changes while testing

[mothur.git] / chimeracheckcommand.h

diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h
index b3b49d30bad83f82d5c48b3cf1acf82f80ac766e..8981a14ff5e6e7813ab54123fe3fa1c8b68a0bc4 100644 (file)
--- a/chimeracheckcommand.h
+++ b/chimeracheckcommand.h
@@ -13,6 +13,7 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "chimera.h"
+#include "chimeracheckrdp.h"
 
 
 /***********************************************************/
@@ -20,18 +21,30 @@
 class ChimeraCheckCommand : public Command {
 public:
        ChimeraCheckCommand(string);
-       ~ChimeraCheckCommand();
-       int execute();
-       void help();
+       ChimeraCheckCommand();
+       ~ChimeraCheckCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "chimera.check";               }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "CHIMERA_CHECK version 2.7 written by Niels Larsen (http://wdcm.nig.ac.jp/RDP/docs/chimera_doc.html) \nhttp://www.mothur.org/wiki/Chimera.check"; }
+       string getDescription()         { return "detect chimeric sequences"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
-               
 private:
 
        struct linePair {
-               int start;
-               int numSeqs;
-               linePair(long int i, int j) : start(i), numSeqs(j) {}
+               unsigned long long start;
+               unsigned long long end;
+               linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
        };
+
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
        
@@ -39,17 +52,16 @@ private:
        int createProcesses(string, string);
                
        #ifdef USE_MPI
-       int driverMPI(int, int, MPI_File&, MPI_File&, vector<long>&);
+       int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long long>&);
        #endif
 
-       bool abort, svg;
+       bool abort, svg, save;
        string fastafile, templatefile, namefile, outputDir;
        int processors, increment, ksize, numSeqs, templateSeqsLength;
        Chimera* chimera;
        vector<string> fastaFileNames;
        vector<string> nameFileNames;
        vector<string> outputNames;
-               
 };
 
 /***********************************************************/