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The current TierGlyph has all the logic for displaying the data in various ways (Graph, Annotation, ...)
The new design will have a subclass of TierGlyph, TierGlyphViewMode, that will contain another
Glyph, ViewModeGlyph (an abstract class), and will delegate all calls to the viewModeGlyph. To display
the data (object model SeqSymmetry) in a different manner, just change the ViewModeGlyph. For example,
for a Wiggle file (Graph track), the TierGlyph can have a FillBarGraphGlyph, then replace that with a
HeatMapGraphGlyph, then replace that with a StairStepGraphGlyph, all subclasses of ViewModeGlyph.
Each ViewModeGlyph will specify what data it can display, so only only the view mode glyphs that can
handle the data will be available. This is done by specifying a FileTypeCategory for each data set.
FileTypeCategories are: Annotation, Alignment, Graph, Sequence, Probeset, Scored, Mismatch, or Variant.
The method com.affymetrix.igb.util.TrackUtils.useViewMode(String method), is used to specify whether
to use the old code (regular TierGlyph) or new code (TierGlyphViewMode). The method takes in the
uri, and passes back true to use new code, or false to use old code. To test all data using the
new code, change this method to always return true.
Annotations/Alignments
- MaxExpanded @
- Collapsed /Expanded @
- ScrollExpanded - like MaxExpandedExpanded, but with a vertical scroll, and no max stack depth
- Depth @
- Tabular - show the data in a table like the Selection Info tab (rows/columns reversed)
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View Modes can be the result of an operation or series of operations on the SeqSymmetry data
e.g the not annotation operation, or the log graph operation. The view mode is on the output
SeqSymmetry of the operation.
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Semantic Zooming
View Modes can be varying, depending on the view state, for example for a zoomed out annotation,
the depth view mode is shown, but when zoomed in, the MaxExpanded annotation view mode is shown.
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- The different View Modes can have parameters, like the user options in the track preferences.
These same options can be instead linked to the data.
Bugs
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- .
Discussion
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Hi,
For Operation View Mode,
I have added a popup menu called "Transform". It holds all transformation that applies to current file type category. Once a transform is applied, it starts with a default view mode based on output.
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