Issue :- Zoom stripe label blocking the residue sequence.

Solution :- Moved the zoom stripe label up on the Y-axis to prevent it from overlapping the genome residue sequence.

Files changed:-
genoviz_sdk/pom.xml
genoviz_sdk/src/main/java/com/affymetrix/genoviz/glyph/StringGlyph.java
genoviz_sdk/src/main/java/com/affymetrix/genoviz/widget/Shadow.java
pom.xml

Testing steps:-
1) Click on any genome to load the sequence in IGB project.
2) Click on Load Sequence button from top right corner to load the genome residue.
3) Click anywhere to see the zoom stripe label.

Test results:-
Please find the attached screenshots for test results.

Code changes:-
https://bitbucket.org/rpatil14/riddhi-genovizsdk/branch/IGBF-1230#diff

Note:- Changed the genoviz_sdk and genovizTutorial jar verrsion from 1.7 to 1.8. We need to change pom.xml of IGB project to use 1.8 version og genoviz module. So, the file pom.xml of IGB project will be committed once, these changes are pushed to the team repository in order to prevent any breakage.

For the next step:

• Rebase your topic branch on the latest Genoviz SDK maste branch
• Issue pull request from your Genoviz SDK fork/branch to team Genoviz SDK repository master branch, move this issue to "Pull Request Submitted"
• Make a branch on your IGB fork for issue IGBF-1230
• In that branch only, update the POM.xml to use Genoviz SDK 1.8
• Push your changes.

Once you push your changes and I have deployed Genoviz SDK 1.8 onto Loraine Lab Nexus (https://nexus.bioviz.org), the installer should get built on your fork, and we can test how it looks. However, the build on your fork should fail before I deploy Genoviz SDK 1.8. Build failure in this case would be a good test of our dependency management system. So keep an eye on your build process to make sure system is behaving as expected.

Testing:

• Examine how new zoom stripe looks in all places where it is being used (that we know about).

This includes:

• ProtAnnot (IGB App accessible via App Manager GUI)
• Sliced View tab in IGB
• Main view in IGB

I checked ProtAnnot's POM.xml
This POM.xml does not mention the Genoviz SDK version but instead inherits that from its parent POM, which is the POM for the entire project. This means that if we update the parent POM, ProtAnnot bundle deployed on https://bioviz.org/igbserver should work fine. It is using the provided Genoviz SDK bundle in IGB.

• Please check the attached Test_Document_IGBF_1230.xls for the testing results and the next steps.
• Created pull request :-
  https://bitbucket.org/lorainelab/genoviz-sdk/pull-requests/11/igbf-1230-zoom-stripe-label-blocking-the/diff
• Updated pom.xml of IGB project to use latest version of genoviz jar
  https://bitbucket.org/rpatil14/riddhifork-igb/branch/IGBF-1230#diff

I am not able to see the images in my Excel (could be a Mac vs Windows issue)
Can you attach the PNGs separately?

Merged pull request https://bitbucket.org/lorainelab/genoviz-sdk/pull-requests/11/igbf-1230-zoom-stripe-label-blocking-the/diff into master on team repository. Build failed, but was easy to fix by changing reference to parent POM version from 1.1.7 to 1.1.8 in tutorial module. Now it builds. Version 1.1.8 of library and tutorials are now deployed on https://nexus.bioviz.org.

Ready now to increment version of of Genoviz SDK used in IGB to 1.1.8 to pick up the change in zoom stripe label location.

Pull request submitted for IGB project:- (Use updated genoviz jar in IGB)
https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/663/igbf-1230-point-igb-to-use-18-version-of/diff

Note:- I have attached the images from Test_Document_IGBF_1230.xls separately to the ticket.

Please re-run pipeline for IGBF-1230.
It should now run properly and build the installer as I have deployed the new 1.1.8 Genoviz artifacts on https://nexus.bioviz.org.

Build was successful for IGBF-1230

Ready for pull request.

MacOS - When multiple tracks are selected, one with merged strands and one without, upon zooming - the zoom stripe label still blocks residues. Screen shot added.

RP and AL discussed next steps. We realized that the best way to fix this would be to modify Shadow.java (in Genoviz SDK library) to enable users of this class to change y-position of the label (a StringGlyph) based on what it is covering in the container NeoMap. In light of this, we have decided to revert the changes to the library and re-visit this issue at a later date. AL will take care of reverting the changes and also updating version numbers as required. When that is done, we will make a new issue to modify Shadow.java (as noted) and close this.

After using the new feature in 9.1.0, it appears to be working reasonably well and is a big improvement in usability. In light of this, this issue is now closed.