//**********************************************************************************************************************
int GetRAbundCommand::processList(ofstream& out){
try {
CountTable ct;
ct.readTable(countfile, false, false);
InputData input(inputfile, format);
ListVector* list = input.getListVector();
string lastLabel = list->getLabel();
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
if (m->control_pressed) { delete list; return 0; }
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if(allLines == 1 || labels.count(list->getLabel()) == 1){
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
if (m->control_pressed) { delete list; return 0; }
RAbundVector* rabund = new RAbundVector();
createRabund(ct, list, rabund);
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
delete rabund;
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
}
if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
delete list;
list = input.getListVector(lastLabel);
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
if (m->control_pressed) { delete list; return 0; }
RAbundVector* rabund = new RAbundVector();
createRabund(ct, list, rabund);
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
delete rabund;
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
//restore real lastlabel to save below
list->setLabel(saveLabel);
}
lastLabel = list->getLabel();
delete list;
list = input.getListVector();
}
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
//run last label if you need to
if (needToRun == true) {
if (list != NULL) { delete list; }
list = input.getListVector(lastLabel);
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
if (m->control_pressed) { delete list; return 0; }
RAbundVector* rabund = new RAbundVector();
createRabund(ct, list, rabund);
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
delete rabund;
delete list;
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetRAbundCommand", "processList");
exit(1);
}
}
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; }
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;
map<string, int> counts;
if(namefile != ""){
nameMap = new NameAssignment(namefile);
nameMap->readMap();
read->read(nameMap);
}else if (countfile != "") {
ct = new CountTable();
ct->readTable(countfile, false, false);
read->read(ct);
counts = ct->getNameMap();
}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);
list->printHeaders(listFile);
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;
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 && 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", counts);
}
else if(rndDist != rndPreviousDist){
printData(toString(rndPreviousDist, length-1), counts);
}
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", counts);
}
else if(rndPreviousDist<cutoff){
printData(toString(rndPreviousDist, length-1), counts);
}
delete matrix;
delete list;
delete rabund;
delete cluster;
if (countfile == "") {
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);
}
}
