Details
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Type: Task
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Status: Closed (View Workflow)
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Priority: Blocker
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:
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Story Points:2
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Epic Link:
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Sprint:Spring 3 : 3 Feb to 14 Feb
Description
Describe how code will be structured - package names, class names, location in the code base.
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Ann Loraine
created issue -
Ann Loraine
made changes -
Field | Original Value | New Value |
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Epic Link |
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Ann Loraine
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Labels | Advanced |
Ann Loraine
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Description | Describe how code will be structured - package names, class names, locatoin in the code base. | Describe how code will be structured - package names, class names, location in the code base. |
Ann Loraine
made changes -
Sprint | Spring 3 : 3 Feb to 14 Feb [ 86 ] |
Ann Loraine
made changes -
Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Ann Loraine
made changes -
Ann Loraine
made changes -
Ann Loraine
made changes -
Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] | Srishti Tiwari [ stiwari8 ] |
Ann Loraine
made changes -
Priority | Major [ 3 ] | Critical [ 2 ] |
Ann Loraine
made changes -
Priority | Critical [ 2 ] | Blocker [ 1 ] |
Srishti Tiwari (Inactive)
made changes -
Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Srishti Tiwari (Inactive)
made changes -
Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Srishti Tiwari (Inactive)
made changes -
Assignee | Srishti Tiwari [ stiwari8 ] | Ann Loraine [ aloraine ] |
Ann Loraine
made changes -
Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Ann Loraine
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Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
Ann Loraine
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Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Ann Loraine
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Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Ann Loraine
made changes -
Resolution | Done [ 10000 ] | |
Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
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