Suggested structure for the project:
Module name: File Handler Plugin - Genotyping Results
Description: A plugin for loading and visualization results from genotyping assays, such as the 23 and Me SNP chip test results
Code location: integrated-genome-browser/plugins/GenotypingResults
java source code files and packages:
- all are in package: org.lorainelab.igb.genotyping
- GenotypeFileHandler.java - implements FileTypeHandler
- TwentyThreeAndMeSymLoader.java - a SymLoader for reading 23 and Me results
- TwentyThreeAndMeVariationSym.java - data structure for representing a single-base location on the genome where individuals vary (SNP) as assayed by 23 and Me genotyping chip
- TwentyThreeAndMeVariationGlyph.java - a subclass of Glyph that draws a TwentyThreeAndMeVariationSym.java
- GenotypingResultsFactory.java - implements factory methods for adding above Glyphs to a SeqMapView
One doubt: The package com.affymetrix.igb.view.factories contains many classes that implement MapTierGlyphFactoryI.java. This interface seems to be the key to adding new types of data as new IGB tracks.
One implementation class in particular seems to be doing most of the work in IGB - AnnotationGlyphFactory.java. Its first commit is 2012-09-11 by Hiral Vora and its latest commit is 2018-10-22 by Nowlan Freese. However, it is not the only such class currently in use. ProbeSetGlyphFactory.java is used to draw Affymetrix expression array probesets - see https://wiki.transvar.org/display/igbman/Visualizing+probe+sets and https://bitbucket.org/lorainelab/affyprobesetsforigb/src/master/.
Also, all the factory classes in om.affymetrix.igb.view.factories are annotated as Components, suggesting that if we configure our project correctly, our to-be-written GenotypingResultsFactory can be selected by the framework to populate a 23 and Me track with Glyphs.
How do we use to ensure that our new factory gets selected instead of the others? To be answered in https://jira.transvar.org/browse/IGBF-2248
Task
Blocker
Suggested structure for the project:
Module name: File Handler Plugin - Genotyping Results
Description: A plugin for loading and visualization results from genotyping assays, such as the 23 and Me SNP chip test results
Code location: integrated-genome-browser/plugins/GenotypingResults
java source code files and packages:
One doubt: The package com.affymetrix.igb.view.factories contains many classes that implement MapTierGlyphFactoryI.java. This interface seems to be the key to adding new types of data as new IGB tracks.
One implementation class in particular seems to be doing most of the work in IGB - AnnotationGlyphFactory.java. Its first commit is 2012-09-11 by Hiral Vora and its latest commit is 2018-10-22 by Nowlan Freese. However, it is not the only such class currently in use. ProbeSetGlyphFactory.java is used to draw Affymetrix expression array probesets - see https://wiki.transvar.org/display/igbman/Visualizing+probe+sets and https://bitbucket.org/lorainelab/affyprobesetsforigb/src/master/.
Also, all the factory classes in om.affymetrix.igb.view.factories are annotated as Components, suggesting that if we configure our project correctly, our to-be-written GenotypingResultsFactory can be selected by the framework to populate a 23 and Me track with Glyphs.
How do we use to ensure that our new factory gets selected instead of the others? To be answered in https://jira.transvar.org/browse/IGBF-2248