working on pam

[mothur.git] / chimerabellerophoncommand.h

diff --git a/chimerabellerophoncommand.h b/chimerabellerophoncommand.h
index e450b52bbe3326f5677cd914f0fa19c9c7970962..23e555d6914482d9a2c819b079715d1a178d0f53 100644 (file)
--- 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;
 };
 
 /***********************************************************/