designfile = m->getDesignFile();
if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current designfile and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setDesignFile(designfile); }
//make sure the user has already run the read.otu command
sharedfile = validParameter.validFile(parameters, "shared", true);
sharedfile = m->getSharedFile();
if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setSharedFile(sharedfile); }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
process(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); }
process(lookup, out);
processedLabels.insert(lookup[0]->getLabel());
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
process(lookup, out);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }