working on current change

[mothur.git] / distancecommand.h

diff --git a/distancecommand.h b/distancecommand.h
index 3b2d345d73fc46244446cd136366869f92a6e6d6..81267d1604ca2ba2a4551b2520cc6eeee7182a0f 100644 (file)
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -22,18 +22,23 @@ 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 linePair {
+       struct distlinePair {
                int start;
                int end;
+               
        };
        
        Dist* distCalculator;
@@ -43,12 +48,11 @@ private:
 
        int processors, numNewFasta;
        float cutoff;
-       map<int, int> processIDS;   //end line, processid
-       vector<linePair*> lines;
+       vector<int> processIDS;   //end line, processid
+       vector<distlinePair> lines;
        
        bool abort;
        vector<string>  Estimators, outputNames; //holds estimators to be used
-       map<string, vector<string> > outputTypes;
        
        //void m->appendFiles(string, string);
        void createProcesses(string);