it = parameters.find("list");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["list"] = inputDir + it->second; }
}
it = parameters.find("fasta");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
it = parameters.find("phylip");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["phylip"] = inputDir + it->second; }
}
it = parameters.find("column");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["column"] = inputDir + it->second; }
}
it = parameters.find("name");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ 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; }
}
it = parameters.find("group");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["group"] = inputDir + it->second; }
}
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; allLines = 1; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
m->mothurOut("You must provide a groupfile to use groups."); m->mothurOutEndLine();
abort = true;
}else {
- splitAtDash(groups, Groups);
+ m->splitAtDash(groups, Groups);
}
}
globaldata->Groups = Groups;
string temp = validParameter.validFile(parameters, "large", false); if (temp == "not found") { temp = "F"; }
- large = isTrue(temp);
+ large = m->isTrue(temp);
temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
convert(temp, precision);
delete nameMap;
//openfile for getMap to use
- openInputFile(distFile, inRow);
+ m->openInputFile(distFile, inRow);
if (m->control_pressed) { inRow.close(); remove(distFile.c_str()); return 0; }
}
names.clear();
binnames = globaldata->gListVector->get(i);
- splitAtComma(binnames, names);
+ m->splitAtComma(binnames, names);
for (int j = 0; j < names.size(); j++) {
nameToIndex[names[j]] = i;
userLabels.erase(list->getLabel());
}
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
delete list;
void GetOTURepCommand::readNamesFile() {
try {
vector<string> dupNames;
- openInputFile(namefile, inNames);
+ m->openInputFile(namefile, inNames);
string name, names, sequence;
dupNames.clear();
//parse names into vector
- splitAtComma(names, dupNames);
+ m->splitAtComma(names, dupNames);
//store names in fasta map
sequence = fasta->getSequence(name);
fasta->push_back(dupNames[i], sequence);
}
- gobble(inNames);
+ m->gobble(inNames);
}
inNames.close();
string nameRep;
//create output file
- if (outputDir == "") { outputDir += hasPath(listfile); }
+ if (outputDir == "") { outputDir += m->hasPath(listfile); }
ofstream newNamesOutput;
string outputNamesFile;
map<string, ofstream*> filehandles;
if (Groups.size() == 0) { //you don't want to use groups
- outputNamesFile = outputDir + getRootName(getSimpleName(listfile)) + processList->getLabel() + ".rep.names";
- openOutputFile(outputNamesFile, newNamesOutput);
+ outputNamesFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + ".rep.names";
+ m->openOutputFile(outputNamesFile, newNamesOutput);
outputNames.push_back(outputNamesFile);
outputNameFiles[outputNamesFile] = processList->getLabel();
}else{ //you want to use groups
for (int i=0; i<Groups.size(); i++) {
temp = new ofstream;
filehandles[Groups[i]] = temp;
- outputNamesFile = outputDir + getRootName(getSimpleName(listfile)) + processList->getLabel() + "." + Groups[i] + ".rep.names";
+ outputNamesFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." + Groups[i] + ".rep.names";
- openOutputFile(outputNamesFile, *(temp));
+ m->openOutputFile(outputNamesFile, *(temp));
outputNames.push_back(outputNamesFile);
outputNameFiles[outputNamesFile] = processList->getLabel() + "." + Groups[i];
}
string temp = processList->get(i);
vector<string> namesInBin;
- splitAtComma(temp, namesInBin);
+ m->splitAtComma(temp, namesInBin);
if (Groups.size() == 0) {
nameRep = findRep(namesInBin);
if (thisgroup == "not found") { m->mothurOut(namesInBin[j] + " is not in your groupfile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
- if (inUsersGroups(thisgroup, Groups)) { //add this name to correct group
+ if (m->inUsersGroups(thisgroup, Groups)) { //add this name to correct group
NamesInGroup[thisgroup].push_back(namesInBin[j]);
}
}
try{
//create output file
- if (outputDir == "") { outputDir += hasPath(listfile); }
- string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + label + ".rep.fasta";
- openOutputFile(outputFileName, out);
+ if (outputDir == "") { outputDir += m->hasPath(listfile); }
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + label + ".rep.fasta";
+ m->openOutputFile(outputFileName, out);
vector<repStruct> reps;
outputNames.push_back(outputFileName);
ofstream out2;
string tempNameFile = filename + ".temp";
- openOutputFile(tempNameFile, out2);
+ m->openOutputFile(tempNameFile, out2);
ifstream in;
- openInputFile(filename, in);
+ m->openInputFile(filename, in);
int i = 0;
while (!in.eof()) {
string rep, binnames;
- in >> i >> rep >> binnames; gobble(in);
+ in >> i >> rep >> binnames; m->gobble(in);
out2 << rep << '\t' << binnames << endl;
vector<string> names;
- splitAtComma(binnames, names);
+ m->splitAtComma(binnames, names);
int binsize = names.size();
//if you have a groupfile
out << sequence << endl;
}
}
-
+
+ in.close();
out.close();
out2.close();