X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.h;h=42070e53a57cf05c6d5674e022c602636fa374bf;hb=3504e4e2feeb05aabb0c79aa42cb696522030924;hp=0f606ffb59ac884b46ac97d861aa3542786d1793;hpb=f6b5fea6e0fcc395235dfbfb466b9b6a031b540a;p=mothur.git

diff --git a/getseqscommand.h b/getseqscommand.h
index 0f606ff..42070e5 100644
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -23,7 +23,9 @@ class GetSeqsCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "get.seqs";				}
 		string getCommandCategory()		{ return "Sequence Processing";		}
-		string getHelpString();	
+		
+	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"; }
 
@@ -34,7 +36,7 @@ class GetSeqsCommand : public Command {
 	private:
 		set<string> names;
 		vector<string> outputNames;
-		string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+		string accnosfile, accnosfile2, fastafile, namefile, countfile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
 		bool abort, dups;
     
         //for debug
@@ -43,8 +45,8 @@ class GetSeqsCommand : public Command {
 		int readFasta();
 		int readName();
 		int readGroup();
+        int readCount();
 		int readAlign();
-		int readAccnos();
 		int readList();
 		int readTax();
 		int readQual();