fixes while testing 1.33.0

[mothur.git] / makebiomcommand.h

diff --git a/makebiomcommand.h b/makebiomcommand.h
index ee9bd1c99cf415c93b57fc85087a06d870298115..8f07c40d439529355af3fb3ee78e11b6b23aab7a 100644 (file)
--- a/makebiomcommand.h
+++ b/makebiomcommand.h
@@ -25,8 +25,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "make.biom";   }
        string getCommandCategory()             { return "General";             }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://biom-format.org/documentation/biom_format.html, http://www.mothur.org/wiki/Make.biom"; }
        string getDescription()         { return "creates a biom file"; }
     
@@ -35,16 +36,19 @@ public:
        
 private:
     
-       string sharedfile, contaxonomyfile, metadatafile, groups, outputDir, format, label;
+       string sharedfile, contaxonomyfile, metadatafile, groups, outputDir, format, label, referenceTax, picrustOtuFile;
        vector<string> outputNames, Groups, sampleMetadata;
        set<string> labels;
     
-       bool abort, allLines;
+       bool abort, allLines, picrust;
     
     int getBiom(vector<SharedRAbundVector*>&);
     vector<string> getMetaData(vector<SharedRAbundVector*>&);
     vector<string> parseTax(string tax, vector<string>& scores);
     int getSampleMetaData(vector<SharedRAbundVector*>&);
+    //for picrust
+    int getGreenGenesOTUIDs(vector<SharedRAbundVector*>&, map<string, string>&);
+    map<string, string> readGGOtuMap();
 };