public:
PairwiseSeqsCommand(string);
PairwiseSeqsCommand();
- ~PairwiseSeqsCommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
+ ~PairwiseSeqsCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "pairwise.seqs"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+ string getCitation() { return "Needleman SB, Wunsch CD (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-53. [ for needleman ]\nGotoh O (1982). An improved algorithm for matching biological sequences. J Mol Biol 162: 705-8. [ for gotoh ] \nhttp://www.mothur.org/wiki/Pairwise.seqs"; }
+ string getDescription() { return "calculates pairwise distances from an unaligned fasta file"; }
+
int execute();
- void help();
+ void help() { m->mothurOut(getHelpString()); }
private:
struct distlinePair {
int end;
};
-
vector<int> processIDS; //end line, processid
vector<distlinePair> lines;
- map<string, vector<string> > outputTypes;
Alignment* alignment;
Dist* distCalculator;
#ifdef USE_MPI
int driverMPI(int, int, MPI_File&, float);
- int driverMPI(int, int, string, unsigned long int&);
- int driverMPI(int, int, string, unsigned long int&, string);
+ int driverMPI(int, int, string, unsigned long long&);
+ int driverMPI(int, int, string, unsigned long long&, string);
#endif
string fastaFileName, align, calc, outputDir, output;