merged pat's trim seqs edits with sarah's major overhaul of global data; also added...

[mothur.git] / validcommands.cpp

diff --git a/validcommands.cpp b/validcommands.cpp
index 2127758094b2e3cff802fd567ec78ad522c7fd8a..e5f93a91e125798f556c8769cbe51af9ae0e3e65 100644 (file)
--- a/validcommands.cpp
+++ b/validcommands.cpp
@@ -17,8 +17,12 @@ ValidCommands::ValidCommands() {
                commands["read.dist"]                   = "read.dist"; 
                commands["read.otu"]                    = "read.otu";
                commands["read.tree"]                   = "read.tree"; 
+               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"; 
@@ -29,11 +33,24 @@ ValidCommands::ValidCommands() {
                commands["unifrac.weighted"]    = "unifrac.weighted"; 
                commands["unifrac.unweighted"]  = "unifrac.unweighted"; 
                commands["libshuff"]                    = "libshuff";
-               commands["heatmap"]                             = "heatmap";
+               commands["tree.shared"]                 = "tree.shared";
+               commands["heatmap.bin"]                 = "heatmap.bin";
+               commands["heatmap.sim"]                 = "heatmap.sim";
+               commands["venn"]                                = "venn";
                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["reverse.seqs"]                = "reverse.seqs";
+               commands["trim.seqs"]                   = "trim.seqs";
                commands["quit"]                                = "quit";