X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimerabellerophoncommand.h;h=23e555d6914482d9a2c819b079715d1a178d0f53;hp=e450b52bbe3326f5677cd914f0fa19c9c7970962;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=fdc1f6eaf544f695fc1511f24bddd7e6069c33ba

diff --git a/chimerabellerophoncommand.h b/chimerabellerophoncommand.h
index e450b52..23e555d 100644
--- a/chimerabellerophoncommand.h
+++ b/chimerabellerophoncommand.h
@@ -20,9 +20,21 @@
 class ChimeraBellerophonCommand : public Command {
 public:
 	ChimeraBellerophonCommand(string);
-	~ChimeraBellerophonCommand();
-	int execute();
-	void help();
+	ChimeraBellerophonCommand();
+	~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:
 
@@ -30,6 +42,8 @@ private:
 	string fastafile, outputDir;
 	int processors, window, increment, numSeqs;
 	Chimera* chimera;
+	vector<string> outputNames;
+	vector<string> fastaFileNames;
 };
 
 /***********************************************************/