working on current change

[mothur.git] / distancecommand.h

diff --git a/distancecommand.h b/distancecommand.h
index 595483d2b3e84aef55478a78bd84906771949e5d..81267d1604ca2ba2a4551b2520cc6eeee7182a0f 100644 (file)
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -22,13 +22,17 @@ class DistanceCommand : public Command {
 public:
        DistanceCommand(string);
        DistanceCommand();
-       ~DistanceCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();  
-       void help();
+       ~DistanceCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "dist.seqs";                   }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       string getHelpString(); 
+       string getCitation() { return "Schloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844. \nhttp://www.mothur.org/wiki/Dist.seqs"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
        struct distlinePair {
@@ -49,7 +53,6 @@ private:
        
        bool abort;
        vector<string>  Estimators, outputNames; //holds estimators to be used
-       map<string, vector<string> > outputTypes;
        
        //void m->appendFiles(string, string);
        void createProcesses(string);