X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getoturepcommand.h;h=ca3439d809f96f6eff93dcf3948abd1a8274a7f5;hp=390632975afc85aac5b714c7194c81e74d58e16e;hb=615301e57c25e241356a9c2380648d117709458d;hpb=90708fe9701e3827e477c82fb3652539c3bf2a0d

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 3906329..ca3439d 100644
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -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"; }
 
@@ -55,14 +56,12 @@ public:
 	
 private:
 	ListVector* list;
-	InputData* input;
-	FastaMap* fasta;
 	GroupMap* groupMap;
 	ReadMatrix* readMatrix;
 	FormatMatrix* formatMatrix;
 	NameAssignment* nameMap;
     CountTable ct;
-	string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, countfile, columnfile, distFile, format, outputDir, groups;
+	string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, countfile, columnfile, distFile, format, outputDir, groups, method;
 	ofstream out;
 	ifstream in, inNames, inRow;
 	bool abort, allLines, groupError, large, weighted, hasGroups;
@@ -77,13 +76,14 @@ private:
 									// for all distances related to a certain sequence
 	vector<int> rowPositions;
 
-	void readNamesFile();
+	void readNamesFile(FastaMap*&);
 	void readNamesFile(bool);
 	int process(ListVector*);
 	SeqMap getMap(int);
 	string findRep(vector<string>, string); 	// returns the name of the "representative" sequence of given bin or subset of a bin, for groups
+    string findRepAbund(vector<string>, string);
 	int processNames(string, string);
-	int processFastaNames(string, string);
+	int processFastaNames(string, string, FastaMap*&);
     int readDist();
 };