X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsabundcommand.h;h=b5363e1bce548af4af74408593d855cac4da973c;hb=257eaa172451ede9d63a0715f6cdb7336a52996b;hp=27d25c2f2c3d2739bb6cfecd85f7b059b4867442;hpb=0024441c1ff9a98467ba53cc7420a37c98f32e86;p=mothur.git

diff --git a/getsabundcommand.h b/getsabundcommand.h
index 27d25c2..b5363e1 100644
--- 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