Next step:

Please identify the following:

• Implementation class that draws gene models with a adaptive arrow in the intron part
• Implementation class parent classes and/or interfaces (what the class inherited from)
• Location of the classes in the code base file system (where are in the tree)
• Last branch where you can find it (so that we easily view the class code in bitbucket)
• Last commit for the above

Goal: We need to find the code that implemented the "look" we want to try.

Setting the preferences to default and deactivating all the data sources using IGB 9.1.8 worked and I was able to run IGB 6.7.3.

Implementation class that draws gene models with a adaptive arrow in the intron part

• Up until igb_6_7, the adaptive arrow is implemented in ArrowHeadGlyph

Implementation class parent classes and/or interfaces (what the class inherited from)

• ArrowHeadGlyph extends DirectedGlyph

Location of the classes in the code base file system (where are in the tree)

• Path: integrated-genome-browser/igb/src/com/affymetrix/igb/glyph

Last branch where you can find it (so that we easily view the class code in bitbucket)

• The last branch ArrowHeadGlyph class is available on is igb_6_7
• Link to the code

Last commit for the above

• Last commit involving the class: 4e1e1d9 "move all SeqSymmetry classes to package com.affymetrix.genometry.symmetry"
• Last commit with changes on the class: c2b9cd2 "Reverting back to previous behavior. Do not allow to select intron."

Screenshots of the ArrowHeadGlyph implemented in BedSequenceDemo is attached above. ArrowHeadGlyph is possibly used with EfficientLabelledLineGlyph for the intron structure

Question for Karthik Raveendran:

• Which method of which file implements the arrow shown within the intron part of the gene model?

(After you answer this last question, I will close the ticket. Thank you for your work on this!)

Question answered in IGBF-2900. Moving to Done.