From: Lincoln Stein [mailto:lincoln.stein-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org]
Sent: Monday, March 10, 2008 4:41 PM
To: Sunshine, Margot (NIH/NCI) [C]
Cc: Scott Cain; Gbrowse (E-mail)
Subject: Re: [Gmod-gbrowse] Track disappearing from overview when clicking area without data

On Mon, Mar 10, 2008 at 1:02 PM, Sunshine, Margot (NIH/NCI) [C] <margots-2loH/HJHQuifRvmTrFJqzg@public.gmane.org> wrote:

Hi Scott,

Please help me out. I continue to have problems with GBrowse. I have
installed gbrowse from Thursday's stable development version. I have set
up a public area that will allow you to see the issues I am referring
to. All of this issues occur when using IE from a PC. The URL for my
instance of GBrowse is
http://undiscovered.nci.nih.gov/cgi-bin/gbrowse/gbhuman/

1) Wrong area displaying when clicking on overview
       a) go to URL above
       b) Then in the box for a remote url paste the following link:
http://undiscovered.nci.nih.gov/cellminerdata/gbrowseChr7_RNA_T47D.gff
       c) In the landmark field paste the following: chr7:1..5000000
       d) RNA:T47D displayed in both the overview and the Details
section
       e) Now click on the 60M tick mark in to overview.
       f) The overview repainted with the highlighted area 64M-69M -
not where I clicked.

2) Track disappearing from overview when selecting area without data
       a) this can be done after the last test.
       b) if you click on the 40M tick mark it redisplayed highlighting
45M-50M, again not where it was supposed to and the RNA:T47D track is no
longer displayed in the overview or detail. I can understand in
disappearing from the details, but not from the overview.
       c) sometimes the amount it misses by varies so if perchance it
hits an area with data, instead paste chr7:42000000..47000000 in the
Landmark field and what is described in b should occur.

3) New URL not displayed, continues to display old data
       a) Our usage model of gbrowse involves coming from another query
tool that writes a gff file and then passing that file in as part of the
URL. So this issue involves coming from that approach.
       b) This follows after the last test. Paste the following URL
into the browse address window.
http://undiscovered.nci.nih.gov/cgi-bin/gbrowse/gbhuman?eurl=http://undi
scovered.nci.nih.gov/cellminerdata/gBrowseChr7cDNAArrayMelanoma.gff&name
=chr7%3A1..5000000
       c) The new data does not appear.
       d) In the landmark field paste the following:
chr7:45000000..55000000
       e) the new data appears and the old data vanishes
       f) In the landmark field paste the following:
chr7:35000000..40000000
       g) Now the old data is back and the new data is gone.

Please let me know if you have any ideas on how to resolve these issues.

Sincerely,
Margot Sunshine



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