public:
AlignCommand(string);
+ AlignCommand();
~AlignCommand();
+
+ vector<string> setParameters();
+ string getCommandName() { return "align.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+
int execute();
- void help();
+ void help() { m->mothurOut(getHelpString()); }
private:
struct linePair {
float match, misMatch, gapOpen, gapExtend, threshold;
int processors, kmerSize;
vector<string> candidateFileNames;
+ vector<string> outputNames;
- bool abort, flip;
+ bool abort, flip, calledHelp;
+
};
#endif