X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=degapseqscommand.h;h=3b03c9b0ca1d8a61704dd3c13885d12d8204100a;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=5501d49b6affcdfe7e24fb8b444f837800d08ff5;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/degapseqscommand.h b/degapseqscommand.h
index 5501d49..3b03c9b 100644
--- a/degapseqscommand.h
+++ b/degapseqscommand.h
@@ -17,13 +17,19 @@ class DegapSeqsCommand : public Command {
 public:
 	DegapSeqsCommand(string);
 	DegapSeqsCommand();
-	~DegapSeqsCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~DegapSeqsCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "degap.seqs";		}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Degap.seqs"; }
+	string getDescription()		{ return "removes gap characters from sequences"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 
@@ -31,7 +37,7 @@ private:
 	string fastafile, outputDir;
 	vector<string> outputNames;
 	vector<string> fastaFileNames;
-	map<string, vector<string> > outputTypes;
+	
 };
 
 #endif