*
*/
+#include "mothur.h"
#include "command.hpp"
-#include "globaldata.hpp"
+#include "database.hpp"
+#include "alignment.hpp"
+#include "alignmentdb.h"
class AlignCommand : public Command {
public:
- AlignCommand();
+ AlignCommand(string);
+ AlignCommand();
~AlignCommand();
- int execute();
-
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
+ int execute();
+ void help();
+
private:
- GlobalData* globaldata;
- string candidateFileName, templateFileName, distanceFileName;
- int kmerSize;
- float match, misMatch, gapOpen, gapExtend;
- ofstream out;
- ifstream in;
-
+ struct linePair {
+ 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;
+ bool MPIWroteAccnos;
+ map<string, vector<string> > outputTypes;
+
+ AlignmentDB* templateDB;
+ Alignment* alignment;
+
+ int driver(linePair*, string, string, string, string);
+ int createProcesses(string, string, string, string);
+ void appendAlignFiles(string, string);
+ void appendReportFiles(string, string);
+
+ #ifdef USE_MPI
+ int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+ #endif
+
+ string candidateFileName, templateFileName, distanceFileName, search, align, outputDir;
+ float match, misMatch, gapOpen, gapExtend, threshold;
+ int processors, kmerSize;
+ vector<string> candidateFileNames;
+ vector<string> outputNames;
+
+ bool abort, flip;
};
-
-
-#endif
\ No newline at end of file
+#endif