X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clustercommand.h;h=cd9f47b07d9e8af9a6f04c014fabcfaf36a2818e;hp=f70bb322c76cd3bf897fd5498333e5da379557fd;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=5a4ac4f954c4b4445bcee272f1f8220ddcc9c1e4

diff --git a/clustercommand.h b/clustercommand.h
index f70bb32..cd9f47b 100644
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -21,7 +21,7 @@
 	The cluster command outputs a .list , .rabund and .sabund files.  
 	The cluster command parameter options are method, cuttoff and precision. No parameters are required.  
 	The cluster command should be in the following format: cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision).  
-	The acceptable methods are furthest, nearest and average.  If you do not provide a method the default algorythm is furthest neighbor.  
+	The acceptable methods are furthest, nearest and average.  If you do not provide a method the default algorithm is furthest neighbor.  
 	The cluster() command outputs three files *.list, *.rabund, and *.sabund.   */
 
 
@@ -35,9 +35,10 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "cluster";		}
 	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"; }
+    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.\nSchloss PD, Handelsman J (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-6.\nhttp://www.mothur.org/wiki/Cluster"; }
 	string getDescription()		{ return "cluster your sequences into OTUs using a distance matrix"; }
 	
 	int execute(); 
@@ -55,6 +56,7 @@ private:
 
 	string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile, countfile;
 	double cutoff;
+    float adjust;
 	string showabund, timing;
 	int precision, length;
 	ofstream sabundFile, rabundFile, listFile;