Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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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:None
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Story Points:1
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Epic Link:
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Sprint:Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May
Description
Add breakpoints to the annotation factory class in com.affymetrix.igb.view.factories and observe what happens when you click Load Data after opening a narrowpeak file.
Based on looking at the code, it looks like this method:
private void addAnnotationGlyphs(SeqMapView smv, RootSeqSymmetry annotSym, BioSeq seq)
in
com.affymetrix.igb.view.TrackView
Is where the MapTierGlyphFactoryI for a given data set is identified and used to add Glyphs to IGB's SeqMapView
We need to confirm this.
Ideally, we can write a new new factory class that will let us add custom Glyphs to a genotyping results class, simply by adding the factory to the service registry for same.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
|
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description |
Add breakpoints to the annotation factory class in com.affymetrix.igb.view.factories and observe what happens when you click *Load Data* after opening a narrowpeak file.
Based on looking at the code, it looks like this method: private void addAnnotationGlyphs(SeqMapView smv, RootSeqSymmetry annotSym, BioSeq seq) in com.affymetrix.igb.view.TrackView Is where the MapTierGlyphFactoryI for a given data set is identified and used to add Glyphs to IGB's SeqMapView We need to confirm this. Ideally, we can write a new new factory class that will let us add custom Glyphs to a genotyping results class, simply by adding the factory to the service registry for same. |
Add breakpoints to the annotation factory class in com.affymetrix.igb.view.factories and observe what happens when you click *Load Data* after opening a narrowpeak file.
Based on looking at the code, it looks like this method: private void addAnnotationGlyphs(SeqMapView smv, RootSeqSymmetry annotSym, BioSeq seq) in com.affymetrix.igb.view.TrackView Is where the MapTierGlyphFactoryI for a given data set is identified and used to add Glyphs to IGB's SeqMapView We need to confirm this. Ideally, we can write a new new factory class that will let us add custom Glyphs to a genotyping results class, simply by adding the factory to the service registry for same. |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
Findings regarding whether Annotation Track is extensible to proposed user-created file type categories:
In AnnotationTrackPanel and AnnotationOperationImpl classes there is a static array of file type categories defined, which contains only three values - Annotation, Alignment, and ProbeSet.
Srishti Tiwari - follow-up question:
If you were to remove "Annotation" from the static array, would that cause the Annotation tab to stop becoming active when users click on an "Annotation" track label?
| Sprint | Spring 3 : 3 Feb to 14 Feb [ 86 ] | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 21 Feb [ 86, 87 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb [ 86, 87 ] | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 86, 87, 89 ] |
| Rank | Ranked higher |
| Sprint | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 86, 87, 89 ] | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar [ 86, 87, 89, 90 ] |
| Rank | Ranked higher |
| Sprint | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar [ 86, 87, 89, 90 ] | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10 [ 86, 87, 89, 90, 91 ] |
| Rank | Ranked higher |
| Sprint | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10 [ 86, 87, 89, 90, 91 ] | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr [ 86, 87, 89, 90, 91, 92 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr [ 86, 87, 89, 90, 91, 92 ] | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May [ 86, 87, 89, 90, 91, 92, 93 ] |
| Rank | Ranked higher |
| Sprint | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May [ 86, 87, 89, 90, 91, 92, 93 ] | Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May [ 86, 87, 89, 90, 91, 92, 93, 94 ] |
| Rank | Ranked higher |
If you have some tips or advice for the next developer who works on this, please add them to this ticket. Then move to Done. If not, also move to Done.
cc: Srishti Tiwari
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Hi Dr. [~aloraine],
The above understanding is correct. However, as per current implementation, we cannot have multiple GylphFactories for one File type category. (Please refer: MapTierTypeRegistry.java > getDefaultFactoryFor(FileTypeCategory) This method returns the first GlyphFactory in the list of preprocessors it has)
For our case, we could change this behavior by making a change in the above method or add a new file type category.
Also,
In FileTypeHolder there is a Map that stores file extensions and their FileTypeHandlers.
As per current implementation, the number of FileTypeCategories is fixed (as enums). Every new extension must belong to one of the predefined file type categories. If the new file type category needs to be added, we have to touch the core IGB codebase. We can change this by making the FileTypeCategory extensible. The way to do that is mentioned below:
https://dzone.com/articles/java-extensible-enum-with-interface