X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clustersplitcommand.h;h=e1f17b1bd0b8c4088d5deb3c06691fb3ccf26999;hp=0e32ffaea7710189859f458de4adc897362e12ef;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=43ed0accfbc2852849e104ff7eccdd2c42acd4ec

diff --git a/clustersplitcommand.h b/clustersplitcommand.h
index 0e32ffa..e1f17b1 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 {
 	
@@ -34,8 +35,10 @@ public:
 	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 getOutputPattern(string);	
+	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 77:3219. \nhttp://www.mothur.org/wiki/Cluster.split"; }
 	string getDescription()		{ return "splits your sequences by distance or taxonomy then clusters into OTUs"; }
 	
 	int execute(); 
@@ -45,19 +48,22 @@ private:
 	vector<int> processIDS;   //processid
 	vector<string> outputNames;
 	
-	string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
+	string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, countfile, 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, runCluster;
 	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> >);
+    int createRabund(CountTable*& ct, ListVector*& list, RAbundVector*& rabund);
 };
 
 /////////////////not working for Windows////////////////////////////////////////////////////////////
@@ -71,7 +77,7 @@ private:
 // anything to do with mothur's use of copy constructors in many of our data structures. ie. listvector 
 // is copied by nameassignment and passed to read which passes to the thread?  -westcott 2-8-12
 ////////////////////////////////////////////////////////////////////////////////////////////////////
-/**************************************************************************************************/
+/**************************************************************************************************
 //custom data structure for threads to use.
 // This is passed by void pointer so it can be any data type
 // that can be passed using a single void pointer (LPVOID).
@@ -101,7 +107,7 @@ struct clusterData {
 	}
 };
 
-/**************************************************************************************************/
+/**************************************************************************************************
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyClusterThreadFunction(LPVOID lpParam){ 
@@ -253,7 +259,7 @@ static DWORD WINAPI MyClusterThreadFunction(LPVOID lpParam){
 } 
 #endif
 
-
+*/
 
 
 #endif