--- /dev/null
+/*
+ * mgclustercommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/11/09.
+ * Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mgclustercommand.h"
+
+//**********************************************************************************************************************
+vector<string> MGClusterCommand::setParameters(){
+ try {
+ CommandParameter pblast("blast", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pblast);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter plength("length", "Number", "", "5", "", "", "",false,false); parameters.push_back(plength);
+ CommandParameter ppenalty("penalty", "Number", "", "0.10", "", "", "",false,false); parameters.push_back(ppenalty);
+ CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pcutoff);
+ CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
+ CommandParameter pmethod("method", "Multiple", "furthest-nearest-average", "average", "", "", "",false,false); parameters.push_back(pmethod);
+ CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
+ CommandParameter pmin("min", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmin);
+ CommandParameter pmerge("merge", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmerge);
+ CommandParameter phcluster("hcluster", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phcluster);
+ 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, "MGClusterCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string MGClusterCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The mgcluster command parameter options are blast, name, cutoff, precision, hard, method, merge, min, length, penalty and hcluster. The blast parameter is required.\n";
+ helpString += "The mgcluster command reads a blast and name file and clusters the sequences into OPF units similiar to the OTUs.\n";
+ helpString += "This command outputs a .list, .rabund and .sabund file that can be used with mothur other commands to estimate richness.\n";
+ helpString += "The cutoff parameter is used to specify the maximum distance you would like to cluster to. The default is 0.70.\n";
+ helpString += "The precision parameter's default value is 100. \n";
+ helpString += "The acceptable mgcluster methods are furthest, nearest and average. If no method is provided then average is assumed.\n";
+ helpString += "The min parameter allows you to specify is you want the minimum or maximum blast score ratio used in calculating the distance. The default is true, meaning you want the minimum.\n";
+ helpString += "The length parameter is used to specify the minimum overlap required. The default is 5.\n";
+ helpString += "The penalty parameter is used to adjust the error rate. The default is 0.10.\n";
+ helpString += "The merge parameter allows you to shut off merging based on overlaps and just cluster. By default merge is true, meaning you want to merge.\n";
+ helpString += "The hcluster parameter allows you to use the hcluster algorithm when clustering. This may be neccessary if your file is too large to fit into RAM. The default is false.\n";
+ helpString += "The mgcluster command should be in the following format: \n";
+ helpString += "mgcluster(blast=yourBlastfile, name=yourNameFile, cutoff=yourCutOff).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. balst), '=' and parameters (i.e.yourBlastfile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MGClusterCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+MGClusterCommand::MGClusterCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MGClusterCommand", "MGClusterCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+MGClusterCommand::MGClusterCommand(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;
+ map<string,string>::iterator it;
+
+ //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 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("blast");
+ //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["blast"] = 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
+ blastfile = validParameter.validFile(parameters, "blast", true);
+ if (blastfile == "not open") { blastfile = ""; abort = true; }
+ else if (blastfile == "not found") { blastfile = ""; }
+
+ //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 = "";
+ outputDir += m->hasPath(blastfile); //if user entered a file with a path then preserve it
+ }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
+
+ if ((blastfile == "")) { m->mothurOut("When executing a mgcluster command you must provide a blastfile."); m->mothurOutEndLine(); abort = true; }
+
+ //check for optional parameter and set defaults
+ string temp;
+ temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
+ precisionLength = temp.length();
+ m->mothurConvert(temp, precision);
+
+ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "0.70"; }
+ 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")) { }
+ else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
+
+ temp = validParameter.validFile(parameters, "length", false); if (temp == "not found") { temp = "5"; }
+ m->mothurConvert(temp, length);
+
+ temp = validParameter.validFile(parameters, "penalty", false); if (temp == "not found") { temp = "0.10"; }
