string getTaxonomyFile() { return taxonomyfile; }
string getFlowFile() { return flowfile; }
string getBiomFile() { return biomfile; }
+ string getCountTableFile() { return counttablefile; }
string getProcessors() { return processors; }
void setListFile(string f) { listfile = getFullPathName(f); }
void setTaxonomyFile(string f) { taxonomyfile = getFullPathName(f); }
void setFlowFile(string f) { flowfile = getFullPathName(f); }
void setBiomFile(string f) { biomfile = getFullPathName(f); }
+ void setCountTableFile(string f) { counttablefile = getFullPathName(f); }
void setProcessors(string p) { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n"); }
void printCurrentFiles();
processors = "1";
flowfile = "";
biomfile = "";
+ counttablefile = "";
gui = false;
printedHeaders = false;
commandInputsConvertError = false;
string releaseDate, version;
string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
- string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
+ string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile;
vector<string> Groups;
vector<string> namesOfGroups;