added oligos class. added check orient parameter to trim.flows, sffinfo, fastq.info...

[mothur.git] / collectcommand.h

diff --git a/collectcommand.h b/collectcommand.h
index 1d8734fa5d713ad4535e067af55d3c56d699573c..8423b7b762233c549ce62283d5ecb800c7ceb08f 100644 (file)
--- a/collectcommand.h
+++ b/collectcommand.h
@@ -38,8 +38,9 @@ public:
        string getCommandName()                 { return "collect.single";                      }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getCitation() { return "Schloss PD, Handelsman J (2006). Introducing SONS, A tool that compares the membership of microbial communities. Appl Environ Microbiol 72: 6773-9. \nhttp://www.mothur.org/wiki/Collect.single"; }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getDescription()         { return "generates collector's curves using calculators, that describe the richness, diversity, and other features of individual samples"; }
        
        int execute(); 
@@ -51,7 +52,7 @@ private:
        InputData* input;
        Collect* cCurve;
        vector<Display*> cDisplays;
-       int abund, size;
+       int abund, size, alpha;
        float freq;
        vector<string> outputNames;