public:
AlignCommand(string);
+ AlignCommand();
~AlignCommand();
+
+ vector<string> setParameters();
+ string getCommandName() { return "align.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+ string getCitation() { return "DeSantis TZ, Jr., Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL (2006). NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394-9.\nSchloss PD (2009). A high-throughput DNA sequence aligner for microbial ecology studies. PLoS ONE 4: e8230.\nSchloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844.\nhttp://www.mothur.org/wiki/Align.seqs http://www.mothur.org/wiki/Align.seqs"; }
+ string getDescription() { return "align sequences"; }
+
int execute();
- void help();
+ void help() { m->mothurOut(getHelpString()); }
private:
struct linePair {
- int start;
- int numSeqs;
- linePair(long 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;
+ bool MPIWroteAccnos;
AlignmentDB* templateDB;
Alignment* alignment;
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;
+ bool abort, flip, calledHelp, save;
+
};
#endif