*/
#include "clustercommand.h"
+#include "readphylip.h"
+#include "readcolumn.h"
+#include "readmatrix.hpp"
+#include "clusterdoturcommand.h"
+
+//**********************************************************************************************************************
+vector<string> 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<string> 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<string> 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) {
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<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
ValidParameters validParameter;
//check to make sure all parameters are valid for command
- for (map<string,string>::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<string> 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)) {
- m->mothurOut("Before you use the cluster command, you first need to read in a distance matrix."); m->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; }
+ }
+
+ 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
if (temp == "not found") { temp = "100"; }
//saves precision legnth for formatting below
length = temp.length();
- convert(temp, precision);
+ m->mothurConvert(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);
+
+ //bool cutoffSet = false;
temp = validParameter.validFile(parameters, "cutoff", false);
if (temp == "not found") { temp = "10"; }
- convert(temp, cutoff);
+ //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;
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 { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average."); m->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"; }
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);
-
- outputNames.push_back(fileroot+ tag + ".sabund");
- outputNames.push_back(fileroot+ tag + ".rabund");
- outputNames.push_back(fileroot+ tag + ".list");
- }
}
}
catch(exception& e) {
exit(1);
}
}
-
//**********************************************************************************************************************
-
-void ClusterCommand::help(){
- try {
- m->mothurOut("The cluster command can only be executed after a successful read.dist command.\n");
- m->mothurOut("The cluster command parameter options are method, cuttoff, precision, showabund and timing. No parameters are required.\n");
- m->mothurOut("The cluster command should be in the following format: \n");
- m->mothurOut("cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
- m->mothurOut("The acceptable cluster methods are furthest, nearest and average. If no method is provided then furthest is assumed.\n\n");
- }
- catch(exception& e) {
- m->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; }
+
+ //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<string, string> 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);
- //int ndist = matrix->getNNodes();
float previousDist = 0.00000;
float rndPreviousDist = 0.00000;
oldRAbund = *rabund;
loops = 0;
double saveCutoff = cutoff;
- while (matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){
-
+ while (matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){
+
if (m->control_pressed) { //clean up
- delete globaldata->gSparseMatrix; globaldata->gSparseMatrix = NULL;
- delete globaldata->gListVector; globaldata->gListVector = NULL;
- if (globaldata->getFormat() == "phylip") { globaldata->setPhylipFile(""); }
- else if (globaldata->getFormat() == "column") { globaldata->setColumnFile(""); }
- sabundFile.close();rabundFile.close();listFile.close();
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- return 0;
+ 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 && isTrue(timing)) {
+ if (print_start && m->isTrue(timing)) {
m->mothurOut("Clustering (" + tag + ") dist " + toString(matrix->getSmallDist()) + "/"
- + toString(roundDist(matrix->getSmallDist(), precision))
+ + 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 = roundDist(dist, precision);
+
+ 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");
oldList = *list;
}
- if (print_start && isTrue(timing)) {
+ 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");
}
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();
- //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 (saveCutoff != cutoff) {
+ if (hard) { saveCutoff = m->ceilDist(saveCutoff, precision); }
+ else { saveCutoff = m->roundDist(saveCutoff, precision); }
+
+ m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine();
+ }
- globaldata->setListFile(fileroot+ tag + ".list");
- globaldata->setNameFile("");
- globaldata->setFormat("list");
+ //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); }
+ }
- sabundFile.close();
- rabundFile.close();
- listFile.close();
-
- if (saveCutoff != cutoff) { m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine(); }
+ //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();
m->mothurOutEndLine();
- //if (isTrue(timing)) {
+ //if (m->isTrue(timing)) {
m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster"); m->mothurOutEndLine();
//}
void ClusterCommand::printData(string label){
try {
- if (isTrue(timing)) {
+ 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)) {
- oldRAbund.getSAbundVector().print(cout);
- }
- oldRAbund.print(rabundFile);
- oldRAbund.getSAbundVector().print(sabundFile);
-
+
+ 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);
}
}
//**********************************************************************************************************************
+
+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<string> 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);
+ }
+
+}
+//**********************************************************************************************************************
projects / mothur.git / blobdiff