This mode is used to upgrade goby files to a new version of Goby offline. We try to devise Goby format to avoid upgrade steps, but sometimes upgrading the data structures cannot be avoided (e.g., when we fix bugs that existed in earlier versions). This tool converts data structures to the latest Goby format. Two upgrades are currently implemented by this mode, that apply to Goby 1.9.6- and Goby 220.127.116.11-.
To perform off-line upgrade a set of alignment in the current directory, do the following:
goby 3g upgrade *.entries
The previous command will scan the input alignments to determine which ones need upgrading and will apply perform the upgrade. Online upgrade is transparent to the end-user, except that the initial loading of an alignment will appear to take a long time (loading requires applying all upgrades to bring the data in compatibility with the current version). Since upgrade will not change alignments that do not need to upgrade, you may consider scanning all alignments with the off-line upgrade mode.
It is implemented by edu.cornell.med.icb.goby.modes.UpgradeMode.java.
The following options are available in this mode
|input||yes||Name of the alignment files to upgrade.|