Bookmarks originally only saved location data and zoom; you needed to remember which files were open.
The updated Bookmarks feature now will record location information, zoom, but also which files were open at the time. This gives the user a huge advantage. As before, you can zoom in to a specific gene region and create a bookmark. When you open this bookmark again, it will zoom into that region. However, if the file is not open, or you are looking at a different speciaespecies, IGB will now open the file that was bookmarked at the region of interest; you no longer have to reset IGB for the species, genome and file before using your bookmarks! IGB Bookmarks will now do this for you.
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Bookmarks are still subject to the normal functionality of IGB. If you have Arabidopsis thaliana, 2009 genome open, but your bookmark is for the 2008 genome, when you open the bookmark, only the files listed in the Bookmark will be open. Tracks opened in the 2009 genome will go away. On the other hand, if you have a track opened in the 2009 genome for instance, and the bookmark is also from the 2009 genome, then the bookmarked files will open and maintain the originally opened track.
The old bookmark function is still sometimes useful; when sharing bookmarks involving local files where the recipient needs to load up those local files, the new Bookmark feature would not be able to find the file. By using the old 'Add position bookmark' the recipient can load the files themselves and then use the old-style bookmark to move to the location and the zoom level. However, once the location of the local file has been established on their computer, they can use the new 'Add position and file bookmark' to create a new bookmark that will record location and zoom, but also be able to open the local file(s).