Tested on Windows environment, it is working fine. I tried loading a bookmark and it zoomed in to the location where bookmark was saved. No "zoom in and click load data" message shown.

See:

plugins/Bookmark/src/main/java/com/affymetrix/igb/bookmarks/BookmarkUnibrowControlServlet.java

PR submitted.

I am reassigning this to Sneha to rebase and make the pull request.

When you submit the pull request, please mention that should review my comment.

git review:
single commit with appropriate message.
Needs to be rebased on master.

Code review:
Changes are simple and intuitive.
Need to check: is line 239 the only time that the loadData method is called? --> yes, it is a private method, called exactly once in this class.

Functional review:
This has been challenging. Just in testing with 9.0.1, IGB is not responding to links the way I think it should.
With my example link in the last comment and with the example given with the issue, IGB 9.0.1 gave me a message saying that I should zoom in a load data. On Sneha's branch, I did not get that message using those links. However I do get the message using the Galaxy View link which makes sense because it does not contain start and end values.

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Overall, this looks good. Before merging, I think Ann should consider weather or not this is a good idea.
This removes an inconvenience for advanced users. We already have a preferences option, so if you find the box annoying you can check the box to never see it again.
However, the general scenario of a track appearing, and being tiny and users not knowing that they need to load data (or zoom in and load data), is why we have that message in the first place. Many new users will be in exactly that position when they use BAR or Galaxy and are directed to use IGB for the first time. Even if the coordinates (start and stop) are specified, they may still specify a wide region. If the data is not loaded automatically, then the track will be tiny, and easy to not notice. See the image I attached.

The example link does not seem to be working.
The example link specifies Chr2, but when I tried it, the region that I saw was in Chr1. And no new track is added.

Consider this url:
http://localhost:7085/IGBControl?version=A_thaliana_Jun_2009&seqid=Chr1&start=0&end=30427671&loadresidues=true&create=2018%2F08%2F14+15%3A33%3A20&modified=2018%2F08%2F14+15%3A33%3A20&feature_url_0=http%3A%2F%2Fs3.amazonaws.com%2Fiplant-cdn%2Fiplant%2Fhome%2Faraport%2Frnaseq_bam%2FKlepikova%2FSRR3581899%2Faccepted_hits.bam&sym_method_0=http%3A%2F%2Fs3.amazonaws.com%2Fiplant-cdn%2Fiplant%2Fhome%2Faraport%2Frnaseq_bam%2FKlepikova%2FSRR3581899%2Faccepted_hits.bam&sym_ypos_0=0&sym_yheight_0=50&sym_col_0=0x0B539C&sym_bg_0=0xFFFFFF&sym_name_0=+SRR3581899+Senescent+internode&query_url=http%3A%2F%2Fs3.amazonaws.com%2Fiplant-cdn%2Fiplant%2Fhome%2Faraport%2Frnaseq_bam%2FKlepikova%2FSRR3581899%2Faccepted_hits.bam&server_url=http%3A%2F%2Florainelab-quickload.scidas.org%2Fbar%2F

If a link has start and end positions, but they are really wide, do we assume that the user does not need to zoom in? Does IGB automatically start trying to load all of the data in view?

I also tested it with Galaxy. This the link I was redirected to from Galaxy.
http://bioviz.org/galaxy.html?version=Arabidopsis_thaliana_TAIR10&loadresidues=false&feature_url_0=https://usegalaxy.org/display_application/bbd44e69cb8906b55f6744890fdd33ed/igb_bedgraph/View/None/data/BEDGRAPH.bed.bedgraph&sym_name_0=BEDGRAPH&sym_method_0=https://usegalaxy.org/display_application/bbd44e69cb8906b55f6744890fdd33ed/igb_bedgraph/View/None/data/BEDGRAPH.bed.bedgraph&query_url=https://usegalaxy.org/display_application/bbd44e69cb8906b55f6744890fdd33ed/igb_bedgraph/View/None/data/BEDGRAPH.bed.bedgraph&server_url=galaxy

Fixed the issue of "Zoom in " dialogue box appearing even when start and end positions are given in the request URL from bar site.
Now when there are start and end parameters in the URL, the dialogue doesn't appear.

Work is in the branch : https://bitbucket.org/swathark/integrated-genome-browser/branch/IGBF-1364#diff

How to test?
1) Click the link present in the html file attached to this issue. (BarLinksExample.html) . The URL contains start and end parameters so the user should not get dialogue box to "Zoom in and load data".

2) URL can be modified to delete start and end parameters and try hitting the link. Now we should be able to see the dialogue box.

Needs reviewing and first level testing.
Keeping the issue unassigned.