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.