Greatting All,
We have a need to feed a features file to the jalviewLite, but we do not want all those features to be highlighted on the alignment by default, since we are providing GUI for the user to pick which feature to be highlighted through the new javascript api. Is there a way we can do this without modify the code?
Thanks,
Wei
Hi Wei!
On 19/10/2011 17:17, Wei Jen wrote:
We have a need to feed a features file to the jalviewLite, but we do not want all those features to be highlighted on the alignment by default, since we are providing GUI for the user to pick which feature to be highlighted through the new javascript api. Is there a way we can do this without modify the code?
ah. good question! 
I presume you are using the ‘setFeatureGroupState(String, boolean)’ to control the visibility of a group of features on the alignment. In that case, all you need do is specify the list of feature groups that you don’t want displayed when jalview starts up using the ‘hidefeaturegroups’ parameter (you should use a | to separate the groups you want to hide).
If you want to have finer control of the feature display state, then you’re out of luck - the Jalview javascript API simply doesn’t have the methods. I do plan to extend it, though - with mechanisms so you can control which feature types are displayed via javascript. Email me if your interested in this and I’ll see how hard it’ll be to fit in in to the next development phase…
Jim.