public:
ScreenSeqsCommand(string);
ScreenSeqsCommand();
- ~ScreenSeqsCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
+ ~ScreenSeqsCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "screen.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
private:
int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria;
vector<string> outputNames;
vector<string> optimize;
- map<string, vector<string> > outputTypes;
map<string, int> nameMap;
int readNames();