added cutoff change to hcluster

[mothur.git] / chimerapintailcommand.h

diff --git a/chimerapintailcommand.h b/chimerapintailcommand.h
index 9fc6f437c6724f3424e412b3af5ad0d59c06066e..acb078173501a7d7cf48cc88f5c305e12eccc225 100644 (file)
--- a/chimerapintailcommand.h
+++ b/chimerapintailcommand.h
@@ -22,17 +22,26 @@ class ChimeraPintailCommand : public Command {
 public:
 
        ChimeraPintailCommand(string);
-       ~ChimeraPintailCommand();
-       int execute();
-       void help();
+       ChimeraPintailCommand();
+       ~ChimeraPintailCommand(){}
        
+       vector<string> setParameters();
+       string getCommandName()                 { return "chimera.pintail";             }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       string getHelpString(); 
+       string getCitation() { return "Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2005). At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71: 7724-36. \nAshelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2006). New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72: 5734-41. \nhttp://www.mothur.org/wiki/Chimera.pintail"; }
+       string getDescription()         { return "detect chimeric sequences"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }          
 private:
 
        struct linePair {
                unsigned long int start;
-               int numSeqs;
-               linePair(unsigned long int i, int j) : start(i), numSeqs(j) {}
+               unsigned long int end;
+               linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
        };
+
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
        
@@ -40,7 +49,7 @@ private:
        int createProcesses(string, string, string);
        
        #ifdef USE_MPI
-       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<long>&);
+       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
        #endif
 
        bool abort, filter;
@@ -49,8 +58,6 @@ private:
        Chimera* chimera;
        vector<string> outputNames;
        vector<string> fastaFileNames;
-       
-       
 };
 
 /***********************************************************/