X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustersplitcommand.h;h=c4b236cb12dbfc535c1de5da7840b39f21176fb7;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=e838bc41ee1b3616d3f0f95e6a512c5bde136d33;hpb=8ab46c171b45ae3782d839539792d049017a361b;p=mothur.git

diff --git a/clustersplitcommand.h b/clustersplitcommand.h
index e838bc4..c4b236c 100644
--- a/clustersplitcommand.h
+++ b/clustersplitcommand.h
@@ -16,33 +16,42 @@
 #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;
+	bool print_start, abort, hard, large;
 	time_t start;
 	ofstream outList, outRabund, outSabund;
 	
 	void printData(ListVector*);
 	int createProcesses(vector < vector < map<string, string> > >);
 	vector<string> cluster(vector< map<string, string> >, set<string>&);
-	int mergeLists(vector<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