//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
treefile = m->getTreeFile();
if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setTreeFile(treefile); }
//check for required parameters
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
if (m->control_pressed) {
delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
m->Groups.clear();
return 0;
}
for (int i = 0; i < T.size(); i++) {
if (m->control_pressed) { delete tmap; delete weighted;
- for (int i = 0; i < T.size(); i++) { delete T[i]; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ for (int i = 0; i < T.size(); i++) { delete T[i]; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
counter = 0;
rScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC...
userData = weighted->getValues(T[i], processors, outputDir); //userData[0] = weightedscore
if (m->control_pressed) { delete tmap; delete weighted;
- for (int i = 0; i < T.size(); i++) { delete T[i]; } if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ for (int i = 0; i < T.size(); i++) { delete T[i]; } if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//save users score
for (int s=0; s<numComp; s++) {
#endif
if (m->control_pressed) { delete tmap; delete weighted;
- for (int i = 0; i < T.size(); i++) { delete T[i]; } delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ for (int i = 0; i < T.size(); i++) { delete T[i]; } delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//report progress
// m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();
if (m->control_pressed) { delete tmap; delete weighted;
- for (int i = 0; i < T.size(); i++) { delete T[i]; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ for (int i = 0; i < T.size(); i++) { delete T[i]; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
printWSummaryFile();
if (m->control_pressed) {
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
return 0;
}
double tempScore;
for (int j = lines[(i+1)].start; j < (lines[(i+1)].start + lines[(i+1)].num); j++) { in >> tempScore; scores[j].push_back(tempScore); }
in.close();
- remove(s.c_str());
+ m->mothurRemove(s);
}
return 0;
void UnifracWeightedCommand::printWSummaryFile() {
try {
//column headers
- outSum << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t' << "WSig" << endl;
- m->mothurOut("Tree#\tGroups\tWScore\tWSig"); m->mothurOutEndLine();
+ outSum << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t';
+ m->mothurOut("Tree#\tGroups\tWScore\t");
+ if (random) { outSum << "WSig"; m->mothurOut("WSig"); }
+ outSum << endl; m->mothurOutEndLine();
//format output
outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" + toString((1/float(iters))) + "\n");
}
}else{
- outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl;
- cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl;
- m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t0.00\n");
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << endl;
+ m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\n");
}
count++;
}