X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=subsamplecommand.h;h=db4001a5c07337d51ea96aedfa9d3f20458b6685;hp=d1fb1226236dc3842b9ace53536cf95a266f1d5e;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=035f86272c776e1cccaa47021e26782e49cd41e7

diff --git a/subsamplecommand.h b/subsamplecommand.h
index d1fb122..db4001a 100644
--- a/subsamplecommand.h
+++ b/subsamplecommand.h
@@ -28,9 +28,10 @@ public:
 	
 	vector<string> setParameters();
 	string getCommandName()			{ return "sub.sample";	}
-	string getCommandCategory()		{ return "General";		}
-	string getOutputFileNameTag(string, string);
+	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"; }
 
@@ -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>&);
 	
 };