*/
#include "command.hpp"
-#include "mothur.h"
-#include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-
-using namespace std;
+#include "filters.h"
+#include "mpi.h"
+class Sequence;
class FilterSeqsCommand : public Command {
public:
- FilterSeqsCommand();
+ FilterSeqsCommand(string);
~FilterSeqsCommand() {};
int execute();
+ void help();
private:
- void doTrump();
- void doSoft();
- void doHard();
- void doVertical();
-
- int alignmentLength;
+ struct linePair {
+ int start;
+ int numSeqs;
+ linePair(long int i, int j) : start(i), numSeqs(j) {}
+ };
+ vector<linePair*> lines;
+ vector<int> processIDS;
+
+ string vertical, filter, fasta, hard, outputDir, filterFileName;
+ vector<string> fastafileNames;
+ int alignmentLength, processors;
+ vector<int> bufferSizes;
+ vector<string> outputNames;
+
+ char trump;
+ bool abort;
+ float soft;
int numSeqs;
- GlobalData* globaldata;
- ReadSeqs* readSeqs;
- SequenceDB* db;
+ string createFilter();
+ int filterSequences();
+ int createProcessesCreateFilter(Filters&, string);
+ int createProcessesRunFilter(string, string);
+ int driverCreateFilter(Filters&, string, linePair*);
+ int driverRunFilter(string, string, string, linePair*);
+ int driverMPIRun(istringstream&, MPI_File&);
+ int MPICreateFilter(Filters&, string);
+ int setLines(string);
+ int parseBuffer(string, vector<string>&);
- string filter;
-
};
-#endif
\ No newline at end of file
+#endif