sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / setcurrentcommand.h

diff --git a/setcurrentcommand.h b/setcurrentcommand.h
index 5a40e4a20f97377e86d973c2412cc17e12e3fcb0..190bf77f2889211f90a0be91c5f3073d02c017b9 100644 (file)
--- a/setcurrentcommand.h
+++ b/setcurrentcommand.h
@@ -23,8 +23,12 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "set.current"; }
        string getCommandCategory()             { return "General";             }
-       string getHelpString(); 
        
+       string getHelpString(); 
+    string getOutputPattern(string){ return ""; }      
+       string getCitation() { return "http://www.mothur.org/wiki/Set.current"; }
+       string getDescription()         { return "set current files for mothur"; }
+
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
        
@@ -36,8 +40,8 @@ private:
        string clearTypes;
        vector<string> types;
        
-       string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
-       string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile;
+       string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile, countfile;
+       string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
 
        
 };