public:
ClassifySeqsCommand(string);
+ ClassifySeqsCommand();
~ClassifySeqsCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
private:
struct linePair {
- int start;
- int numSeqs;
- linePair(int i, int j) : start(i), numSeqs(j) {}
+ unsigned long int start;
+ unsigned long int end;
+ linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
};
+
vector<int> processIDS; //processid
vector<linePair*> lines;
vector<string> fastaFileNames;
vector<string> namefileNames;
vector<string> groupfileNames;
- map<string, int> nameMap;
- map<string, int>::iterator itNames;
+ vector<string> outputNames;
+ map<string, vector<string> > nameMap;
+ map<string, vector<string> >::iterator itNames;
+ map<string, vector<string> > outputTypes;
Classify* classify;
int driver(linePair*, string, string, string);
void appendTaxFiles(string, string);
- void createProcesses(string, string, string);
+ int createProcesses(string, string, string);
string addUnclassifieds(string, int);
int MPIReadNamesFile(string);
#ifdef USE_MPI
- int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<long>&);
+ int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
#endif
};