--- /dev/null
+/*
+ * clusterdoturcommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 10/27/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "clusterdoturcommand.h"
+#include "clusterclassic.h"
+
+//**********************************************************************************************************************
+vector<string> ClusterDoturCommand::setParameters(){
+ try {
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ 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 phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
+ CommandParameter psim("sim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psim);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ 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, "ClusterDoturCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ClusterDoturCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The cluster.classic command clusters using the algorithm from dotur. \n";
+ helpString += "The cluster.classic command parameter options are phylip, name, method, cuttoff, hard, sim, precision. Phylip is required, unless you have a valid current file.\n";
+ helpString += "The cluster.classic command should be in the following format: \n";
+ helpString += "cluster.classic(phylip=yourDistanceMatrix, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n";
+ helpString += "The acceptable cluster methods are furthest, nearest, weighted and average. If no method is provided then average is assumed.\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterDoturCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ClusterDoturCommand::ClusterDoturCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterDoturCommand", "ClusterCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//This function checks to make sure the cluster command has no errors and then clusters based on the method chosen.
+ClusterDoturCommand::ClusterDoturCommand(string option) {
+ try{
+
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ map<string,string>::iterator it;
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {
+ abort = true;
+ }
+ }
+
+ //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);
+ 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("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; }
+ }
+
+ }
+
+ //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 = ""; }
+
+ //check for required parameters
+ phylipfile = validParameter.validFile(parameters, "phylip", true);
+ if (phylipfile == "not open") { abort = true; }
+ else if (phylipfile == "not found") {
+ phylipfile = m->getPhylipFile();
+ if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You need to provide a phylip file with the cluster.classic command."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }else { m->setPhylipFile(phylipfile); }
+
+
+ //check for optional parameter and set defaults
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
+
+ string temp;
+ temp = validParameter.validFile(parameters, "precision", false);
+ if (temp == "not found") { temp = "100"; }
+ //saves precision legnth for formatting below
+ length = temp.length();
+ m->mothurConvert(temp, precision);
+
+ temp = validParameter.validFile(parameters, "cutoff", false);
+ if (temp == "not found") { temp = "10"; }
+ m->mothurConvert(temp, cutoff);
+ cutoff += (5 / (precision * 10.0));
+
+ 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);
+
+ method = validParameter.validFile(parameters, "method", false);
+ if (method == "not found") { method = "average"; }
+
+ if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) {
+ if (method == "furthest") { tag = "fn"; }
+ else if (method == "nearest") { tag = "nn"; }
+ else if (method == "average") { tag = "an"; }
+ else if (method == "weighted") { tag = "wn"; }
+ }else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest, average, weighted."); m->mothurOutEndLine(); abort = true; }
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterDoturCommand", "ClusterCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int ClusterDoturCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ if(namefile != ""){
+ nameMap = new NameAssignment(namefile);
+ nameMap->readMap();
+ }else{
+ nameMap = NULL;
+ }
+
+ //reads phylip file storing data in 2D vector, also fills list and rabund
+ ClusterClassic* cluster = new ClusterClassic(cutoff, method, sim);
+ cluster->readPhylipFile(phylipfile, nameMap);
+
+ if (m->control_pressed) { delete cluster; delete list; delete rabund; return 0; }
+
+ list = cluster->getListVector();
+ rabund = cluster->getRAbundVector();
+
+ if (outputDir == "") { outputDir += m->hasPath(phylipfile); }
+ fileroot = outputDir + m->getRootName(m->getSimpleName(phylipfile));
+
+ 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");
+
+ float previousDist = 0.00000;
+ float rndPreviousDist = 0.00000;
+ oldRAbund = *rabund;
+ oldList = *list;
+
+ //double saveCutoff = cutoff;
+
+ int estart = time(NULL);
+
+ while ((cluster->getSmallDist() < cutoff) && (cluster->getNSeqs() > 1)){
+ if (m->control_pressed) { delete cluster; delete list; delete rabund; sabundFile.close();rabundFile.close();listFile.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; }
+
+ cluster->update(cutoff);
+
+ float dist = cluster->getSmallDist();
+ float rndDist;
+ if (hard) {
+ rndDist = m->ceilDist(dist, precision);
+ }else{
+ rndDist = m->roundDist(dist, precision);
+ }
+
+ if(previousDist <= 0.0000 && dist != previousDist){
+ printData("unique");
+ }
+ else if(rndDist != rndPreviousDist){
+ printData(toString(rndPreviousDist, length-1));
+ }
+
+ previousDist = dist;
+ rndPreviousDist = rndDist;
+ oldRAbund = *rabund;
+ oldList = *list;
+ }
+
+ if(previousDist <= 0.0000){
+ printData("unique");
+ }
+ else if(rndPreviousDist<cutoff){
+ printData(toString(rndPreviousDist, length-1));
+ }
+
+ sabundFile.close();
+ rabundFile.close();
+ listFile.close();
+
+ delete cluster; delete nameMap; delete list; delete rabund;
+
+ //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();
+
+ m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster"); m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterDoturCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+void ClusterDoturCommand::printData(string label){
+ try {
+
+ oldRAbund.setLabel(label);
+ oldRAbund.print(rabundFile);
+ oldRAbund.getSAbundVector().print(sabundFile);
+
+ oldRAbund.getSAbundVector().print(cout);
+
+ oldList.setLabel(label);
+ oldList.print(listFile);
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterDoturCommand", "printData");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
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