working on pam

[mothur.git] / subsamplecommand.h

diff --git a/subsamplecommand.h b/subsamplecommand.h
index 5656dab49e7ac7d58665369e58c1950c17b93542..db4001a5c07337d51ea96aedfa9d3f20458b6685 100644 (file)
--- a/subsamplecommand.h
+++ b/subsamplecommand.h
@@ -16,6 +16,7 @@
 #include "rabundvector.hpp"
 #include "inputdata.h"
 #include "sequence.hpp"
+#include "counttable.h"
 
 
 class SubSampleCommand : public Command {
@@ -27,35 +28,39 @@ public:
        
        vector<string> setParameters();
        string getCommandName()                 { return "sub.sample";  }
-       string getCommandCategory()             { return "General";             }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        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()); }  
        
 private:       
        bool abort, pickedGroups, allLines, persample;
-       string listfile, groupfile, sharedfile, rabundfile, sabundfile, fastafile, namefile;
+       string listfile, groupfile, countfile, sharedfile, rabundfile, sabundfile, fastafile, namefile, taxonomyfile;
        set<string> labels; //holds labels to be used
        string groups, label, outputDir;
        vector<string> Groups, outputNames;
        int size;
        vector<string> names;
        map<string, vector<string> > nameMap;
+    CountTable ct;
        
-       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>&);
+       int processList(ListVector*&, set<string>&);
        int getNames();
        int readNames();
+    int getTax(set<string>&);
        
 };