fixed metastats, added resize to cluster.classic, added code to kill children if...

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index c2d9c45cfa931e9510981a4ff0c82c1d1e0fa890..aa9b5e7102a324bce97095c2fce7d78f470ab3fc 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();
        
@@ -29,9 +34,10 @@ 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;
        
@@ -39,7 +45,7 @@ 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, realign;
@@ -49,6 +55,7 @@ private:
        Chimera* chimera;
        
        vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        vector<string> fastaFileNames;
        
 };