X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chopseqscommand.h;h=cc22c751483a75f246f69e4955985f158d041638;hb=38491018f166c7c5517518cfa64832582f20dd85;hp=dbf4d23b71ebc1302672e66bc65472331117713f;hpb=8f909cf6870cc2e4d8ed8cff69a203f6f83a160b;p=mothur.git

diff --git a/chopseqscommand.h b/chopseqscommand.h
index dbf4d23..cc22c75 100644
--- a/chopseqscommand.h
+++ b/chopseqscommand.h
@@ -21,23 +21,25 @@ class ChopSeqsCommand : public Command {
 		ChopSeqsCommand(string);
 		ChopSeqsCommand();	
 		~ChopSeqsCommand(){};
-		vector<string> getRequiredParameters();
-		vector<string> getValidParameters();
-		vector<string> getRequiredFiles();
-		map<string, vector<string> > getOutputFiles() { return outputTypes; }
-		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, countGaps, Short;
 		int numbases;
 		vector<string> outputNames;
-		map<string, vector<string> > outputTypes;
 		
 		string getChopped(Sequence);
-		
-		
 };
 
 #endif