X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustercommand.h;h=787f835a0f33d1d157aeab41568286c28a752520;hb=1e0359c041eedc99670c93d824a2cf7fa72577cc;hp=9dfd2a063ada813ce96be831e55263fafe132c1a;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/clustercommand.h b/clustercommand.h
index 9dfd2a0..787f835 100644
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -9,11 +9,10 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
+#include "globaldata.hpp"
 #include "rabundvector.hpp"
+#include "sabundvector.hpp"
 #include "listvector.hpp"
 #include "cluster.hpp"
 #include "sparsematrix.hpp"
@@ -27,14 +26,18 @@
 	The cluster() command outputs three files *.list, *.rabund, and *.sabund.   */
 
 
-class GlobalData;
-
 class ClusterCommand : public Command {
 	
 public:
-	ClusterCommand();	
+	ClusterCommand(string);
+	ClusterCommand();
 	~ClusterCommand();
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
 	int execute();	
+	void help();
 	
 private:
 	GlobalData* globaldata;
@@ -44,13 +47,22 @@ 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;
+	map<string, vector<string> > outputTypes;
 };
 
-#endif
\ No newline at end of file
+#endif