X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chopseqscommand.h;h=e73714d2e98406da2a05e54bb34f61398bd0143c;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=2da134e4660202410c86f86d6c1ef1e1139bff5e;hpb=62568a297aaf939ab753334f17abde82ec8e8531;p=mothur.git

diff --git a/chopseqscommand.h b/chopseqscommand.h
index 2da134e..e73714d 100644
--- a/chopseqscommand.h
+++ b/chopseqscommand.h
@@ -18,18 +18,27 @@ 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 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, fromend;
+		string fastafile, outputDir, keep;
+		bool abort, countGaps, Short;
+		int numbases;
+		vector<string> outputNames;
 		
-		string getChoppedAligned(Sequence);
-		string getChoppedUnaligned(Sequence);
+		string getChopped(Sequence);
 };
 
 #endif