changes while testing

[mothur.git] / chimeracheckcommand.h

diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h
index 6e81812e469772b18a737930354f1bdf943a9ef9..8981a14ff5e6e7813ab54123fe3fa1c8b68a0bc4 100644 (file)
--- a/chimeracheckcommand.h
+++ b/chimeracheckcommand.h
@@ -22,21 +22,27 @@ class ChimeraCheckCommand : public Command {
 public:
        ChimeraCheckCommand(string);
        ChimeraCheckCommand();
-       ~ChimeraCheckCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~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 {
-               unsigned long int start;
-               unsigned long int end;
-               linePair(unsigned long int i, unsigned long int j) : start(i), end(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
@@ -46,18 +52,16 @@ private:
        int createProcesses(string, string);
                
        #ifdef USE_MPI
-       int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long int>&);
+       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;
-       map<string, vector<string> > outputTypes;
-               
 };
 
 /***********************************************************/