X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chopseqscommand.h;h=cc22c751483a75f246f69e4955985f158d041638;hb=5a4ac4f954c4b4445bcee272f1f8220ddcc9c1e4;hp=b6af15466c3f7fde3062760335c12e11025e7393;hpb=3604ddb078ae09215ec1ddc2b8c183232e3b5f89;p=mothur.git

diff --git a/chopseqscommand.h b/chopseqscommand.h
index b6af154..cc22c75 100644
--- a/chopseqscommand.h
+++ b/chopseqscommand.h
@@ -18,18 +18,28 @@ class ChopSeqsCommand : public Command {
 	
 	public:
 	
-		ChopSeqsCommand(string);	
+		ChopSeqsCommand(string);
+		ChopSeqsCommand();	
 		~ChopSeqsCommand(){};
-		int execute();
-		void help();	
-		
+	
+		vector<string> setParameters();
+		string getCommandName()			{ return "chop.seqs";		}
+		string getCommandCategory()		{ return "Sequence Processing"; }
+		string getOutputFileNameTag(string, string);
+        string getHelpString();	
+		string getCitation() { return "http://www.mothur.org/wiki/Chops.seqs"; }
+		string getDescription()		{ return "trim sequence length"; }
+	
+		int execute(); 
+		void help() { m->mothurOut(getHelpString()); }		
+	
 	private:
 		string fastafile, outputDir, keep;
-		bool abort;
+		bool abort, countGaps, Short;
 		int numbases;
+		vector<string> outputNames;
 		
 		string getChopped(Sequence);
-		
 };
 
 #endif