+ m->mothurConvert(temp, penalty);
+
+ temp = validParameter.validFile(parameters, "min", false); if (temp == "not found") { temp = "true"; }
+ minWanted = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "merge", false); if (temp == "not found") { temp = "true"; }
+ merge = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "hcluster", false); if (temp == "not found") { temp = "false"; }
+ hclusterWanted = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "T"; }
+ hard = m->isTrue(temp);
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MGClusterCommand", "MGClusterCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int MGClusterCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ //read names file
+ if (namefile != "") {
+ nameMap = new NameAssignment(namefile);
+ nameMap->readMap();
+ }else{ nameMap= new NameAssignment(); }
+
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(blastfile));
+ string tag = "";
+ time_t start;
+ float previousDist = 0.00000;
+ float rndPreviousDist = 0.00000;
+
+ //read blastfile - creates sparsematrices for the distances and overlaps as well as a listvector
+ //must remember to delete those objects here since readBlast does not
+ read = new ReadBlast(blastfile, cutoff, penalty, length, minWanted, hclusterWanted);
+ read->read(nameMap);
+
+ list = new ListVector(nameMap->getListVector());
+ RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
+
+ if (m->control_pressed) { outputTypes.clear(); delete nameMap; delete read; delete list; delete rabund; return 0; }
+
+ start = time(NULL);
+ oldList = *list;
+ map<string, int> Seq2Bin;
+ map<string, int> oldSeq2Bin;
+
+ if (method == "furthest") { tag = "fn"; }
+ else if (method == "nearest") { tag = "nn"; }
+ else { tag = "an"; }
+
+ //open output files
+ m->openOutputFile(fileroot+ tag + ".list", listFile);
+ m->openOutputFile(fileroot+ tag + ".rabund", rabundFile);
+ m->openOutputFile(fileroot+ tag + ".sabund", sabundFile);
+
+ if (m->control_pressed) {
+ delete nameMap; delete read; delete list; delete rabund;
+ listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+ outputTypes.clear();
+ return 0;
+ }
+
+ double saveCutoff = cutoff;
+
+ if (!hclusterWanted) {
+ //get distmatrix and overlap
+ SparseMatrix* distMatrix = read->getDistMatrix();
+ overlapMatrix = read->getOverlapMatrix(); //already sorted by read
+ delete read;
+
+ //create cluster
+ if (method == "furthest") { cluster = new CompleteLinkage(rabund, list, distMatrix, cutoff, method); }
+ else if(method == "nearest"){ cluster = new SingleLinkage(rabund, list, distMatrix, cutoff, method); }
+ else if(method == "average"){ cluster = new AverageLinkage(rabund, list, distMatrix, cutoff, method); }
+ cluster->setMapWanted(true);
+ Seq2Bin = cluster->getSeqtoBin();
+ oldSeq2Bin = Seq2Bin;
+
+ if (m->control_pressed) {
+ delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster;
+ listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+ outputTypes.clear();
+ return 0;
+ }
+
+ //cluster using cluster classes
+ while (distMatrix->getSmallDist() < cutoff && distMatrix->getNNodes() > 0){
+
+ cluster->update(cutoff);
+
+ if (m->control_pressed) {
+ delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster;
+ listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+ outputTypes.clear();
+ return 0;
+ }
+
+ float dist = distMatrix->getSmallDist();
+ float rndDist;
+ if (hard) {
+ rndDist = m->ceilDist(dist, precision);
+ }else{
+ rndDist = m->roundDist(dist, precision);
+ }
+
+ if(previousDist <= 0.0000 && dist != previousDist){
+ oldList.setLabel("unique");
+ printData(&oldList);
+ }
+ else if(rndDist != rndPreviousDist){
+ if (merge) {
+ ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist);
+
+ if (m->control_pressed) {
+ delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster; delete temp;
+ listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+ outputTypes.clear();
+ return 0;
+ }
+
+ temp->setLabel(toString(rndPreviousDist, precisionLength-1));
+ printData(temp);
+ delete temp;
+ }else{
+ oldList.setLabel(toString(rndPreviousDist, precisionLength-1));
+ printData(&oldList);
+ }
+ }
+
+ previousDist = dist;
+ rndPreviousDist = rndDist;
+ oldList = *list;
+ Seq2Bin = cluster->getSeqtoBin();
+ oldSeq2Bin = Seq2Bin;
+ }
+
+ if(previousDist <= 0.0000){
+ oldList.setLabel("unique");
+ printData(&oldList);
+ }
+ else if(rndPreviousDist<cutoff){
+ if (merge) {
+ ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist);
+
+ if (m->control_pressed) {
+ delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster; delete temp;
+ listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+ outputTypes.clear();
+ return 0;
+ }
+
+ temp->setLabel(toString(rndPreviousDist, precisionLength-1));
+ printData(temp);
+ delete temp;
+ }else{
+ oldList.setLabel(toString(rndPreviousDist, precisionLength-1));
+ printData(&oldList);
+ }
+ }
+
+ //free memory
+ overlapMatrix.clear();
+ delete distMatrix;
+ delete cluster;
+
+ }else { //use hcluster to cluster
+ //get distmatrix and overlap
+ overlapFile = read->getOverlapFile();
