*
*/
+#include "mothur.h"
#include "command.hpp"
-#include "globaldata.hpp"
-
-
+#include "database.hpp"
+#include "alignment.hpp"
class AlignCommand : public Command {
void help();
private:
- GlobalData* globaldata;
- OptionParser* parser;
- map<string, string> parameters;
- map<string, string>::iterator it;
- bool abort;
+ struct linePair {
+ int start;
+ int numSeqs;
+ linePair(int i, int j) : start(i), numSeqs(j) {}
+ };
+ map<int, int> processIDS; //end line, processid
+ vector<linePair*> lines;
+
+ Database* templateDB;
+ Alignment* alignment;
+
+ int driver(linePair*, string, string);
+ void createProcesses(string, string);
+ void appendAlignFiles(string, string);
+ void appendReportFiles(string, string);
+
string candidateFileName, templateFileName, distanceFileName, search, align;
- int kmerSize;
float match, misMatch, gapOpen, gapExtend;
- ofstream out;
- ifstream in;
- int ableToOpen;
-
+ int processors, kmerSize;
+ bool abort;
};
-
-
-#endif
\ No newline at end of file
+#endif