removed UWSig and WSig from output if user does not set random=T

[mothur.git] / chimerauchimecommand.h

diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index 36e4a39aae24570e6f6cb5965f19261f0b3c9b63..8478117f3c99cd2f31224e614d3a95943fc1b4b0 100644 (file)
--- a/chimerauchimecommand.h
+++ b/chimerauchimecommand.h
@@ -26,23 +26,19 @@ public:
        string getCommandName()                 { return "chimera.uchime";              }
        string getCommandCategory()             { return "Sequence Processing"; }
        string getHelpString(); 
-       string getCitation() { return "http://drive5.com/uchime/ \nhttp://www.mothur.org/wiki/Chimera.uchime"; }
-       
+       string getCitation() { return "uchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\nhttp://www.mothur.org/wiki/Chimera.uchime\nEdgar,R.C., Haas,B.J., Clemente,J.C., Quince,C. and Knight,R. (2011), UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, in press.\n"; }
+       string getDescription()         { return "detect chimeric sequences"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }          
        
 private:
        vector<int> processIDS;   //processid
-       int driver(string, string, string);
-       int createProcesses(string, string, string);
-       
-#ifdef USE_MPI
-       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
-#endif
-       
-       bool abort;
-       string fastafile, templatefile, outputDir, namefile;
+       int driver(string, string, string, string);
+       int createProcesses(string, string, string, string);
+               
+       bool abort, useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract;
+       string fastafile, templatefile, outputDir, namefile, abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract;
        int processors;
        
        vector<string> outputNames;