//**********************************************************************************************************************
int RemoveRareCommand::processList(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);
string outputGroupFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
ofstream out, outGroup;
m->openOutputFile(outputFileName, out);
bool wroteSomething = false;
//you must provide a label because the names in the listfile need to be consistent
string thisLabel = "";
if (allLines) { m->mothurOut("For the listfile you must select one label, using first label in your listfile."); m->mothurOutEndLine(); }
else if (labels.size() > 1) { m->mothurOut("For the listfile you must select one label, using " + (*labels.begin()) + "."); m->mothurOutEndLine(); thisLabel = *labels.begin(); }
else { thisLabel = *labels.begin(); }
InputData input(listfile, "list");
ListVector* list = input.getListVector();
//get first one or the one we want
if (thisLabel != "") {
//use smart distancing
set<string> userLabels; userLabels.insert(thisLabel);
set<string> processedLabels;
string lastLabel = list->getLabel();
while((list != NULL) && (userLabels.size() != 0)) {
if(userLabels.count(list->getLabel()) == 1){
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
break;
}
if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
delete list;
list = input.getListVector(lastLabel);
break;
}
lastLabel = list->getLabel();
delete list;
list = input.getListVector();
}
if (userLabels.size() != 0) {
m->mothurOut("Your file does not include the label " + thisLabel + ". I will use " + lastLabel + "."); m->mothurOutEndLine();
list = input.getListVector(lastLabel);
}
}
//if groupfile is given then use it
GroupMap* groupMap;
if (groupfile != "") {
groupMap = new GroupMap(groupfile); groupMap->readMap();
SharedUtil util;
vector<string> namesGroups = groupMap->getNamesOfGroups();
util.setGroups(Groups, namesGroups);
m->openOutputFile(outputGroupFileName, outGroup);
}
if (list != NULL) {
//make a new list vector
ListVector newList;
newList.setLabel(list->getLabel());
//for each bin
for (int i = 0; i < list->getNumBins(); i++) {
if (m->control_pressed) { if (groupfile != "") { delete groupMap; outGroup.close(); m->mothurRemove(outputGroupFileName); } out.close(); m->mothurRemove(outputFileName); return 0; }
//parse out names that are in accnos file
string binnames = list->get(i);
vector<string> names;
string saveBinNames = binnames;
m->splitAtComma(binnames, names);
vector<string> newGroupFile;
if (groupfile != "") {
vector<string> newNames;
saveBinNames = "";
for(int k = 0; k < names.size(); k++) {
string group = groupMap->getGroup(names[k]);
if (m->inUsersGroups(group, Groups)) {
newGroupFile.push_back(names[k] + "\t" + group);
newNames.push_back(names[k]);
saveBinNames += names[k] + ",";
}
}
names = newNames;
saveBinNames = saveBinNames.substr(0, saveBinNames.length()-1);
}
if (names.size() > nseqs) { //keep bin
newList.push_back(saveBinNames);
for(int k = 0; k < newGroupFile.size(); k++) { outGroup << newGroupFile[k] << endl; }
}
}
//print new listvector
if (newList.getNumBins() != 0) {
wroteSomething = true;
newList.print(out);
}
}
out.close();
if (groupfile != "") { outGroup.close(); outputTypes["group"].push_back(outputGroupFileName); outputNames.push_back(outputGroupFileName); }
if (wroteSomething == false) { m->mothurOut("Your file contains only rare sequences."); m->mothurOutEndLine(); }
outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveRareCommand", "processList");
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);
}
}