cmd

var RootCmd = &cobra.Command{
	Use:   "gotree",
	Short: "gotree: A set of tools to handle phylogenetic trees in go",
	Long: `gotree is a set of tools to handle phylogenetic trees in go.

Different usages are implemented: 
- Generating random trees
- Transforming trees (renaming tips, pruning/removing tips)
- Comparing trees (computing bootstrap supports, counting common edges)
`,
	PersistentPreRun: func(cmd *cobra.Command, args []string) {
		switch rootInputFormat {
		case "newick":
			treeformat = utils.FORMAT_NEWICK
		case "nexus":
			treeformat = utils.FORMAT_NEXUS
		case "phyloxml":
			treeformat = utils.FORMAT_PHYLOXML
		default:
			treeformat = utils.FORMAT_NEWICK
		}
		if seed == -1 {
			seed = time.Now().UTC().UnixNano()
		}
		rand.Seed(seed)
	},

	Run: func(cmd *cobra.Command, args []string) {
		s := cobrashell.New()

		s.Println(fmt.Sprintf("Welcome to Gotree Console %s", Version))
		s.Println("type \"help\" to get a list of available commands")
		cobrashell.AddCommands(s, cmd.Root(), nil, cmd.Root().Commands()...)

		s.Run()
	},

	PersistentPostRun: func(cmd *cobra.Command, args []string) {
	},
}

var Version string