public:
PairwiseSeqsCommand(string);
PairwiseSeqsCommand();
- ~PairwiseSeqsCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
+ ~PairwiseSeqsCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "pairwise.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+
int execute();
- void help();
+ void help() { m->mothurOut(getHelpString()); }
private:
struct distlinePair {
int end;
};
-
vector<int> processIDS; //end line, processid
vector<distlinePair> lines;
- map<string, vector<string> > outputTypes;
Alignment* alignment;
Dist* distCalculator;