X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustersplitcommand.h;h=c4b236cb12dbfc535c1de5da7840b39f21176fb7;hb=ba2b95b22ab8947d5583ca2c2da74557870b6861;hp=c696329af7c14c1ff4252e3496a4905dd3faf2d4;hpb=2a7d1455e8cfe4f67a7173f3a7249762c5436217;p=mothur.git

diff --git a/clustersplitcommand.h b/clustersplitcommand.h
index c696329..c4b236c 100644
--- a/clustersplitcommand.h
+++ b/clustersplitcommand.h
@@ -16,23 +16,30 @@
 #include "listvector.hpp"
 #include "cluster.hpp"
 #include "sparsematrix.hpp"
-#include "globaldata.hpp"
 
 
 class ClusterSplitCommand : public Command {
 	
 public:
 	ClusterSplitCommand(string);
-	~ClusterSplitCommand();
-	int execute();	
-	void help();
+	ClusterSplitCommand();
+	~ClusterSplitCommand() {}
 	
+	vector<string> setParameters();
+	string getCommandName()			{ return "cluster.split";		}
+	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.split"; }
+	string getDescription()		{ return "splits your sequences by distance or taxonomy then clusters into OTUs"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+
 private:
-	GlobalData* globaldata;
 	vector<int> processIDS;   //processid
 	vector<string> outputNames;
-
-	string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile;
+	
+	string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
 	double cutoff, splitcutoff;
 	int precision, length, processors, taxLevelCutoff;
 	bool print_start, abort, hard, large;
@@ -44,6 +51,7 @@ private:
 	vector<string> cluster(vector< map<string, string> >, set<string>&);
 	int mergeLists(vector<string>, map<float, int>, ListVector*);
 	map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
+	int createMergedDistanceFile(vector< map<string, string> >);
 };
 
 #endif