vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
vector<string> Treenames;
//map<string, string> names;
- vector<string> binLabelsInFile;
- vector<string> currentBinLabels;
+ vector<string> sharedBinLabelsInFile;
+ vector<string> currentSharedBinLabels;
+ vector<string> listBinLabelsInFile;
+ //vector<string> currentListBinLabels;
string saveNextLabel, argv, sharedHeaderMode, groupMode;
- bool printedHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
+ bool printedSharedHeaders, printedListHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
//functions from mothur.h
//file operations
counttablefile = "";
summaryfile = "";
gui = false;
- printedHeaders = false;
+ printedSharedHeaders = false;
+ printedListHeaders = false;
commandInputsConvertError = false;
mothurCalling = false;
debug = false;