X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimerabellerophoncommand.h;h=23e555d6914482d9a2c819b079715d1a178d0f53;hp=6e1ae50794f23d92c75d0224011251e385ae8f43;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281

diff --git a/chimerabellerophoncommand.h b/chimerabellerophoncommand.h
index 6e1ae50..23e555d 100644
--- a/chimerabellerophoncommand.h
+++ b/chimerabellerophoncommand.h
@@ -21,13 +21,20 @@ class ChimeraBellerophonCommand : public Command {
 public:
 	ChimeraBellerophonCommand(string);
 	ChimeraBellerophonCommand();
-	~ChimeraBellerophonCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map< string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~ChimeraBellerophonCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "chimera.bellerophon";	}
+	string getCommandCategory()		{ return "Sequence Processing"; }
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "Huber T, Faulkner G, Hugenholtz P (2004). Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 2317-9. \nhttp://www.mothur.org/wiki/Chimera.bellerophon"; }
+	string getDescription()		{ return "detect chimeric sequences"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 		
 private:
 
@@ -36,7 +43,6 @@ private:
 	int processors, window, increment, numSeqs;
 	Chimera* chimera;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 	vector<string> fastaFileNames;
 };