X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.h;h=c5b6ca4141afc00c12b646ea34604b898b1c4131;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=60e471eebf7865d5924406ef7c720c3bdcdf4648;hpb=90708fe9701e3827e477c82fb3652539c3bf2a0d;p=mothur.git

diff --git a/getseqscommand.h b/getseqscommand.h
index 60e471e..c5b6ca4 100644
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -23,8 +23,9 @@ class GetSeqsCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "get.seqs";				}
 		string getCommandCategory()		{ return "Sequence Processing";		}
-		string getOutputFileNameTag(string, string);
+		
 	string getHelpString();	
+    string getOutputPattern(string);	
 		string getCitation() { return "http://www.mothur.org/wiki/Get.seqs"; }
 		string getDescription()		{ return "gets sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
 
@@ -37,7 +38,7 @@ class GetSeqsCommand : public Command {
 		vector<string> outputNames;
 		string accnosfile, accnosfile2, fastafile, namefile, countfile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
 		bool abort, dups;
-    
+        map<string, string> uniqueMap;
         //for debug
         map<string, set<string> > sanity; //maps file type to names chosen for file. something like "fasta" -> vector<string>. If running in debug mode this is filled and we check to make sure all the files have the same names. If they don't we output the differences for the user.