added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / pairwiseseqscommand.h

diff --git a/pairwiseseqscommand.h b/pairwiseseqscommand.h
index b40d6c97ea10bbc708ddc2c4985be7b960843fab..a3a91f7bcd1f4ad2bbd52024d36153399ebc1414 100644 (file)
--- a/pairwiseseqscommand.h
+++ b/pairwiseseqscommand.h
@@ -23,22 +23,26 @@ class PairwiseSeqsCommand : public Command {
 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 linePair {
+       struct distlinePair {
                int start;
                int end;
        };
-       map<int, int> processIDS;   //end line, processid
-       vector<linePair*> lines;
-       map<string, vector<string> > outputTypes;
+       
+       vector<int> processIDS;   //end line, processid
+       vector<distlinePair> lines;
        
        Alignment* alignment;
        Dist* distCalculator;
@@ -50,8 +54,8 @@ private:
        
        #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;