I have designed the GUI for the new parameter. I have attached. Let me know if it looks fine.

I had a doubt. I do need to add the entire block that I have attached right?

Please also attach an image showing the entire panel.

I have attached the panel.

Can you make it more compact so that it fits the available space?

For example, the long sentence "Primer pair....DNA" could wrap around to fit better.

Possible problem with submitting accessions in place of sequence to resolve the issue with exon junction span option:

Some of the IGB genomes (human, mouse, rat) have the NCBI accession number in the id field for each gene (NM_000133.3). But many of the other genomes (Arabidopsis) do not have the accession as the id field, since these gene annotations came from other sources (not NCBI).

The exon junction span will work with just sequence if that sequence matches exactly with the NCBI sequence annotation for that gene. However, the tested gene in IGB Human 2013 (NM_000133.3) has a few base pair differences at the start and end of the annotation, which causes it to fail in primer blast.

I was testing for different species and looks like it works fine for genome sequence for Rattus norvegicus from IGB. So I have just handled the error it throws when no primers are found with exon/intron.

Code Changes - https://bitbucket.org/noorzahara/ncbi-primer-local/branch/IGBF-2348#diff

I guess the test cases written currently tests my changes as well. So there is no need for new test cases.

Observations:
Following features are working fine:

• Exon/ Intron options are set to default options (as in NCBI site) and properly sent while sending a request to NCBI set.
• Options are set default by "Reset Default" Option.

Observed the following issues:

• When Exon Junction span is set to default "No Preference". Primer blast for all seq and organism works fine.
  But when it is set to other 2 options - "Primer must span an exon-exon junction", "Primer may not span an exon-exon junction" for few of the sym exception is being thrown. As for these options, NCBI Site redirects to an Info page , the Info page details are to be handled.
  Can be reproduced by testing with Rat genome - Taar7a .
• According to the NCBI site A refseq mRNA seq is required for exon/intron selection. Can we send default options of exon/intron option as "No Preference" if the database type selected is other than "refseq mRNA" ?
  Because other combination ends up in info page, which user has to see in console.
• Few parameters have been added in NCBI site like Max target size, Allow splice variants under Primer Pair Specificity Checking Parameters. And Post processing option is removed.

If required test cases for different options of Exon Junction span can be added. Test case exists for default options "No preference".

For this ticket. kindly use branch IGBF-2320.
https://bitbucket.org/noorzahara/ncbi-primer-local/branch/IGBF-2320#diff

Tested branch: https://bitbucket.org/noorzahara/ncbi-primer-local/branch/IGBF-2320

• Cloned the repo. Ran "mvn install", builds the NCBI app properly without exception.
• Added https://bitbucket.org/noorzahara/ncbi-primer-local/downloads/ as a repository.
  Install the app. NCBI App got installed and the Primer option tab can be seen in bottom tab.
• Select a genome. To test default options of Exon junction span options ("No preference")
  select syms, right click on primer blast option. It opens the NCBI primer blast site.
  -Tested different param values for exon/intron selection panel, database, and other genomes. If the parameters are valid NCBI Primer site opens else Error or Info page is captured in console without exception.
• Click on "Reset Default". All options are set to default.

PR submitted
https://bitbucket.org/lorainelab/ncbi-primer/pull-requests/1/igbf-2320/diff

• Added https://bitbucket.org/lorainelab/ncbi-primer/downloads/ (team repos downloads) as a repository in IGB.
• New parameters can be seen in Exon/intron selection panel under primer options tab.
• Tested for different parameter values.
  Moving the ticket to Done.