Fix minor issues with insertion markers. (1) markers not in sync wit…#1809
Merged
Fix minor issues with insertion markers. (1) markers not in sync wit…#1809
Conversation
… "hide small indels option. (2) expanded color (blue) too dark for dark mode.
Contributor
There was a problem hiding this comment.
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 |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
…h "hide small indels option. (2) expanded color (blue) too dark for dark mode.