//**********************************************************************************************************************
int CorrAxesCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thislookup) {
try {
vector<SharedRAbundFloatVector*> newLookup;
for (int i = 0; i < thislookup.size(); i++) {
SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
temp->setLabel(thislookup[i]->getLabel());
temp->setGroup(thislookup[i]->getGroup());
newLookup.push_back(temp);
}
//for each bin
vector<string> newBinLabels;
string snumBins = toString(thislookup[0]->getNumBins());
for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
//look at each sharedRabund and make sure they are not all zero
bool allZero = true;
for (int j = 0; j < thislookup.size(); j++) {
if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; }
}
//if they are not all zero add this bin
if (!allZero) {
for (int j = 0; j < thislookup.size(); j++) {
newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
}
//if there is a bin label use it otherwise make one
string binLabel = "Otu";
string sbinNumber = toString(i+1);
if (sbinNumber.length() < snumBins.length()) {
int diff = snumBins.length() - sbinNumber.length();
for (int h = 0; h < diff; h++) { binLabel += "0"; }
}
binLabel += sbinNumber;
if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; }
newBinLabels.push_back(binLabel);
}
}
for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
thislookup = newLookup;
m->currentBinLabels = newBinLabels;
return 0;
}
catch(exception& e) {
m->errorOut(e, "CorrAxesCommand", "eliminateZeroOTUS");
exit(1);
}
}
//this function is just used to convert files to test the differences between the metastats version and mothurs version
int MetaStatsCommand::convertToShared(string filename) {
try {
ifstream in;
m->openInputFile(filename, in);
string header = m->getline(in); m->gobble(in);
vector<string> groups = m->splitWhiteSpace(header);
vector<SharedRAbundFloatVector*> newLookup;
cout << groups.size() << endl;
for (int i = 0; i < groups.size(); i++) {
cout << "creating group " << groups[i] << endl;
SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
temp->setLabel("0.03");
temp->setGroup(groups[i]);
newLookup.push_back(temp);
}
int otuCount = 0;
while (!in.eof()) {
if (m->control_pressed) { break; }
string otuname;
in >> otuname; m->gobble(in);
otuCount++;
cout << otuname << endl;
for (int i = 0; i < groups.size(); i++) {
double temp;
in >> temp; m->gobble(in);
newLookup[i]->push_back(temp, groups[i]);
}
m->gobble(in);
}
in.close();
ofstream out;
m->openOutputFile(filename+".shared", out);
out << "label\tgroup\tnumOTUs\t";
string snumBins = toString(otuCount);
for (int i = 0; i < otuCount; i++) {
string binLabel = "Otu";
string sbinNumber = toString(i+1);
if (sbinNumber.length() < snumBins.length()) {
int diff = snumBins.length() - sbinNumber.length();
for (int h = 0; h < diff; h++) { binLabel += "0"; }
}
binLabel += sbinNumber;
out << binLabel << '\t';
}
out << endl;
for (int i = 0; i < groups.size(); i++) {
out << "0.03" << '\t' << groups[i] << '\t';
newLookup[i]->print(out);
}
out.close();
cout << filename+".shared" << endl;
return 0;
}
catch(exception& e) {
m->errorOut(e, "MetaStatsCommand", "convertToShared");
exit(1);
}
}
int CorrAxesCommand::getMetadata(){
try {
vector<string> groupNames;
ifstream in;
m->openInputFile(metadatafile, in);
string headerLine = m->getline(in); m->gobble(in);
istringstream iss (headerLine,istringstream::in);
//read the first label, because it refers to the groups
string columnLabel;
iss >> columnLabel; m->gobble(iss);
//save names of columns you are reading
while (!iss.eof()) {
iss >> columnLabel; m->gobble(iss);
metadataLabels.push_back(columnLabel);
}
int count = metadataLabels.size();
//read rest of file
while (!in.eof()) {
if (m->control_pressed) { in.close(); return 0; }
string group = "";
in >> group; m->gobble(in);
groupNames.push_back(group);
SharedRAbundFloatVector* tempLookup = new SharedRAbundFloatVector();
tempLookup->setGroup(group);
tempLookup->setLabel("1");
for (int i = 0; i < count; i++) {
float temp = 0.0;
in >> temp;
tempLookup->push_back(temp, group);
}
lookupFloat.push_back(tempLookup);
m->gobble(in);
}
in.close();
//remove any groups the user does not want, and set globaldata->groups with only valid groups
SharedUtil* util;
util = new SharedUtil();
Groups = m->getGroups();
util->setGroups(Groups, groupNames);
m->setGroups(Groups);
for (int i = 0; i < lookupFloat.size(); i++) {
//if this sharedrabund is not from a group the user wants then delete it.
if (util->isValidGroup(lookupFloat[i]->getGroup(), m->getGroups()) == false) {
delete lookupFloat[i]; lookupFloat[i] = NULL;
lookupFloat.erase(lookupFloat.begin()+i);
i--;
}
}
delete util;
return 0;
}
catch(exception& e) {
m->errorOut(e, "CorrAxesCommand", "getMetadata");
exit(1);
}
}