AlignCommand(string);
AlignCommand();
~AlignCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
+
+ 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 {
vector<int> processIDS; //processid
vector<linePair*> lines;
bool MPIWroteAccnos;
- map<string, vector<string> > outputTypes;
AlignmentDB* templateDB;
Alignment* alignment;
vector<string> candidateFileNames;
vector<string> outputNames;
- bool abort, flip;
+ bool abort, flip, calledHelp;
+
};
#endif