X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustersplitcommand.h;h=d46bb8ed9be115e229cd1ed0ea39a993aa6f61f0;hb=5a4ac4f954c4b4445bcee272f1f8220ddcc9c1e4;hp=0e32ffaea7710189859f458de4adc897362e12ef;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;p=mothur.git

diff --git a/clustersplitcommand.h b/clustersplitcommand.h
index 0e32ffa..d46bb8e 100644
--- a/clustersplitcommand.h
+++ b/clustersplitcommand.h
@@ -15,7 +15,7 @@
 #include "sabundvector.hpp"
 #include "listvector.hpp"
 #include "cluster.hpp"
-#include "sparsematrix.hpp"
+#include "sparsedistancematrix.h"
 #include "readcluster.h"
 #include "splitmatrix.h"
 #include "readphylip.h"
@@ -23,6 +23,7 @@
 #include "readmatrix.hpp"
 #include "inputdata.h"
 #include "clustercommand.h"
+#include "clusterclassic.h"
 
 class ClusterSplitCommand : public Command {
 	
@@ -34,6 +35,7 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "cluster.split";		}
 	string getCommandCategory()		{ return "Clustering";			}
+	string getOutputFileNameTag(string, string);
 	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"; }
@@ -48,13 +50,15 @@ private:
 	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;
+	bool print_start, abort, hard, large, classic;
 	time_t start;
 	ofstream outList, outRabund, outSabund;
 	
 	void printData(ListVector*);
 	vector<string> createProcesses(vector< map<string, string> >, set<string>&);
 	vector<string> cluster(vector< map<string, string> >, set<string>&);
+    string clusterFile(string, string, set<string>&, double&);
+    string clusterClassicFile(string, string, set<string>&, double&);
 	int mergeLists(vector<string>, map<float, int>, ListVector*);
 	map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
 	int createMergedDistanceFile(vector< map<string, string> >);