public:
AlignCommand(string);
+ AlignCommand();
~AlignCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
vector<int> processIDS; //processid
vector<linePair*> lines;
bool MPIWroteAccnos;
+ map<string, vector<string> > outputTypes;
AlignmentDB* templateDB;
Alignment* alignment;
float match, misMatch, gapOpen, gapExtend, threshold;
int processors, kmerSize;
vector<string> candidateFileNames;
+ vector<string> outputNames;
bool abort, flip;
};