public:
AlignCheckCommand(string);
- ~AlignCheckCommand(){};
+ AlignCheckCommand();
+ ~AlignCheckCommand(){}
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
vector<int> structMap;
string mapfile, fastafile, outputDir;
bool abort;
- int seqLength;
+ int seqLength, haderror;
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
void readMap();
statData getStats(string sequence);