added set.current and get.current commands and modified existing commands to update...

[mothur.git] / chimeracheckcommand.h

diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h
index 84c75ac8b8ff49e85cec777ffb8d2beeec544990..6e81812e469772b18a737930354f1bdf943a9ef9 100644 (file)
--- a/chimeracheckcommand.h
+++ b/chimeracheckcommand.h
@@ -21,7 +21,12 @@
 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();
        
@@ -30,9 +35,10 @@ 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;
        
@@ -50,6 +56,7 @@ private:
        vector<string> fastaFileNames;
        vector<string> nameFileNames;
        vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
                
 };