X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=makebiomcommand.h;h=7ea381f145af343213a25bd32109d20fa1fb1dee;hp=31077aecb64add7041ec1ac0cb3ae9ecf5bba232;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=aa23898d895a8c04cc4582a8809343df0aef6622

diff --git a/makebiomcommand.h b/makebiomcommand.h
index 31077ae..7ea381f 100644
--- a/makebiomcommand.h
+++ b/makebiomcommand.h
@@ -25,7 +25,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "make.biom";	}
 	string getCommandCategory()		{ return "General";		}
+	
 	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"; }
     
@@ -34,14 +36,16 @@ 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*>&);
 };