added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / rarefactsharedcommand.h

diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
index 54d0495fdc8a1ac5063c8c01ff24970cea2b02fb..a5b45468d7059ad2c9e8877376c0154102d05316 100644 (file)
--- a/rarefactsharedcommand.h
+++ b/rarefactsharedcommand.h
@@ -25,9 +25,11 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "rarefaction.shared";          }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Rarefaction.shared"; }
-       
+       string getCitation() { return "Magurran AE (2004). Measuring biological diversity. Blackwell Pub.: Malden, Ma. \nhttp://www.mothur.org/wiki/Rarefaction.shared"; }
+       string getDescription()         { return "generate inter-sample rarefaction curves using a re-sampling without replacement approach"; }
+
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
        
@@ -35,17 +37,18 @@ public:
 private:
        
        vector<SharedRAbundVector*> lookup;
-       InputData* input;
-       Rarefact* rCurve;
-       vector<Display*> rDisplays;
        int nIters;
        string format;
        float freq;
        
-       bool abort, allLines, jumble;
+     map<int, string> file2Group; //index in outputNames[i] -> group
+       bool abort, allLines, jumble, groupMode;
        set<string> labels; //holds labels to be used
-       string label, calc, groups, outputDir, sharedfile;
-       vector<string>  Estimators, Groups, outputNames;
+       string label, calc, groups, outputDir, sharedfile, designfile;
+       vector<string>  Estimators, Groups, outputNames, Sets;
+    
+    int process(GroupMap&, string);
+    vector<string> createGroupFile(vector<string>&);
 
 };