Details
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Type:
Bug
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Status: To-Do (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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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:3
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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
Description
Situation: If a bedgraph file has the name option within the track definition line at the top of the file, IGB overrides style changes such as color when data are loaded.
For example, open the attached file (BedGraph_HomoSapien_name.bedGraph) in IGB, but do not click Load Data. Change the foreground/background color of the file in the Data Access tab. Click Load Data. Note that the foreground/background color revert to their default colors (blue/white). Now do the same thing for the BedGraph_HomoSapien_noName.bedGraph file.
Hypothesis: When the file is added to IGB, the file itself is not read. IGB sets the style for the file with the key being the file name. When load data is clicked, IGB reads the file and sees the name option in the track definition line. IGB uses this name as a new identifier. IGB then searches for styles associated with this file using the new identifier and finds none. It then uses the default style.
Task: Fix the issue so that a bedgraph file with a name option does not override user selected color options upon clicking Load Data.
Note: This is important for the CyVerse/BioViz Connect project.
Attachments
Issue Links
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- Closed
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Activity
Track Name seems to be tightly coupled with the tier style object.
Whenever data is loaded and a track name is mentioned in the track line then style changes to default since it is not associated with any style.
We could retain the tier style that was changed before loading the data but with the track name being unchanged.
For this change to work we might have to re-architecture the entire feature.
Note - It has been decided not to do any change regarding the ticket. Hence, can be closed.
As this issue may be more complex than initially thought and because any changes could have unintended effects, moving this issue to the backlog. The issue appears to only affect BioViz Connect, as BioViz Connect sets the track color style before loading the file, which is then overridden if a track name is present in the bedgraph file.
Important files:
Bedgraph files are parsed using Wiggle.java. Within the method createGraphSyms there is logic for setting the graph_id and graph_name.
Set a breakpoint within IGBStateProvider.java in the getAnnotStyle method to see whether the style has been overwritten by default values.