Fix minor issues with insertion markers. (1) markers not in sync wit… #1809
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… "hide small indels option. (2) expanded color (blue) too dark for dark mode.
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Pull request overview
This PR fixes two issues with insertion markers in alignment tracks: (1) markers not syncing with the "hide small indels" option, and (2) the expanded insertion color (blue) being too dark in dark mode.
Changes:
- Moved insertion marker filtering logic from InsertionManager to RulerPanel to enable dynamic filtering based on track-specific settings
- Added brightness adjustment for insertion marker colors in dark mode
- Added new menu item "Set indel size threshold..." for easier threshold configuration
- Added IGVPreferences parameter to AlignmentTileLoader.loadTile() method for consistent preference handling
Reviewed changes
Copilot reviewed 8 out of 8 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| src/main/java/org/igv/ui/panel/RulerPanel.java | Updated insertion marker colors for dark mode, moved filtering logic from InsertionManager, added showInsertions flag and mouse event handling for insertion area |
| src/main/java/org/igv/sam/InsertionManager.java | Removed filtering logic for small indels (moved to RulerPanel for dynamic filtering) |
| src/main/java/org/igv/sam/AlignmentTileLoader.java | Added IGVPreferences parameter to loadTile() method for consistent preference access |
| src/main/java/org/igv/sam/AlignmentDataManager.java | Updated loadTile() call to pass preferences parameter |
| src/main/java/org/igv/sam/AlignmentTrackMenu.java | Added "Set indel size threshold..." menu item and updated repaint calls to include header panels |
| src/main/java/org/igv/ui/panel/MainPanel.java | Added repaintHeaderPanels() method to support updating insertion markers |
| src/main/java/org/igv/ui/IGV.java | Added repaintHeaderPanels() method wrapper |
| src/test/java/org/igv/sam/AlignmentTileLoaderTest.java | Updated test to pass IGVPreferences to loadTile() method |
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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…h "hide small indels option. (2) expanded color (blue) too dark for dark mode.