it = parameters.find("taxonomy");
//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["taxonomy"] = 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; }
}
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = "";
- outputDir += hasPath(taxonomyFileName); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(taxonomyFileName); //if user entered a file with a path then preserve it
}
string temp = validParameter.validFile(parameters, "cutoff", false);
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; }
}
if (m->control_pressed) { delete tree; return 0; }
- string fileroot = outputDir + getRootName(getSimpleName(taxonomyFileName));
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
ofstream outList;
string outputListFile = fileroot + "tx.list";
- openOutputFile(outputListFile, outList);
+ m->openOutputFile(outputListFile, outList);
ofstream outSabund;
string outputSabundFile = fileroot + "tx.sabund";
- openOutputFile(outputSabundFile, outSabund);
+ m->openOutputFile(outputSabundFile, outSabund);
ofstream outRabund;
string outputRabundFile = fileroot + "tx.rabund";
- openOutputFile(outputRabundFile, outRabund);
+ m->openOutputFile(outputRabundFile, outRabund);
outputNames.push_back(outputListFile);
outputNames.push_back(outputSabundFile);
try {
ifstream in;
- openInputFile(namefile, in);
+ m->openInputFile(namefile, in);
string first, second;
map<string, string>::iterator itNames;
while(!in.eof()) {
- in >> first >> second; gobble(in);
+ in >> first >> second; m->gobble(in);
itNames = namemap.find(first);
if (itNames == namemap.end()) {