+ bool executing, runParse, jumble, gui, mothurCalling, debug;
+
+ //current files - if you add a new type you must edit optionParser->getParameters, get.current and set.current commands and mothurOut->printCurrentFiles/clearCurrentFiles/getCurrentTypes. add a get and set function.
+ string getPhylipFile() { return phylipfile; }
+ string getColumnFile() { return columnfile; }
+ string getListFile() { return listfile; }
+ string getRabundFile() { return rabundfile; }
+ string getSabundFile() { return sabundfile; }
+ string getNameFile() { return namefile; }
+ string getGroupFile() { return groupfile; }
+ string getOrderFile() { return orderfile; }
+ string getOrderGroupFile() { return ordergroupfile; }
+ string getTreeFile() { return treefile; }
+ string getSharedFile() { return sharedfile; }
+ string getRelAbundFile() { return relabundfile; }
+ string getDesignFile() { return designfile; }
+ string getFastaFile() { return fastafile; }
+ string getSFFFile() { return sfffile; }
+ string getQualFile() { return qualfile; }
+ string getOligosFile() { return oligosfile; }
+ string getAccnosFile() { return accnosfile; }
+ string getTaxonomyFile() { return taxonomyfile; }
+ string getFlowFile() { return flowfile; }
+ string getBiomFile() { return biomfile; }
+ string getCountTableFile() { return counttablefile; }
+ string getSummaryFile() { return summaryfile; }
+ string getProcessors() { return processors; }
+
+ void setListFile(string f) { listfile = getFullPathName(f); }
+ void setTreeFile(string f) { treefile = getFullPathName(f); }
+ void setGroupFile(string f) { groupfile = getFullPathName(f); groupMode = "group"; }
+ void setPhylipFile(string f) { phylipfile = getFullPathName(f); }
+ void setColumnFile(string f) { columnfile = getFullPathName(f); }
+ void setNameFile(string f) { namefile = getFullPathName(f); }
+ void setRabundFile(string f) { rabundfile = getFullPathName(f); }
+ void setSabundFile(string f) { sabundfile = getFullPathName(f); }
+ void setSharedFile(string f) { sharedfile = getFullPathName(f); }
+ void setRelAbundFile(string f) { relabundfile = getFullPathName(f); }
+ void setOrderFile(string f) { orderfile = getFullPathName(f); }
+ void setOrderGroupFile(string f) { ordergroupfile = getFullPathName(f); }
+ void setDesignFile(string f) { designfile = getFullPathName(f); }
+ void setFastaFile(string f) { fastafile = getFullPathName(f); }
+ void setSFFFile(string f) { sfffile = getFullPathName(f); }
+ void setQualFile(string f) { qualfile = getFullPathName(f); }
+ void setOligosFile(string f) { oligosfile = getFullPathName(f); }
+ void setAccnosFile(string f) { accnosfile = getFullPathName(f); }
+ void setTaxonomyFile(string f) { taxonomyfile = getFullPathName(f); }
+ void setFlowFile(string f) { flowfile = getFullPathName(f); }
+ void setBiomFile(string f) { biomfile = getFullPathName(f); }
+ void setSummaryFile(string f) { summaryfile = getFullPathName(f); }
+ void setCountTableFile(string f) { counttablefile = getFullPathName(f); groupMode = "count"; }
+ void setProcessors(string p) { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n"); }
+
+ void printCurrentFiles();
+ bool hasCurrentFiles();
+ void clearCurrentFiles();
+ set<string> getCurrentTypes();