private:
bool abort;
string fastafile, namefile, outputDir;
+ int diffs, percent;
vector<seqRNode> alignSeqs;
map<string, string> names; //represents the names file first column maps to second column
map<string, int> sizes; //this map a seq name to the number of identical seqs in the names file
int readFASTA();
void readNameFile();
void printData(string, string); //fasta filename, names file name
+ bool isFragment(string, string);
};