X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeseqscommand.h;h=e26e751032402cd39dac933acf3f57814ab2fc0f;hb=79a7d3273749b08d4f9f8dfe350c964ff0c4351e;hp=df96e4514bc84787ad901e137bbc794588681705;hpb=a44542a3c740cf957cff72ac71742f2fe48b0eaf;p=mothur.git

diff --git a/removeseqscommand.h b/removeseqscommand.h
index df96e45..e26e751 100644
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -23,7 +23,8 @@ class RemoveSeqsCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "remove.seqs";				}
 		string getCommandCategory()		{ return "Sequence Processing";		}
-		string getHelpString();	
+		string getOutputFileNameTag(string, string);
+	string getHelpString();	
 		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"; }
 
@@ -33,15 +34,16 @@ 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();
-		void readAccnos();
 		int readList();
 		int readTax();
 		int readQual();