Juicebox

[jrobinso]

No description provided.

[Copilot]

Pull request overview

This pull request adds Hi-C contact map visualization functionality to IGV, likely inspired by the Juicebox tool. The main changes include:

• A new interactive contact map viewer (ContactMapView) with normalization support, dynamic color scaling, and synchronized ruler display
• Enhanced HicFile class with normalization vector support and block request deduplication for improved performance
• Integration of the contact map view into InteractionTrack with a popup menu option
• Cleanup of legacy template comments across 130+ files

Reviewed changes

Copilot reviewed 230 out of 231 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
src/main/java/org/igv/bedpe/ContactMapView.java	New 766-line class implementing interactive Hi-C contact map visualization with async data loading, color scale controls, and event-driven updates
src/main/java/org/igv/hic/HicFile.java	Added normalization support, getBinSize helper method, and block deduplication to prevent redundant I/O operations
src/main/java/org/igv/bedpe/InteractionTrack.java	Integrated ContactMapView with menu option to open contact map popup
src/main/java/org/igv/hic/NormalizationVector.java	Added ByteOrder.LITTLE_ENDIAN support and accessor method
src/main/java/org/igv/bedpe/HicSource.java	Refactored to use HicFile.getBinSize instead of local implementation
src/test/java/org/igv/hic/HicFileTest.java	Updated test to pass normalization parameter
src/test/java/org/igv/hic/HicFileLocalTest.java	New test class for normalization vector functionality
test/sessions/4dn_hic.xml	New test session file for Hi-C data
130+ files	Removed boilerplate template comments and JDK import separators

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