X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getoturepcommand.h;h=a1bf3f0229a98231e9a627e4fc98f9d23ad897ea;hb=e0c50fc42e953dbe258feb9bc1d1d7dc10fafff0;hp=5af0340b4b920a4fab3decc79bd2b3b4237f85ef;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96;p=mothur.git

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 5af0340..a1bf3f0 100644
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -18,8 +18,8 @@
 #include "groupmap.h"
 #include "readmatrix.hpp"
 #include "formatmatrix.h"
+#include "counttable.h"
 
-typedef list<PCell>::iterator MatData;
 typedef map<int, float> SeqMap;
 
 struct repStruct {
@@ -43,8 +43,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "get.oturep";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Get.oturep"; }
 	string getDescription()		{ return "gets a representative sequence for each OTU"; }
 
@@ -61,10 +62,11 @@ private:
 	ReadMatrix* readMatrix;
 	FormatMatrix* formatMatrix;
 	NameAssignment* nameMap;
-	string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir, groups;
+    CountTable ct;
+	string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, countfile, columnfile, distFile, format, outputDir, groups;
 	ofstream out;
 	ifstream in, inNames, inRow;
-	bool abort, allLines, groupError, large, weighted;
+	bool abort, allLines, groupError, large, weighted, hasGroups;
 	set<string> labels; //holds labels to be used
 	map<string, int> nameToIndex;  //maps sequence name to index in sparsematrix
 	map<string, string> nameFileMap;
@@ -80,9 +82,10 @@ private:
 	void readNamesFile(bool);
 	int process(ListVector*);
 	SeqMap getMap(int);
-	string findRep(vector<string>); 	// returns the name of the "representative" sequence of given bin or subset of a bin, for groups
+	string findRep(vector<string>, string); 	// returns the name of the "representative" sequence of given bin or subset of a bin, for groups
 	int processNames(string, string);
 	int processFastaNames(string, string);
+    int readDist();
 };
 
 #endif