changed reading of name file to use buffered reads. note the splitAtWhiteSpace functi...

[mothur.git] / subsamplecommand.h

diff --git a/subsamplecommand.h b/subsamplecommand.h
index 6716903105f2fc25d018b77d977d6fa57875a148..7235a7b68ec569412bb97d1b98f076ff3b439bdb 100644 (file)
--- a/subsamplecommand.h
+++ b/subsamplecommand.h
@@ -29,7 +29,9 @@ public:
        string getCommandName()                 { return "sub.sample";  }
        string getCommandCategory()             { return "General";             }
        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()); }  
        
@@ -43,13 +45,12 @@ 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>&);