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);
}
}
int HClusterCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
NameAssignment* nameMap = NULL;
if(namefile != ""){
nameMap = new NameAssignment(namefile);
nameMap->readMap();
}
time_t estart = time(NULL);
if (!sorted) {
read = new ReadCluster(distfile, cutoff, outputDir, true);
read->setFormat(format);
read->read(nameMap);
if (m->control_pressed) {
delete read;
sabundFile.close();
rabundFile.close();
listFile.close();
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
return 0;
}
distfile = read->getOutputFile();
list = read->getListVector();
delete read;
}else {
list = new ListVector(nameMap->getListVector());
}
if (m->control_pressed) {
sabundFile.close();
rabundFile.close();
listFile.close();
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
return 0;
}
m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to sort. "); m->mothurOutEndLine();
estart = time(NULL);
//list vector made by read contains all sequence names
if(list != NULL){
rabund = new RAbundVector(list->getRAbundVector());
}else{
m->mothurOut("Error: no list vector!"); m->mothurOutEndLine(); return 0;
}
list->printHeaders(listFile);
float previousDist = 0.00000;
float rndPreviousDist = 0.00000;
oldRAbund = *rabund;
oldList = *list;
print_start = true;
start = time(NULL);
cluster = new HCluster(rabund, list, method, distfile, nameMap, cutoff);
vector<seqDist> seqs; seqs.resize(1); // to start loop
if (m->control_pressed) {
delete cluster;
sabundFile.close();
rabundFile.close();
listFile.close();
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
return 0;
}
float saveCutoff = cutoff;
while (seqs.size() != 0){
seqs = cluster->getSeqs();
//to account for cutoff change in average neighbor
if (seqs.size() != 0) {
if (seqs[0].dist > cutoff) { break; }
}
if (m->control_pressed) {
delete cluster;
sabundFile.close();
rabundFile.close();
listFile.close();
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
return 0;
}
for (int i = 0; i < seqs.size(); i++) { //-1 means skip me
if (seqs[i].seq1 != seqs[i].seq2) {
cutoff = cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
if (m->control_pressed) {
delete cluster;
sabundFile.close();
rabundFile.close();
listFile.close();
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } 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)){
printData("unique");
}
else if((rndDist != rndPreviousDist)){
printData(toString(rndPreviousDist, length-1));
}
previousDist = seqs[i].dist;
rndPreviousDist = rndDist;
oldRAbund = *rabund;
oldList = *list;
}
}
}
if (m->control_pressed) {
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(previousDist <= 0.0000){
printData("unique");
}
else if(rndPreviousDist<cutoff){
printData(toString(rndPreviousDist, length-1));
}
sabundFile.close();
rabundFile.close();
listFile.close();
delete cluster;
if (m->control_pressed) {
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
return 0;
}
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, "HClusterCommand", "execute");
exit(1);
}
}
int ClusterDoturCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
ClusterClassic* cluster = new ClusterClassic(cutoff, method, sim);
NameAssignment* nameMap = NULL;
CountTable* ct = NULL;
map<string, int> counts;
if(namefile != "") {
nameMap = new NameAssignment(namefile);
nameMap->readMap();
cluster->readPhylipFile(phylipfile, nameMap);
delete nameMap;
}else if (countfile != "") {
ct = new CountTable();
ct->readTable(countfile, false, false);
cluster->readPhylipFile(phylipfile, ct);
counts = ct->getNameMap();
delete ct;
}else {
cluster->readPhylipFile(phylipfile, nameMap);
}
tag = cluster->getTag();
if (m->getControl_pressed()) { delete cluster; return 0; }
list = cluster->getListVector();
rabund = cluster->getRAbundVector();
if (outputDir == "") { outputDir += util.hasPath(phylipfile); }
fileroot = outputDir + util.getRootName(util.getSimpleName(phylipfile));
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 == "") {
util.openOutputFile(sabundFileName, sabundFile);
util.openOutputFile(rabundFileName, rabundFile);
outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
}
util.openOutputFile(listFileName, listFile);
outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
float previousDist = 0.00000;
float rndPreviousDist = 0.00000;
oldRAbund = *rabund;
oldList = *list;
bool printHeaders = true;
int estart = time(NULL); int loop = 0;
while ((cluster->getSmallDist() <= cutoff) && (cluster->getNSeqs() > 1)){
if (m->getControl_pressed()) { delete cluster; delete list; delete rabund; if(countfile == "") {rabundFile.close(); sabundFile.close(); util.mothurRemove((fileroot+ tag + ".rabund")); util.mothurRemove((fileroot+ tag + ".sabund")); }
