X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=clustercommand.h;h=c8e01749de20baac9fe523e9cbf0b5f158b35941;hb=6e81846c8e5b2614f6b06643a9f558fb0e6669fa;hp=5dbeb73e2a5e133669f1d5ffd0d61a85731ed9a5;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed;p=mothur.git

diff --git a/clustercommand.h b/clustercommand.h
index 5dbeb73..c8e0174 100644
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -9,10 +9,8 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include "globaldata.hpp"
 #include "command.hpp"
+#include "globaldata.hpp"
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
 #include "listvector.hpp"
@@ -28,14 +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;
@@ -45,13 +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