+ distFile = read->getDistFile();
+ delete read;
+
+ //sort the distance and overlap files
+ sortHclusterFiles(distFile, overlapFile);
+
+ if (m->control_pressed) {
+ delete nameMap; delete list; delete rabund;
+ listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+ outputTypes.clear();
+ return 0;
+ }
+
+ //create cluster
+ hcluster = new HCluster(rabund, list, method, distFile, nameMap, cutoff);
+ hcluster->setMapWanted(true);
+ Seq2Bin = cluster->getSeqtoBin();
+ oldSeq2Bin = Seq2Bin;
+
+ vector<seqDist> seqs; seqs.resize(1); // to start loop
+ //ifstream inHcluster;
+ //m->openInputFile(distFile, inHcluster);
+
+ if (m->control_pressed) {
+ delete nameMap; delete list; delete rabund; delete hcluster;
+ listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+ outputTypes.clear();
+ return 0;
+ }
+
+ while (seqs.size() != 0){
+
+ seqs = hcluster->getSeqs();
+
+ //to account for cutoff change in average neighbor
+ if (seqs.size() != 0) {
+ if (seqs[0].dist > cutoff) { break; }
+ }
+
+ if (m->control_pressed) {
+ delete nameMap; delete list; delete rabund; delete hcluster;
+ listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+ m->mothurRemove(distFile);
+ m->mothurRemove(overlapFile);
+ outputTypes.clear();
+ return 0;
+ }
+
+ for (int i = 0; i < seqs.size(); i++) { //-1 means skip me
+
+ if (seqs[i].seq1 != seqs[i].seq2) {
+
+ cutoff = hcluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
+
+ if (m->control_pressed) {
+ delete nameMap; delete list; delete rabund; delete hcluster;
+ listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+ m->mothurRemove(distFile);
+ m->mothurRemove(overlapFile);
+ outputTypes.clear();
+ return 0;
+ }
+
+ float rndDist;
+ if (hard) {
+ rndDist = m->ceilDist(seqs[i].dist, precision);
+ }else{
+ rndDist = m->roundDist(seqs[i].dist, precision);
+ }
+
+ if((previousDist <= 0.0000) && (seqs[i].dist != previousDist)){
+ oldList.setLabel("unique");
+ printData(&oldList);
+ }
+ else if((rndDist != rndPreviousDist)){
+ if (merge) {
+ ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist);
+
+ if (m->control_pressed) {
+ delete nameMap; delete list; delete rabund; delete hcluster; delete temp;
+ listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+ m->mothurRemove(distFile);
+ m->mothurRemove(overlapFile);
+ outputTypes.clear();
+ return 0;
+ }
+
+ temp->setLabel(toString(rndPreviousDist, precisionLength-1));
+ printData(temp);
+ delete temp;
+ }else{
+ oldList.setLabel(toString(rndPreviousDist, precisionLength-1));
+ printData(&oldList);
+ }
+ }
+
+ previousDist = seqs[i].dist;
+ rndPreviousDist = rndDist;
+ oldList = *list;
+ Seq2Bin = cluster->getSeqtoBin();
+ oldSeq2Bin = Seq2Bin;
+ }
+ }
+ }
+ //inHcluster.close();
+
+ if(previousDist <= 0.0000){
+ oldList.setLabel("unique");
+ printData(&oldList);
+ }
+ else if(rndPreviousDist<cutoff){
+ if (merge) {
+ ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist);
+
+ if (m->control_pressed) {
+ delete nameMap; delete list; delete rabund; delete hcluster; delete temp;
+ listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+ m->mothurRemove(distFile);
+ m->mothurRemove(overlapFile);
+ outputTypes.clear();
+ return 0;
+ }
+
+ temp->setLabel(toString(rndPreviousDist, precisionLength-1));
+ printData(temp);
+ delete temp;
+ }else{
+ oldList.setLabel(toString(rndPreviousDist, precisionLength-1));
+ printData(&oldList);
+ }
+ }
+
+ delete hcluster;
+ m->mothurRemove(distFile);
+ m->mothurRemove(overlapFile);
+ }
+
+ delete list;
+ delete rabund;
+ listFile.close();
+ sabundFile.close();
+ rabundFile.close();
+
+ if (m->control_pressed) {
+ delete nameMap;
+ listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+ outputTypes.clear();
+ return 0;
+ }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(fileroot+ tag + ".list"); m->mothurOutEndLine(); outputNames.push_back(fileroot+ tag + ".list"); outputTypes["list"].push_back(fileroot+ tag + ".list");
+ m->mothurOut(fileroot+ tag + ".rabund"); m->mothurOutEndLine(); outputNames.push_back(fileroot+ tag + ".rabund"); outputTypes["rabund"].push_back(fileroot+ tag + ".rabund");
+ m->mothurOut(fileroot+ tag + ".sabund"); m->mothurOutEndLine(); outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
+ m->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->mothurOut("It took " + toString(time(NULL) - start) + " seconds to cluster."); m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MGClusterCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+void MGClusterCommand::printData(ListVector* mergedList){
+ try {
+ mergedList->print(listFile);
+ mergedList->getRAbundVector().print(rabundFile);
+
+ SAbundVector sabund = mergedList->getSAbundVector();
+
+ sabund.print(cout);
+ sabund.print(sabundFile);
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MGClusterCommand", "printData");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//this merging is just at the reporting level, after this info is printed to the file it is gone and does not effect the datastructures
+//that are used to cluster by distance. this is done so that the overlapping data does not have more influenece than the distance data.
