groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; globaldata->Groups.clear(); }
else {
- splitAtDash(groups, Groups);
+ m->splitAtDash(groups, Groups);
globaldata->Groups = Groups;
}
T = globaldata->gTree;
tmap = globaldata->gTreemap;
- if(outputDir == "") { outputDir += hasPath(globaldata->getTreeFile()); }
- output = new ColumnFile(outputDir + getSimpleName(globaldata->getTreeFile()) + ".parsimony", itersString);
- outputNames.push_back(outputDir + getSimpleName(globaldata->getTreeFile()) + ".parsimony");
+ if(outputDir == "") { outputDir += m->hasPath(globaldata->getTreeFile()); }
+ output = new ColumnFile(outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".parsimony", itersString);
+ outputNames.push_back(outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".parsimony");
- sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".psummary";
- openOutputFile(sumFile, outSum);
+ sumFile = outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".psummary";
+ m->openOutputFile(sumFile, outSum);
outputNames.push_back(sumFile);
}else { //user wants random distribution
savetmap = globaldata->gTreemap;
getUserInput();
- if(outputDir == "") { outputDir += hasPath(randomtree); }
- output = new ColumnFile(outputDir+ getSimpleName(randomtree), itersString);
- outputNames.push_back(outputDir+ getSimpleName(randomtree));
+ if(outputDir == "") { outputDir += m->hasPath(randomtree); }
+ output = new ColumnFile(outputDir+ m->getSimpleName(randomtree), itersString);
+ outputNames.push_back(outputDir+ m->getSimpleName(randomtree));
}
//set users groups to analyze