Requests for additional worldgen structure support:

~Chromaticraft Ocean Monuments
~Mystcraft Library
~Roguelike Dungeons
~And of course more mod-specific villager houses, such as Witchery's Apothecary and Library, plus Witchery's walled village type, RFTools house, Tinkers Construct house, Thaumcraft tower...

Ill get started on this.

How exactly do you think this should work?

Id like to say somewhat similar to the way you track villages but I'm not sure, Ill have a better idea after I've looked into it further, But first I'm going to familiarize myself with the code.

I see the main design problem as how will the other mods communicate to Atlas what kinds of structures there are and where they are. Also, should it be markers or custom tiles? Several suggestions have been made for these issues in the forum thread (http://www.minecraftforum.net/forums/mapping-and-modding/minecraft-mods/1292324-antique-atlas-v4-2-10-17-12-2015), but I failed to document it, so you might have to look through all the pages again, sorry about that :/
Also it might be worthwhile to consider the possibilities of extension here, e.g. how the players could map their own structures. Or whether we should make it Atlas's responsibility to map structures from other mods, or instead require other people to make changes to their mods (I think the former is preferrable.)
By the way, if you end up needing new tile textures, feel free to tap me.

personally I was going to ask permission to decompile the code and see if there was something I could hook into in the structure files ill brainstorm and let you know what I come up with tommorow.

Do you have skype or teamspeak?

I do have skype with the same name as here. But I'm not currently actively working on the mod, @Kenkron is. I could still discuss the possible approaches with you, but it might be a bit slow, as Minecraft modding is not currently loaded in my brain's RAM, if you know what I mean :)

Its alright I understand all too well seeing as summer is just around the corner.

I mean, I really haven't had the time for modding for more than a year. Right now @Kenkron is sort of leading development of Antique Atlas. I'll do what I can at least on the conceptual side of things, so feel free to contact me.

Ive been poking around a few Ideas and Ive got a general Idea of how id Like it to work.

What's your idea?

Basically my idea is quite simple, add a tab to the side of the book, when clicked it will open up a popup window like the side configuration window in thermal dynamics, in that window it will have a library of icons you can scroll through then drag and drop them onto the books map into the desired position.

That's basically the same thing as markers. What I had in mind originally was to somehow automate this process of locating third-party structures.
Or do you mean to use custom tiles instead of markers? Essentially like an Atlas editor (see #18)

I mean custom tiles, its nearly impossible to do it automatically without permission to de-compile the code of the other mods.

Perhaps some of them have public APIs or events on the event bus that we could use. Or we could ask the modders to implement those, or to add a little line of code using Atlas API to mark their structures. Or in case their mod is open source, we could submit a pull request.

I believe the easiest would be to nicely ask then to add in a line of code into their mod so we can hook the atlas api to it.

I too would like to know the idea

Im going to try to get in contact with the owner of the witchery mod, Is this alright?

Sure, go ahead. See https://github.com/Hunternif/AntiqueAtlasApiExample for how other mods are supposed to call Atlas API.

Im currently waiting for a reply from Emoniph, Im going to try and contact the owner of mystcraft later.