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Welcome to the ScriptableObjectCollection wiki!
It's really hard to make sure those features work perfectly with the system since it depends on to catch up the GUIDs of the collectables, ALWAYS try to use the Add New / Deleting by the inspector itself
For most of the cases, you don't need these objects to be fully serialized when using the references on Save Data and other cases, I recommend taking a look into the fsCollectableScriptableObjectConverter
inside the package, this uses FullSerializer to only serialize the necessary data, and rebuild the connection properly when serialize/deserialize the object
Since the CollectionsRegistry is inside the Resources folder, every reference this has to a collection and to all the collectables will be inside the Unity Resources bundle, and if have a lot of references for expensive stuff, this can decrease your startup time significantly, there's 2 things you should keep in mind:
1- Use the Automatically Loaded items for items that should be available for the lifetime of your game
2- If you want to use this for more expensive stuff, let's say all the gameplay prefabs, you can uncheck the automatic initialization of this collection, and register the collection on your loading by using CollectionsRegistry.Instance.RegisterCollection(Collection);
and removing it when they are not necessary anymore.