public:
PreClusterCommand(string);
- ~PreClusterCommand();
- int execute();
- void help();
+ PreClusterCommand();
+ ~PreClusterCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "pre.cluster"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Pre.cluster"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
int diffs, length;
map<string, int> sizes; //this map a seq name to the number of identical seqs in the names file
map<string, int>::iterator itSize;
// map<string, bool> active; //maps sequence name to whether it has already been merged or not.
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
int readFASTA();
void readNameFile();