line and label no longer persist between commands. Added phylip formated output...

[mothur.git] / validcommands.cpp

diff --git a/validcommands.cpp b/validcommands.cpp
index 696214e236be1b44cfc63335ee9caecc96249ea8..ec60b3b974ad832be1b71092bf3cfbdf9bf28e71 100644 (file)
--- a/validcommands.cpp
+++ b/validcommands.cpp
@@ -20,7 +20,9 @@ ValidCommands::ValidCommands() {
                commands["bin.seqs"]                    = "bin.seqs"; 
                commands["get.oturep"]                  = "get.oturep";
                commands["cluster"]                             = "cluster"; 
-               commands["deconvolute"]                 = "deconvolute"; 
+               commands["unique.seqs"]                 = "unique.seqs"; 
+               commands["dist.seqs"]                   = "dist.seqs";
+               commands["dist.shared"]                 = "dist.shared";
                commands["collect.single"]              = "collect.single"; 
                commands["collect.shared"]              = "collect.shared"; 
                commands["rarefaction.single"]  = "rarefaction.single"; 
@@ -37,8 +39,15 @@ ValidCommands::ValidCommands() {
                commands["get.group"]           = "get.group";
                commands["get.label"]           = "get.label";
                commands["get.line"]            = "get.line";
+               commands["get.sabund"]          = "get.sabund";
+               commands["get.rabund"]          = "get.rabund";
                commands["bootstrap.shared"]    = "bootstrap.shared";
+               commands["concensus"]                   = "concensus";
                commands["help"]                                = "help"; 
+               commands["filter.seqs"]                 = "filter.seqs";
+               commands["align.seqs"]                  = "align.seqs";
+               commands["summary.seqs"]                = "summary.seqs";
+               commands["screen.seqs"]                 = "screen.seqs";
                commands["quit"]                                = "quit";