fixed metastats, added resize to cluster.classic, added code to kill children if...

[mothur.git] / getsabundcommand.h

diff --git a/getsabundcommand.h b/getsabundcommand.h
index 27d25c2f2c3d2739bb6cfecd85f7b059b4867442..b5363e1bce548af4af74408593d855cac4da973c 100644 (file)
--- a/getsabundcommand.h
+++ b/getsabundcommand.h
@@ -20,9 +20,15 @@ class GlobalData;
 
 class GetSAbundCommand : public Command {
 public:
+       GetSAbundCommand(string);
        GetSAbundCommand();
        ~GetSAbundCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -30,9 +36,15 @@ private:
        ofstream out;
        ReadOTUFile* read;
        OrderVector* order;
-       OrderVector* lastOrder;
        InputData* input;
        SAbundVector* sabund;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
+
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
+       string label;
+
 };
 
 #endif