X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustercommand.h;h=c8e01749de20baac9fe523e9cbf0b5f158b35941;hb=c5f38b0c83719306fd2e5a7a83e04988b1853f62;hp=ad41a4506e926dc646066964ccdd11c98fc48826;hpb=bfbc55964f1977da72c2cea984288a427d370a59;p=mothur.git

diff --git a/clustercommand.h b/clustercommand.h
index ad41a45..c8e0174 100644
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -26,14 +26,13 @@
 	The cluster() command outputs three files *.list, *.rabund, and *.sabund.   */
 
 
-class GlobalData;
-
 class ClusterCommand : public Command {
 	
 public:
-	ClusterCommand();	
+	ClusterCommand(string);
 	~ClusterCommand();
 	int execute();	
+	void help();
 	
 private:
 	GlobalData* globaldata;
@@ -43,13 +42,21 @@ private:
 	RAbundVector* rabund;
 	RAbundVector oldRAbund;
 	ListVector oldList;
-	
-	string method, fileroot, tag;
+
+	bool abort, hard;
+
+	string method, fileroot, tag, outputDir;
 	double cutoff;
+	string showabund, timing;
 	int precision, length;
 	ofstream sabundFile, rabundFile, listFile;
+
+	bool print_start;
+	time_t start;
+	unsigned long loops;
 	
 	void printData(string label);
+	vector<string> outputNames;
 };
 
 #endif