working on pam

[mothur.git] / subsamplecommand.h

diff --git a/subsamplecommand.h b/subsamplecommand.h
index 7116909e3f97ec758ff4b9de178e0d9ebd0dded1..db4001a5c07337d51ea96aedfa9d3f20458b6685 100644 (file)
--- a/subsamplecommand.h
+++ b/subsamplecommand.h
@@ -29,8 +29,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "sub.sample";  }
        string getCommandCategory()             { return "Sequence Processing";         }
-       string getOutputFileNameTag(string, string);
+       
        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"; }
 
@@ -39,7 +40,7 @@ public:
        
 private:       
        bool abort, pickedGroups, allLines, persample;
-       string listfile, groupfile, countfile, 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;
@@ -56,9 +57,10 @@ private:
        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>&);
        
 };