X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removeseqscommand.h;h=1a6365dac35b9e18669f8827c4054268b9123d9e;hp=474951a9feaee7d497417cf2a03f206367056241;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=f687723a8357916e86a05116978e6869b039ce36

diff --git a/removeseqscommand.h b/removeseqscommand.h
index 474951a..1a6365d 100644
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -23,8 +23,9 @@ class RemoveSeqsCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "remove.seqs";				}
 		string getCommandCategory()		{ return "Sequence Processing";		}
-		string getOutputFileNameTag(string, string);
+		
 	string getHelpString();	
+    string getOutputPattern(string);	
 		string getCitation() { return "http://www.mothur.org/wiki/Remove.seqs"; }
 		string getDescription()		{ return "removes sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
 
@@ -34,13 +35,15 @@ class RemoveSeqsCommand : public Command {
 	
 	private:
 		set<string> names;
-		string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+		string accnosfile, fastafile, namefile, groupfile, countfile, alignfile, listfile, taxfile, qualfile, outputDir;
 		bool abort, dups;
 		vector<string> outputNames;
+        map<string, string> uniqueMap;
 		
 		int readFasta();
 		int readName();
 		int readGroup();
+        int readCount();
 		int readAlign();
 		int readList();
 		int readTax();