removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / chimeraslayercommand.h

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index d201ccb5f1baa2c628f217c7c763523e832d70eb..02ebe722a522d763c309bab0ea2215f0ceac6f85 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -21,15 +21,16 @@ 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();
+       ~ChimeraSlayerCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "chimera.slayer";              }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }          
        
-               
 private:
 
        struct linePair {
@@ -56,7 +57,6 @@ private:
        Chimera* chimera;
        
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        vector<string> fastaFileNames;
        vector<string> nameFileNames;