From: <Loraine>, "Loraine, Ann" <Ann.Loraine@uncc.edu>
Date: Wednesday, November 12, 2014 at 3:42 PM
To: "D. Molnar" <dm516@cam.ac.uk>
Cc: "Norris, David" <dcnorris@uncc.edu>, "Freese, Nowlan" <nfreese@uncc.edu>, Tarun Santosh Kanaparthi <tkanapar@uncc.edu>, Ivory Clabaugh <ieclabau@uncc.edu>
Subject: Re: Redirect loop at forum link & transparent track colours

It is very nice to hear from you - thank you for the great idea! And thank you also for telling us about the bad link.

I am forwarding your email to the team here. Mason, would you add this request to Jira? Also, let’s make a note to get back in touch when the new feature is added and/or we have status updates.

Best wishes,

Ann

From: Mason Meyer <Mason.Meyer@my.lr.edu>
Date: Thu 11/13/2014 2:34 PM
To: David Molnar <dm516@cam.ac.uk>
Cc: "Loraine, Ann" <Ann.Loraine@uncc.edu>, Ivory Clabaugh <ieclabau@uncc.edu>, "Norris, David" <dcnorris@uncc.edu>, "Freese, Nowlan" <nfreese@uncc.edu>, Tarun Santosh Kanaparthi <tkanapar@uncc.edu>
Subject: Re: Redirect loop at forum link & transparent track colours

Hey Mr. Molnar,

My name is Mason Meyer and I’m a user support specialist who is currently working on the IGB project. I wanted to let you know that there is, in fact, a way to add transparency to
the track colour so that both can be seen in the overlay. Our team member, Ivory, has taken some screenshots of the transparency for you and they are attached to this e-mail so you can check out the feature. The appearance is, admittedly, a bit rough when zoomed out (see igbTransparentOverly.png, attached) but it is smoother when more zoomed in (igbTransparentOverly2.png).
Unfortunately, if you zoom out further (see igbTransparentOverly3.png) the transparent color loses its transparency.

*To apply transparency:
When selecting a color, go to “More Colors” and go to the HSL tab, there is a slider for transparency.

We have created a record in our development system in order to improve the feature in the near future. We will make sure to keep you updated on any changes. Thanks again for bringing these issues to our attention and please let us know if you ever have any more tips or questions!

Thanks again,

Mason Meyer

From: Dávid Molnár <zeitgeistmeister@googlemail.com>
Date: Friday, December 12, 2014 at 9:14 PM
To: Mason Meyer <mason.meyer@my.lr.edu>
Cc: "Loraine, Ann" <Ann.Loraine@uncc.edu>, "Clabaugh, Ivory" <ieclabau@uncc.edu>, "Norris, David" <dcnorris@uncc.edu>, "Freese, Nowlan" <nfreese@uncc.edu>, "Kanaparthi, Tarun Santosh" <tkanapar@uncc.edu>
Subject: Re: Redirect loop at forum link & transparent track colours

Hi Mason,

the pictures you sent are exactly what I would like to have; however
on a mac (using the latest version of IGB via java web start) the HSB
tab has no transparency slider (see attached screenshot). Can this be
fixed?

Thanks so far for your help and I admit this is a little late to come
back but I was away from all things genome for a while.

Kind regards,
David

From: <Loraine>, Ann <Ann.Loraine@uncc.edu>
Date: Sunday, December 14, 2014 at 11:00 PM
To: Dávid Molnár <zeitgeistmeister@googlemail.com>
Cc: "Clabaugh, Ivory" <ieclabau@uncc.edu>, "Norris, David" <dcnorris@uncc.edu>, "Freese, Nowlan" <nfreese@uncc.edu>, Mason Meyer <mason.meyer@my.lr.edu>
Subject: Re: Redirect loop at forum link & transparent track colours

Hello,

Thanks for your message - I hope we can help!

I’m wondering if the problem has to do with the Java version?

Please take a look at the attached image. If you follow the steps, do you see an “HSL” tab?

This image is from a preview version of IGB 8.2, but I don’t think the color choosing functionality has changed between 8.1 and 8.2 releases of IGB. If there’s a difference, it might have to do with the Java version. So you should see the same thing with IGB 8.1.

We are planning to release IGB 8.2 some time this week, possibly even on Monday. IGB 8.2 is faster and more user friendly than previous versions - and we added new features, including an option to visualize paired end alignments (from BAM files) as linked. I am also especially excited about the new bridge to R we implemented — it’s very new and we hope people will like it. Some demo code is here: https://bitbucket.org/lorainelab/rtoigb

If you’d like to hear more, Nowlan is doing a presentation on-line of the new features on Wednesday - https://www.biostars.org/p/123516/ If you have time to join in, that would be great, but if not, you can view it on YouTube later.

Best wishes,

Ann

From: <Loraine>, Ann <Ann.Loraine@uncc.edu>
Date: Sat 12/20/2014 5:11 AM
To: Dávid Molnár <zeitgeistmeister@googlemail.com>
Cc: "Clabaugh, Ivory" <ieclabau@uncc.edu>, "Norris, David" <dcnorris@uncc.edu>, "Freese, Nowlan" <nfreese@uncc.edu>, Mason Meyer <mason.meyer@my.lr.edu>
Subject: Re: Redirect loop at forum link & transparent track colours

Just a quick follow-up:

David noticed that the Hue-Saturation-Luminance (HSL) color selection tab was introduced in Java version 7. So I think this means that if you update your Java version, you would see the tab.

Also, I found this:

http://download.java.net/jdk7u2/docs/technotes/guides/swing/7.0/index.html

Best,

Ann