) + "/" - + toString(roundDist(matrix->getSmallDist(), precision)) + + if (m->control_pressed) { //clean up + delete list; delete matrix; delete rabund; delete cluster; + sabundFile.close();rabundFile.close();listFile.close(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } 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; @@ -159,8 +298,14 @@ int ClusterCommand::execute(){ loops++; cluster->update(cutoff); + float dist = matrix->getSmallDist(); - float rndDist = roundDist(dist, precision); + float rndDist; + if (hard) { + rndDist = m->ceilDist(dist, precision); + }else{ + rndDist = m->roundDist(dist, precision); + } if(previousDist <= 0.0000 && dist != previousDist){ printData("unique"); @@ -175,8 +320,8 @@ int ClusterCommand::execute(){ oldList = *list; } - if (print_start && isTrue(timing)) { - mothurOut("Clustering (" + tag + ") for distance " + toString(previousDist) + "/" + toString(rndPreviousDist) + 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; @@ -189,28 +334,56 @@ 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; - - //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(""); } - - globaldata->setListFile(fileroot+ tag + ".list"); - globaldata->setNameFile(""); - globaldata->setFormat("list"); + delete matrix; + delete list; + delete rabund; + delete cluster; sabundFile.close(); rabundFile.close(); listFile.close(); - //if (isTrue(timing)) { - mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster"); mothurOutEndLine(); + + 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(); + + + //if (m->isTrue(timing)) { + m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster"); m->mothurOutEndLine(); //} + + return 0; } catch(exception& e) { - errorOut(e, "ClusterCommand", "execute"); + m->errorOut(e, "ClusterCommand", "execute"); exit(1); } } @@ -219,16 +392,16 @@ int ClusterCommand::execute(){ void ClusterCommand::printData(string label){ try { - if (isTrue(timing)) { - mothurOut("\tTime: " + toString(time(NULL) - start) + "\tsecs for " + toString(oldRAbund.getNumBins()) - + "\tclusters. Updates: " + toString(loops)); mothurOutEndLine(); + 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 (isTrue(showabund)) { + if (m->isTrue(showabund)) { oldRAbund.getSAbundVector().print(cout); } oldRAbund.print(rabundFile); @@ -238,7 +411,7 @@ void ClusterCommand::printData(string label){ oldList.print(listFile); } catch(exception& e) { - errorOut(e, "ClusterCommand", "printData"); + m->errorOut(e, "ClusterCommand", "printData"); exit(1); }