X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chopseqscommand.h;h=cc22c751483a75f246f69e4955985f158d041638;hb=ccae9eef0b44f2d63fdf4a707d0d40243aa1b990;hp=5d8d6c4a87223dd1ec5573563f64b0b658cfcc1d;hpb=21805b1c466a341d64a5a451f156a56d12c75dca;p=mothur.git

diff --git a/chopseqscommand.h b/chopseqscommand.h
index 5d8d6c4..cc22c75 100644
--- a/chopseqscommand.h
+++ b/chopseqscommand.h
@@ -12,20 +12,34 @@
 
 
 #include "command.hpp"
+#include "sequence.hpp"
 
 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;
-		bool abort;
-		int end;
+		string fastafile, outputDir, keep;
+		bool abort, countGaps, Short;
+		int numbases;
+		vector<string> outputNames;
+		
+		string getChopped(Sequence);
 };
 
 #endif