+++ /dev/null
-/*
- * clustercommand.cpp
- * Dotur
- *
- * Created by Sarah Westcott on 1/2/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#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",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<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, 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<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{
- 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();
- map<string,string>::iterator it;
-
- ValidParameters validParameter;
-
- //check to make sure all parameters are valid for command
- 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 = ""; }
-
- 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
- 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, "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"; }
- m->mothurConvert(temp, cutoff);
- cutoff += (5 / (precision * 10.0));
-
- method = validParameter.validFile(parameters, "method", false);
- if (method == "not found") { method = "average"; }
-
- 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"; }
-
- }
- }
- catch(exception& e) {
- m->errorOut(e, "ClusterCommand", "ClusterCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-ClusterCommand::~ClusterCommand(){}
-//**********************************************************************************************************************
-
-int ClusterCommand::execute(){
- try {
-
- 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; }
- 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;
- 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);
- float previousDist = 0.00000;
- float rndPreviousDist = 0.00000;
- oldRAbund = *rabund;
- oldList = *list;
-
- print_start = true;
- start = time(NULL);
- loops = 0;
- double saveCutoff = cutoff;
-
- while (matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){
-
- 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;
- }
-
- 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");
- }
- else if(rndDist != rndPreviousDist){
- printData(toString(rndPreviousDist, length-1));
- }
-
- previousDist = dist;
- rndPreviousDist = rndDist;
- 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");
- }
- else if(rndPreviousDist<cutoff){
- printData(toString(rndPreviousDist, length-1));
- }
-
- delete matrix;
- delete list;
- delete rabund;
- delete cluster;
-
- 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();
-
-
- //if (m->isTrue(timing)) {
- m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster"); m->mothurOutEndLine();
- //}
-
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "ClusterCommand", "execute");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-void ClusterCommand::printData(string label){
- try {
- 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 (m->isTrue(showabund)) {
- oldRAbund.getSAbundVector().print(cout);
- }
- oldRAbund.print(rabundFile);
- oldRAbund.getSAbundVector().print(sabundFile);
-
- oldList.setLabel(label);
- oldList.print(listFile);
- }
- catch(exception& e) {
- m->errorOut(e, "ClusterCommand", "printData");
- exit(1);
- }
-
-
-}
-//**********************************************************************************************************************
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