added dist.shared command

[mothur.git] / validcommands.cpp

diff --git a/validcommands.cpp b/validcommands.cpp
index e0d604543ec564f1e364426a9f61c613e97ffea0..787cc8025a6c62d01be190a63c33e42429fe21a4 100644 (file)
--- a/validcommands.cpp
+++ b/validcommands.cpp
@@ -17,23 +17,36 @@ ValidCommands::ValidCommands() {
                commands["read.dist"]                   = "read.dist"; 
                commands["read.otu"]                    = "read.otu";
                commands["read.tree"]                   = "read.tree"; 
-               commands["read.shared"]                 = "read.shared";
+               commands["read.seqs"]           = "read.seqs";
+               commands["bin.seqs"]                    = "bin.seqs"; 
+               commands["get.repseqs"]                 = "get.repseqs"; 
+               commands["get.oturep"]                  = "get.oturep";
                commands["cluster"]                             = "cluster"; 
                commands["deconvolute"]                 = "deconvolute"; 
-               commands["parsimony"]                   = "parsimony";
-               commands["help"]                                = "help"; 
-               commands["quit"]                                = "quit"; 
+               commands["dist.seqs"]                   = "dist.seqs";
+               commands["dist.shared"]                 = "dist.shared";  //matrix output
                commands["collect.single"]              = "collect.single"; 
                commands["collect.shared"]              = "collect.shared"; 
-               commands["get.group"]           = "get.group";
-               commands["get.label"]           = "get.label";
-               commands["get.line"]            = "get.line";
                commands["rarefaction.single"]  = "rarefaction.single"; 
                commands["rarefaction.shared"]  = "rarefaction.shared"; 
                commands["summary.single"]              = "summary.single"; 
                commands["summary.shared"]              = "summary.shared"; 
+               commands["parsimony"]                   = "parsimony";
                commands["unifrac.weighted"]    = "unifrac.weighted"; 
                commands["unifrac.unweighted"]  = "unifrac.unweighted"; 
+               commands["libshuff"]                    = "libshuff";
+               commands["tree.shared"]                 = "tree.shared";
+               commands["heatmap"]                             = "heatmap";
+               commands["venn"]                                = "venn";
+               commands["get.group"]           = "get.group";
+               commands["get.label"]           = "get.label";
+               commands["get.line"]            = "get.line";
+               commands["bootstrap.shared"]    = "bootstrap.shared";
+               commands["concensus"]                   = "concensus";
+               commands["help"]                                = "help"; 
+               commands["filter.seqs"]                 = "filter.seqs";
+               commands["align.seqs"]                  = "align.seqs";
+               commands["quit"]                                = "quit"; 
 
                                
        }