X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=getsabundcommand.h;h=b5363e1bce548af4af74408593d855cac4da973c;hb=4956d362c5bc6a47cf7a6290258f0e763e3a406e;hp=cd95d94e915f53d947e37b12127b898d65d43fd8;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/getsabundcommand.h b/getsabundcommand.h
index cd95d94..b5363e1 100644
--- a/getsabundcommand.h
+++ b/getsabundcommand.h
@@ -21,7 +21,12 @@ 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();
 	
@@ -31,16 +36,14 @@ private:
 	ofstream out;
 	ReadOTUFile* read;
 	OrderVector* order;
-	OrderVector* lastOrder;
 	InputData* input;
 	SAbundVector* sabund;
-	OptionParser* parser;
-	map<string, string> parameters;
-	map<string, string>::iterator it;
+	vector<string> outputNames;
+	map<string, vector<string> > outputTypes;
+
 	bool abort, allLines;
-	set<int> lines; //hold lines to be used
 	set<string> labels; //holds labels to be used
-	string line, label;
+	string label;
 
 };