+ListVector* MGClusterCommand::mergeOPFs(map<string, int> binInfo, float dist){
+ try {
+ //create new listvector so you don't overwrite the clustering
+ ListVector* newList = new ListVector(oldList);
+
+ bool done = false;
+ ifstream inOverlap;
+ int count = 0;
+
+ if (hclusterWanted) {
+ m->openInputFile(overlapFile, inOverlap);
+ if (inOverlap.eof()) { done = true; }
+ }else { if (overlapMatrix.size() == 0) { done = true; } }
+
+ while (!done) {
+ if (m->control_pressed) {
+ if (hclusterWanted) { inOverlap.close(); }
+ return newList;
+ }
+
+ //get next overlap
+ seqDist overlapNode;
+ if (!hclusterWanted) {
+ if (count < overlapMatrix.size()) { //do we have another node in the matrix
+ overlapNode = overlapMatrix[count];
+ count++;
+ }else { break; }
+ }else {
+ if (!inOverlap.eof()) {
+ string firstName, secondName;
+ float overlapDistance;
+ inOverlap >> firstName >> secondName >> overlapDistance; m->gobble(inOverlap);
+
+ //commented out because we check this in readblast already
+ //map<string,int>::iterator itA = nameMap->find(firstName);
+ //map<string,int>::iterator itB = nameMap->find(secondName);
+ //if(itA == nameMap->end()){ cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1); }
+ //if(itB == nameMap->end()){ cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1); }
+
+ //overlapNode.seq1 = itA->second;
+ //overlapNode.seq2 = itB->second;
+ overlapNode.seq1 = nameMap->get(firstName);
+ overlapNode.seq2 = nameMap->get(secondName);
+ overlapNode.dist = overlapDistance;
+ }else { inOverlap.close(); break; }
+ }
+
+ if (overlapNode.dist < dist) {
+ //get names of seqs that overlap
+ string name1 = nameMap->get(overlapNode.seq1);
+ string name2 = nameMap->get(overlapNode.seq2);
+
+ //use binInfo to find out if they are already in the same bin
+ //map<string, int>::iterator itBin1 = binInfo.find(name1);
+ //map<string, int>::iterator itBin2 = binInfo.find(name2);
+
+ //if(itBin1 == binInfo.end()){ cerr << "AAError: Sequence '" << name1 << "' does not have any bin info.\n"; exit(1); }
+ //if(itBin2 == binInfo.end()){ cerr << "ABError: Sequence '" << name2 << "' does not have any bin info.\n"; exit(1); }
+
+ //int binKeep = itBin1->second;
+ //int binRemove = itBin2->second;
+
+ int binKeep = binInfo[name1];
+ int binRemove = binInfo[name2];
+
+ //if not merge bins and update binInfo
+ if(binKeep != binRemove) {
+
+ //save names in old bin
+ string names = newList->get(binRemove);
+
+ //merge bins into name1s bin
+ newList->set(binKeep, newList->get(binRemove)+','+newList->get(binKeep));
+ newList->set(binRemove, "");
+
+ //update binInfo
+ while (names.find_first_of(',') != -1) {
+ //get name from bin
+ string name = names.substr(0,names.find_first_of(','));
+ //save name and bin number
+ binInfo[name] = binKeep;
+ names = names.substr(names.find_first_of(',')+1, names.length());
+ }
+
+ //get last name
+ binInfo[names] = binKeep;
+ }
+
+ }else { done = true; }
+ }
+
+ //return listvector
+ return newList;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MGClusterCommand", "mergeOPFs");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+void MGClusterCommand::sortHclusterFiles(string unsortedDist, string unsortedOverlap) {
+ try {
+ //sort distFile
+ string sortedDistFile = m->sortFile(unsortedDist, outputDir);
+ m->mothurRemove(unsortedDist); //delete unsorted file
+ distFile = sortedDistFile;
+
+ //sort overlap file
+ string sortedOverlapFile = m->sortFile(unsortedOverlap, outputDir);
+ m->mothurRemove(unsortedOverlap); //delete unsorted file
+ overlapFile = sortedOverlapFile;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MGClusterCommand", "sortHclusterFiles");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+
+
+
+
projects / mothur.git / blobdiff