public:
SplitAbundCommand(string);
+ SplitAbundCommand();
~SplitAbundCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
private:
- int split(ListVector*);
- int split(); //namefile
+ int splitList(ListVector*);
+ int splitNames(); //namefile
+ int writeNames();
+ int writeList(ListVector*);
+ int writeAccnos(string);
+ int parseGroup(string);
+ int parseFasta(string);
+ int readNamesFile(); //namefile
+ int createNameMap(ListVector*);
vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
ListVector* list;
GroupMap* groupMap;
InputData* input;
- string outputDir, listfile, namefile, groupfile, label;
- set<string> labels;
- bool abort, allLines, accnos, wroteRareList, wroteAbundList;
+ string outputDir, listfile, namefile, groupfile, label, groups, fastafile, inputFile;
+ set<string> labels, rareNames, abundNames;
+ vector<string> Groups;
+ bool abort, allLines, accnos;
int cutoff;
+ //map<string, bool> wroteListFile;
+ map<string, string> nameMap;