* Refactoring and simplification of heatmap legend editing and usage

[jrobinso]

• Add dark mode heatmaps for copy number and gene expression.

[Copilot]

Pull request overview

This PR refactors heatmap legend editing and usage, simplifying the codebase by consolidating color scale management and adding dark mode support for heatmaps.

• Introduces dark mode color scales for copy number and gene expression heatmaps
• Refactors color scale management to use string-based keys instead of TrackType enums
• Simplifies heatmap legend editor by removing unused TrackType parameter

Reviewed changes

Copilot reviewed 16 out of 16 changed files in this pull request and generated 9 comments.

Show a summary per file

File	Description
test/sessions/wig_heatmap.xml	New test session for heatmap rendering with ChipSeq data
test/sessions/gbm_subtypes2.xml	New test session for copy number heatmaps
test/sessions/gbm_subtypes.xml	Updates resource URLs to use GitHub raw content
src/main/resources/preferences.tab	Adds dark mode color scale preferences for copy number and gene expression
src/main/java/org/igv/ui/legend/HeatmapLegendEditor.java	Removes TrackType parameter from constructor
src/main/java/org/igv/ui/HeatmapScaleDialog.java	Removes unused main method
src/main/java/org/igv/track/TrackMenuUtils.java	Refactors heatmap scale dialog to use lambda and adds null safety for color scales
src/main/java/org/igv/track/MergedTracks.java	Removes redundant getColorScale override
src/main/java/org/igv/track/FeatureTrack.java	Removes manual color scale range adjustment
src/main/java/org/igv/track/AbstractTrack.java	Refactors getColorScale to check preferences by key and simplifies logic
src/main/java/org/igv/session/Session.java	Simplifies getColorScale to not fall back to preferences
src/main/java/org/igv/session/IGVSessionReader.java	Cleans up comments in color scale parsing
src/main/java/org/igv/prefs/PreferencesEditor.java	Refactors to use LegendPanel and improves combo box handling with SelectionItem wrapper
src/main/java/org/igv/prefs/LegendPanel.java	Renamed from HeatmapLegendPanel, refactored to use string keys and adds dark mode support for labels
src/main/java/org/igv/prefs/IGVPreferences.java	Refactors color scale management to use string keys, adds getColorScale(String) overload, renames get() to getUserPreference()
src/main/java/org/igv/maf/MultipleAlignmentTrack.java	Removes empty setColorScale override

Comments suppressed due to low confidence (3)

src/main/java/org/igv/prefs/LegendPanel.java:7

• The import for TrackType is unused. After the refactoring, this class no longer uses TrackType anywhere in its implementation. Consider removing this unused import.
  src/main/java/org/igv/prefs/LegendPanel.java:52
• The mouseExited() method is empty. Consider resetting the cursor to the default when the mouse exits the component to properly restore the cursor state.
  src/main/java/org/igv/prefs/LegendPanel.java:139
• The label color is set to use dark mode detection (Globals.isDarkMode() ? Color.WHITE : Color.BLACK) in paintHorizontal(). However, the vertical painting method paintVertical() still uses hardcoded Color.BLACK at line 182. For consistency with the dark mode support added in this PR, paintVertical() should also use the same dark mode-aware color selection.

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[Copilot]

The method caches null values in colorScaleCache (line 763) when both the preference lookup and TrackType parsing fail. This could prevent subsequent attempts to retrieve a valid color scale. Consider only caching non-null values or returning early when the scale cannot be determined.