Example:
Open the most recent chicken genome (G_gallus_Mar_2018).
Navigate to 1:79,200,818-79,317,139
Under UCSC REST in the Data Access tab under Available Data, select cpgIslandExt
Load Data
Select one of the data points and look at the Selection Info tab, you should see props such as "perCpg"

For the example above you will either need to be on Sravani's branch, or wait until we merge her changes into the Loraine Lab repo.

• The property filters such as id, name, score, and title available in the Color By panel are assigned during compile time (static variables). For example, see the below code snippet.

  static {
          PROPERTY_VALUES.add(ID);
          PROPERTY_VALUES.add(NAME);
          PROPERTY_VALUES.add(SCORE);
          PROPERTY_VALUES.add(TITLE);
      }
  

• We cannot assign the props at compile time (like the above) if they change from data source to data source. Per the code, the Color By options support three types of file categories: Annotation, Alignment, and ProbSet. Do they all have the same type of props?

• I am still figuring out if I can extract the props of the selected data source so we can display the props w.r.t data source.

This task can be divided into multiple subtasks:

1. How to get / where to store the schema of the loaded data in IGB?
   How to get the schema: UCSC provides a rich set of APIs for getting genome data and its metadata(or schema). We can get the schema of a specific genome using /list/schema API. For example, hit this URL to view the schema of cpgIslandExt.
   Where to store the metadata (or schema): The IGB dataset holds several properties, such as Name, Properties, Data Container, and so on (check in DataSet.java). The variable Properties would be the right place to store the metadata (or schema).
2. will add more details about further steps here.

Kaushik branch: https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/branch/IGBF-3640

Filter and Color by are working mostly as I would expect. I found some existing issues, also present in IGB 10.0.0, where a filter can be applied to the negative strand and a warning is thrown (see below). As this is an existing issue, I have created a separate ticket, IGBF-3698, to fix it.

WARNING: Found a glyph with null info at location java.awt.geom.Rectangle2D$Double[x=0.0,y=53.764827058823535,w=0.0,h=20.0]

Note that Kaushik's changes also fix an issue with certain comparators (for example >) causing an error to appear in IGB.

Kaushik Gopu - When using Color By > Property, can we utilize the heatmap option for properties that are numeric? For example, using the galGal6 genome with cpgIslandExt selected, if I select Color By > Property > perCpG it would be nice if the heatmap Edit option would appear.
UPDATE - Sravani and I discussed this idea. While this idea may be possible, it would require significant refactoring of this code.

While going through the code, found out that the tierLabelManager is available in ColorByAction itself so we don't have to send it from the SeqMapView class, which would let us change only few files to add this functionality. Also, while investigating I found an issue with the existing code when the user selects Color by and chooses the property option there are 4 default options available in the dropdown, if the user selects any option other than the pre-selected one, it shows an error, even though user gives correct data. Nowlan Freese or Kaushik Gopu It would be great if anyone of you can test this and let me know if this issue exists for you as well, I already found the solution too.

Development is completed and the props are populated in the properties dropdown for both color by and filter by, need to test one more scenario. once that is done will move the ticket to review. Updated code is at branch: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3640

Merged all the other code changes and did a few fixes. Updated code is available at: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3640. Tested the code and it is working as expected. Below are screenshots:
Selected single track with extra properties:

Selected single track without extra properties:

Selected two tracks, both have similar extra properties:

Selected two tracks, one has similar extra properties and the other one doesn't have:

To Test:

1. Build the jar file for the branch.
2. Start the application in debug mode, select any species, and select any one of the ucsc rest tracks that has extra properties (bed, bigBed, bedDetail, and bigGenePRed track types have extra properties).
3. Now while loading the empty track, an API call is made and the featureProps are loaded.
4. Load data for the track and right-click on the track name to see the options menu
5. Click on Color by option and select property from the dropdown items
6. Now, in the property dropdown list, you should be able to see the extra properties that are present in that track

Built and tested Sravani's branch locally on my Mac.

Following the testing above, the additional properties show up for the appropriate files from UCSC REST. I am able to filter and color the data appropriately. If multiple tracks are selected, only the shared/common properties appear.

Did code review with Sravani.

Ready for pull request.

Created a single Pull request for both tickets, https://jira.bioviz.org/browse/IGBF-3660 and https://jira.bioviz.org/browse/IGBF-3640. Nowlan Freese already reviewed it, Kaushik Gopu Please review it and let me know if find any issues. Added the test case fix for windows as well in the commit and added a try catch block as per Kaushik Gopu suggestion. Here is the updated PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1008

IGB was built without skipping test cases; all test cases passed on Windows, and no issues occurred during the build process.
Jaya Sravani Sirigineedi incorporated suggested changes in the code.