mods to trim.seqs

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index c5ef88885d9b4c1e7275c998e8a2b35bbbbba99b..ff1933735b2862935b3283b61ca96f180f6df546 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -20,7 +20,12 @@
 class ChimeraSlayerCommand : public Command {
 public:
        ChimeraSlayerCommand(string);
+       ChimeraSlayerCommand();
        ~ChimeraSlayerCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -36,21 +41,23 @@ private:
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
        
-       int driver(linePair*, string, string, string);
-       int createProcesses(string, string, string);
+       int driver(linePair*, string, string, string, string);
+       int createProcesses(string, string, string, string);
                
        #ifdef USE_MPI
-       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
        #endif
 
-       bool abort, realign;
-       string fastafile, templatefile, outputDir, search;
+       bool abort, realign, trim, trimera;
+       string fastafile, templatefile, outputDir, search, namefile, includeAbunds;
        int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
        float divR;
        Chimera* chimera;
        
        vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        vector<string> fastaFileNames;
+       vector<string> nameFileNames;
        
 };