Details
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Type:
Epic
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Status: Open
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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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Component/s: Dev and Dep, Scriptable API
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Labels:None
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Epic Name:groovyJalviewAPI
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Urgency:Not urgent
Description
Groovy scripts in jalview are initialised with a small number of bound objects:
- Jalview: the jalview.bin.Jalview instance - supports getAlignFrames() and getCurrentAlFrame()
- currentAlFrame: the first alignment frame instantiated after parsing command line arguments when running in headless mode.
Every other aspect of Jalview is accessed via its java namespace, which makes it cumbersome to script, and means that scripters have no idea whether their code is guaranteed to run on some future version of Jalview.
Key needs:
* short, memorable symbols for accessing key Jalview objects (e.g. alignment, dataset, view, views, tree, trees, structureview, etc).
- Jalview: the jalview.bin.Jalview instance - supports getAlignFrames() and getCurrentAlFrame()
- currentAlFrame: the first alignment frame instantiated after parsing command line arguments when running in headless mode.
Every other aspect of Jalview is accessed via its java namespace, which makes it cumbersome to script, and means that scripters have no idea whether their code is guaranteed to run on some future version of Jalview.
Key needs:
* short, memorable symbols for accessing key Jalview objects (e.g. alignment, dataset, view, views, tree, trees, structureview, etc).