added get.repseqs command, started matrix output command

[mothur.git] / validcommands.cpp

diff --git a/validcommands.cpp b/validcommands.cpp
index b2e07acae111e10f0324b95b18ca74034249315b..c648585d6b40515be32fa86f0e60804b3ca9c510 100644 (file)
--- a/validcommands.cpp
+++ b/validcommands.cpp
@@ -17,8 +17,13 @@ ValidCommands::ValidCommands() {
                commands["read.dist"]                   = "read.dist"; 
                commands["read.otu"]                    = "read.otu";
                commands["read.tree"]                   = "read.tree"; 
+               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["dist.seqs"]                   = "dist.seqs"; 
                commands["collect.single"]              = "collect.single"; 
                commands["collect.shared"]              = "collect.shared"; 
                commands["rarefaction.single"]  = "rarefaction.single"; 
@@ -29,10 +34,17 @@ ValidCommands::ValidCommands() {
                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";