X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validcommands.cpp;h=787cc8025a6c62d01be190a63c33e42429fe21a4;hb=0e14094b51dd81c07c6a56b7b51533eff2332339;hp=e0d604543ec564f1e364426a9f61c613e97ffea0;hpb=addc715b6d7ea52440751cec10edad03e1a19b37;p=mothur.git

diff --git a/validcommands.cpp b/validcommands.cpp
index e0d6045..787cc80 100644
--- 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"; 
 
 				
 	}