pat's changes to seq.error command

[mothur.git] / chimerapintailcommand.h

diff --git a/chimerapintailcommand.h b/chimerapintailcommand.h
index 0ddfc1c6229758991e74b0def36a778182a74da6..d2b2e03a3196d61cf7036ff879f1a18bec741ae6 100644 (file)
--- a/chimerapintailcommand.h
+++ b/chimerapintailcommand.h
@@ -22,17 +22,23 @@ class ChimeraPintailCommand : public Command {
 public:
 
        ChimeraPintailCommand(string);
+       ChimeraPintailCommand();
        ~ChimeraPintailCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
 private:
 
        struct linePair {
-               int start;
-               int numSeqs;
-               linePair(long int i, int j) : start(i), numSeqs(j) {}
+               unsigned long int start;
+               unsigned long int end;
+               linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
        };
+
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
        
@@ -40,13 +46,16 @@ 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, MPIWroteAccnos;
-       string fastafile, templatefile, consfile, quanfile, maskfile, outputDir;
+       bool abort, filter;
+       string fastafile, templatefile, consfile, quanfile, maskfile, outputDir, inputDir;
        int processors, window, increment, numSeqs, templateSeqsLength;
        Chimera* chimera;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
+       vector<string> fastaFileNames;
        
        
 };