working on pam

[mothur.git] / clustercommand.h

diff --git a/clustercommand.h b/clustercommand.h
index f70bb322c76cd3bf897fd5498333e5da379557fd..cd9f47b07d9e8af9a6f04c014fabcfaf36a2818e 100644 (file)
--- 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;