#include "inputdata.h"
#include "listvector.hpp"
#include "sequence.hpp"
+#include "counttable.h"
/***************************************************************************************/
int splitList(ListVector*);
int splitNames(); //namefile
int writeNames();
- int writeList(ListVector*, string);
+ int writeList(ListVector*, string, int);
int writeAccnos(string);
int parseGroup(string);
int parseFasta(string);
+ int parseCount(string);
+ int splitCount();
int readNamesFile(); //namefile
int createNameMap(ListVector*);
vector<string> outputNames;
- ListVector* list;
- GroupMap* groupMap;
- InputData* input;
+ GroupMap groupMap;
+ CountTable ct;
- string outputDir, listfile, namefile, groupfile, label, groups, fastafile, inputFile;
+ string outputDir, listfile, namefile, groupfile, countfile, 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;