classify.seqs allows sequences to be in taxonomy file that are not in template. ...

[mothur.git] / makebiomcommand.h

diff --git a/makebiomcommand.h b/makebiomcommand.h
index 31077aecb64add7041ec1ac0cb3ae9ecf5bba232..ee9bd1c99cf415c93b57fc85087a06d870298115 100644 (file)
--- a/makebiomcommand.h
+++ b/makebiomcommand.h
@@ -25,6 +25,7 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "make.biom";   }
        string getCommandCategory()             { return "General";             }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        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"; }
@@ -34,14 +35,16 @@ public:
        
 private:
     
-       string sharedfile, contaxonomyfile, groups, outputDir, format, label;
-       vector<string> outputNames, Groups;
+       string sharedfile, contaxonomyfile, metadatafile, groups, outputDir, format, label;
+       vector<string> outputNames, Groups, sampleMetadata;
        set<string> labels;
     
        bool abort, allLines;
     
     int getBiom(vector<SharedRAbundVector*>&);
     vector<string> getMetaData(vector<SharedRAbundVector*>&);
+    vector<string> parseTax(string tax, vector<string>& scores);
+    int getSampleMetaData(vector<SharedRAbundVector*>&);
 };