X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=clustercommand.h;h=3dd4410b6a6a7f5aec286adf2f36338c8b198fad;hb=1e8d08e96f4fe99604a6b3502568de464bf60891;hp=787f835a0f33d1d157aeab41568286c28a752520;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/clustercommand.h b/clustercommand.h
index 787f835..3dd4410 100644
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -10,7 +10,6 @@
  */
 
 #include "command.hpp"
-#include "globaldata.hpp"
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
 #include "listvector.hpp"
@@ -18,7 +17,6 @@
 #include "sparsematrix.hpp"
 
 /* The cluster() command:
-	The cluster command can only be executed after a successful read.phylip or read.column command.   
 	The cluster command outputs a .list , .rabund and .sabund files.  
 	The cluster command parameter options are method, cuttoff and precision. No parameters are required.  
 	The cluster command should be in the following format: cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision).  
@@ -32,15 +30,17 @@ public:
 	ClusterCommand(string);
 	ClusterCommand();
 	~ClusterCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();	
-	void help();
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "cluster";		}
+	string getCommandCategory()		{ return "Clustering";	}
+	string getHelpString();	
+	string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Cluster"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	GlobalData* globaldata;
 	Cluster* cluster;
 	SparseMatrix* matrix;
 	ListVector* list;
@@ -48,9 +48,9 @@ private:
 	RAbundVector oldRAbund;
 	ListVector oldList;
 
-	bool abort, hard;
+	bool abort, hard, sim;
 
-	string method, fileroot, tag, outputDir;
+	string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile;
 	double cutoff;
 	string showabund, timing;
 	int precision, length;
@@ -62,7 +62,6 @@ private:
 	
 	void printData(string label);
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 };
 
 #endif