added count file to get.groups and remove.groups. added shortcut parameter to classif...

[mothur.git] / subsamplecommand.h

diff --git a/subsamplecommand.h b/subsamplecommand.h
index 5656dab49e7ac7d58665369e58c1950c17b93542..c746e144119dc4d4c0d45ef10872b1f7c9951129 100644 (file)
--- a/subsamplecommand.h
+++ b/subsamplecommand.h
@@ -28,9 +28,11 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "sub.sample";  }
        string getCommandCategory()             { return "General";             }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Sub.sample"; }
-       
+       string getDescription()         { return "get a sampling of sequences from a list, shared, rabund, sabund or fasta file"; }
+
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
        
@@ -44,13 +46,12 @@ private:
        vector<string> names;
        map<string, vector<string> > nameMap;
        
-       int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
        int getSubSampleShared();
        int getSubSampleList();
        int getSubSampleRabund();
        int getSubSampleSabund();
        int getSubSampleFasta();
-       int processShared(vector<SharedRAbundVector*>&, ofstream&);
+       int processShared(vector<SharedRAbundVector*>&);
        int processRabund(RAbundVector*&, ofstream&);
        int processSabund(SAbundVector*&, ofstream&);
        int processList(ListVector*&, ofstream&, set<string>&);