listFile.close(); util.mothurRemove((fileroot+ tag + ".list")); outputTypes.clear(); return 0; }
cluster->update(cutoff);
float dist = cluster->getSmallDist();
float rndDist = util.ceilDist(dist, precision);
//cout << loop << '\t' << dist << '\t' << oldList.getNumBins() << endl; loop++;
if(previousDist <= 0.0000 && dist != previousDist) { printData("unique", counts, printHeaders); }
else if(rndDist != rndPreviousDist) { printData(toString(rndPreviousDist, length-1), counts, printHeaders); }
previousDist = dist;
rndPreviousDist = rndDist;
oldRAbund = *rabund;
oldList = *list;
}
if(previousDist <= 0.0000) { printData("unique", counts, printHeaders); }
else if(rndPreviousDist<cutoff) { printData(toString(rndPreviousDist, length-1), counts, printHeaders); }
if (countfile == "") {
sabundFile.close();
rabundFile.close();
}
listFile.close();
delete cluster; delete list; delete rabund;
//set list file as new current listfile
string currentName = "";
itTypes = outputTypes.find("list");
if (itTypes != outputTypes.end()) { if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setListFile(currentName); } }
//set rabund file as new current rabundfile
itTypes = outputTypes.find("rabund");
if (itTypes != outputTypes.end()) { if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setRabundFile(currentName); } }
//set sabund file as new current sabundfile
itTypes = outputTypes.find("sabund");
if (itTypes != outputTypes.end()) { if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setSabundFile(currentName); } }
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } 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);
}
}
int TreeGroupCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
if (format == "sharedfile") {
InputData input(sharedfile, "sharedfile", Groups);
SharedRAbundVectors* lookup = input.getSharedRAbundVectors();
lastLabel = lookup->getLabel();
Groups = lookup->getNamesGroups();
if (lookup->size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command.\n"); return 0; }
//create treemap class from groupmap for tree class to use
CountTable ct;
set<string> nameMap;
map<string, string> groupMap;
set<string> gps;
for (int i = 0; i < Groups.size(); i++) {
nameMap.insert(Groups[i]);
gps.insert(Groups[i]);
groupMap[Groups[i]] = Groups[i];
}
ct.createTable(nameMap, groupMap, gps);
//fills tree names with shared files groups
Treenames = lookup->getNamesGroups();
if (m->getControl_pressed()) { return 0; }
//create tree file
makeSimsShared(input, lookup, ct);
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
}else{
//read in dist file
filename = inputfile;
ReadMatrix* readMatrix;
if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
readMatrix->setCutoff(cutoff);
ListVector* list;
if(namefile != ""){
NameAssignment* nameMap = new NameAssignment(namefile);
nameMap->readMap();
readMatrix->read(nameMap);
list = readMatrix->getListVector();
delete nameMap;
}else if (countfile != "") {
CountTable* ct = new CountTable();
ct->readTable(countfile, true, false);
readMatrix->read(ct);
list = readMatrix->getListVector();
delete ct;
}else { NameAssignment* nameMap = NULL; readMatrix->read(nameMap); list = readMatrix->getListVector(); }
SparseDistanceMatrix* dMatrix = readMatrix->getDMatrix();
Treenames.clear();
//make treemap
CountTable ct;
set<string> nameMap;
map<string, string> groupMap;
set<string> gps;
for (int i = 0; i < list->getNumBins(); i++) {
string bin = list->get(i);
nameMap.insert(bin);
gps.insert(bin);
groupMap[bin] = bin;
Treenames.push_back(bin);
}
ct.createTable(nameMap, groupMap, gps);
vector<string> namesGroups = ct.getNamesOfGroups();
if (m->getControl_pressed()) { return 0; }
vector< vector<double> > matrix = makeSimsDist(dMatrix, list->getNumBins());
delete readMatrix;
delete dMatrix;
if (m->getControl_pressed()) { return 0; }
//create a new filename
map<string, string> variables;
variables["[filename]"] = outputDir + util.getRootName(util.getSimpleName(inputfile));
string outputFile = getOutputFileName("tree",variables);
outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
Tree* newTree = new Tree(&ct, matrix, Treenames);
if (m->getControl_pressed()) { delete newTree; newTree = NULL; }
else { newTree->assembleTree(); }
if (newTree != NULL) { newTree->createNewickFile(outputFile); delete newTree; }
if (m->getControl_pressed()) { return 0; } m->mothurOut("Tree complete.\n");
}
//set tree file as new current treefile
string currentName = "";
itTypes = outputTypes.find("tree");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setTreeFile(currentName); }
}
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "TreeGroupCommand", "execute");
exit(1);
}
}