//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();
//check for required parameters
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { listfile = ""; abort = true; }
- else if (listfile == "not found") { listfile = ""; }
+ else if (listfile == "not found") { listfile = ""; }
+ else { m->setListFile(listfile); }
sabundfile = validParameter.validFile(parameters, "sabund", true);
if (sabundfile == "not open") { sabundfile = ""; abort = true; }
else if (sabundfile == "not found") { sabundfile = ""; }
+ else { m->setSabundFile(sabundfile); }
rabundfile = validParameter.validFile(parameters, "rabund", true);
if (rabundfile == "not open") { rabundfile = ""; abort = true; }
else if (rabundfile == "not found") { rabundfile = ""; }
+ else { m->setRabundFile(rabundfile); }
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { fastafile = ""; abort = true; }
else if (fastafile == "not found") { fastafile = ""; }
+ else { m->setFastaFile(fastafile); }
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
+ else { m->setSharedFile(sharedfile); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { groupfile = ""; abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
-
+ else { m->setGroupFile(groupfile); }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
processShared(lookup, out);
processedLabels.insert(lookup[0]->getLabel());
lookup = input->getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
processShared(lookup, out);
processedLabels.insert(lookup[0]->getLabel());
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
processShared(lookup, out);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
individual += binnames[j];
}
}
- if (subset.count(individual) != 0) { newNames += individual; }
+ if (subset.count(individual) != 0) { newNames += individual + ","; }
//if there are names in this bin add to new list