added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / pairwiseseqscommand.h

diff --git a/pairwiseseqscommand.h b/pairwiseseqscommand.h
index 69785186caa063419a06a7dc73054344ebcfeae9..a3a91f7bcd1f4ad2bbd52024d36153399ebc1414 100644 (file)
--- a/pairwiseseqscommand.h
+++ b/pairwiseseqscommand.h
@@ -29,8 +29,9 @@ public:
        string getCommandName()                 { return "pairwise.seqs";               }
        string getCommandCategory()             { return "Sequence Processing"; }
        string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Pairwise.seqs"; }
-       
+       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() { m->mothurOut(getHelpString()); }  
        
@@ -53,8 +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;