//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(globaldata->getPhylipFile()); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(globaldata->getPhylipFile()); //if user entered a file with a path then preserve it
}
//make sure the user has already run the read.dist command
if (groups == "not found") { groups = ""; savegroups = groups; }
else {
savegroups = groups;
- splitAtDash(groups, Groups);
+ m->splitAtDash(groups, Groups);
globaldata->Groups = Groups;
}
try {
ofstream outCov;
- summaryFile = outputDir + getRootName(getSimpleName(globaldata->getPhylipFile())) + "libshuff.coverage";
- openOutputFile(summaryFile, outCov);
+ summaryFile = outputDir + m->getRootName(m->getSimpleName(globaldata->getPhylipFile())) + "libshuff.coverage";
+ m->openOutputFile(summaryFile, outCov);
outputNames.push_back(summaryFile);
outCov.setf(ios::fixed, ios::floatfield); outCov.setf(ios::showpoint);
//cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
try {
ofstream outSum;
- summaryFile = outputDir + getRootName(getSimpleName(globaldata->getPhylipFile())) + "libshuff.summary";
- openOutputFile(summaryFile, outSum);
+ summaryFile = outputDir + m->getRootName(m->getSimpleName(globaldata->getPhylipFile())) + "libshuff.summary";
+ m->openOutputFile(summaryFile, outSum);
outputNames.push_back(summaryFile);
outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);