For next step, Sai Charan Reddy Vallapureddy

• squash all changes into one commit
• rebase onto the latest master branch, resolving conflicts as needed
• post a link to the new branch here

Investigate possibly overriding equals method on SeqSymmetry as a possibly more light-weight fix.
Also, investigate what would happen if we were to change other search code to use arraylist instead of hashset.

Note: You need to check two different ways of searching: Using AdvancedSearch and using the "Quick search" box at the top left of the IGB window.

Prof. [~aloraine], I have gone through the code and as mentioned by Charan in the IGBF-1096 the old code has not been removed from the code base. I have checked the functionality of both the "Advanced Search" tab as well he "Quick Search" box at the top of the IGB window and both are working fine. I have also rebased the code on a branch in my fork. Before pushing those changes I wanted to let you know that there was not any major difference between last two commits on Charan's branch so we can put it into one commit. Also, before pushing those changes I wanted to ask you If we should remove the old code as mentioned by you in the IGBF-1096 or we should leave it like that?
Please let me know the same.
Thanks.

Quick request:

• Can you post a link to the rebased branch here and on IGBF-1096?

Prof. [~aloraine], I guess there is some problem with the "Quick search" box. So, I am trying to fix that up. I'll post the rebased branch link once that exception is fixed.
Thanks.

Prof. [~aloraine], I have fixed the quick search issue now.
The code changes can be found at:
https://bitbucket.org/pkulka10/igb_prutha/src/IGBF-2032/

Sorry to request yet another rebase!

Please rebase your branch onto master and then submit a PR.

btw thank you Prutha Kulkarni and Sai Charan Reddy Vallapureddy for putting this into a single commit. I wish there were more comments in the code to explain what is happening, but the link back to the issue page and to the commit itself will help a lot.

Working on merging into master by cherry-picking single commit with all changes.

Cherry picked commit hash 93a12d25f onto new branch IGBF-2031-2.

local aloraine$ git ls
99b78dd7f (HEAD -> IGBF-2031-2) IGBF-2032 : Address search functionality issue.
15ad48d59 (origin/master, origin/HEAD, master) Merged lorainelab/integrated-genome-browser into master
2c638ae83 Merged in pbadzuh/igb_pbdev/IGBF-2102 (pull request #754)
74a8f5e80 IGBF-2102 Handle non-quickload data for information window

Pushed new branch IGBF-2031-2 to my fork:
https://bitbucket.org/aloraine/integrated-genome-browser/src/IGBF-2031-2

To test, download installers from:
https://bitbucket.org/aloraine/integrated-genome-browser/downloads/

Using advanced search for rs1122608 on diseaseMom and diseaseDad files:
Properties - finds both hits
Keyword - finds one hit
ID, Name, or Title - finds both hits

I'm not sure if the Keyword results are correct. I would presume that keyword should also find both hits. Charan and I talked, and there may be an additional method that needs to be altered or overridden for the keyword search (possibly KeyWordSearch.java search). We will take a further look on Wednesday.

Philip Badzuh Nowlan Freese - Should P.B. commence testing? If yes, please use installer from my fork (see above link).

Another odd behavior:
Dr. Loraine pointed out that in 9.0.2 using the advanced search with no input would lead to IGB searching forever. This same behavior is present in this branch (2032-2) that includes Charan's updates. However, in 9.1.0 master (as of November 22, 2019) searching in IGB with no input returns all hits (for example every gene in the annotation) very quickly (even with tens of thousands of results). This behavior in 9.1.0 in master could be useful for users, and it appears to work consistently.

If we merge in 2032-2, we will need to address no input searching forever by forcing the user to enter input before searching.

Won't merge for 9.1.
Will come back to this in Jan (Dec?) for re-factoring search using OSGi pattern demonstrated in KeyWordSearch bundle.

Plan new approach.