Clean main track settings

CHANGELOG.md

@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Various changes to the whole genome alignment used in comparison mode. Improves speed, lower memory, and better handling of repeats and other edge cases
 
 ### Fixed
+- Changing read filters now updates detailed reads immediately, without needing to pan or zoom first.
 - Old background requests are less likely to show stale errors after moving to a new region.
 - Detailed read view now fills in missing regions more reliably when navigating around.
 - Starting and closing the bundled seqhiker server is more reliable, especially while background work is still running.

scripts/annotation_cache_controller.gd

@@ -165,7 +165,7 @@ func prefetch_visible_target(start_bp: int, end_bp: int, bp_per_px: float) -> vo
 
 func update_detailed_read_strips(start_bp: int, end_bp: int, bp_per_px: float) -> void:
 	if not detailed_read_strips_enabled(bp_per_px):
-		_reset_read_strips()
+		invalidate_read_strips()
 		return
 	_ensure_read_strip_scope(bp_per_px)
 	if _strip_range_fully_covered(start_bp, end_bp):
@@ -187,6 +187,16 @@ func cancel_visible_requests() -> void:
 	_latest_visible_serial = -1
 
 
+func invalidate_read_strips() -> void:
+	_strip_segments.clear()
+	_strip_zoom = -1
+	_strip_scope_key = ""
+	_strip_generation = -1
+	_strip_left_pending = false
+	_strip_right_pending = false
+	_strip_pending_requests.clear()
+
+
 func cancel_all_requests() -> void:
 	cancel_visible_requests()
 	_strip_pending_requests.clear()
@@ -220,7 +230,7 @@ func _ensure_read_strip_scope(bp_per_px: float) -> void:
 	var zoom: int = int(host._compute_tile_zoom(bp_per_px))
 	var scope_key: String = str(host._scope_cache_key())
 	if zoom != _strip_zoom or scope_key != _strip_scope_key or host._tile_cache_generation != _strip_generation:
-		_reset_read_strips()
+		invalidate_read_strips()
 		_strip_zoom = zoom
 		_strip_scope_key = scope_key
 		_strip_generation = host._tile_cache_generation

scripts/track_settings_controller.gd.uid

@@ -0,0 +1 @@
+uid://do3pkxqjoboc3

tests/godot/run_tests.gd

@@ -2,7 +2,8 @@ extends SceneTree
 
 const TEST_SCRIPTS := [
 	"res://tests/godot/test_annotation_cache_controller.gd",
-	"res://tests/godot/test_local_zem_manager.gd"
+	"res://tests/godot/test_local_zem_manager.gd",
+	"res://tests/godot/test_track_settings_controller.gd"
 ]
 
 

tests/godot/test_annotation_cache_controller.gd

@@ -229,6 +229,27 @@ func test_missing_read_strip_request_fills_internal_gap() -> void:
 	assert_eq(str(request.get("request_kind", "")), "read_strip")
 
 
+func test_invalidate_read_strips_clears_cached_reads_without_visible_requests() -> void:
+	controller._strip_zoom = 1
+	controller._strip_scope_key = "scope"
+	controller._strip_generation = 0
+	controller._strip_segments = _strip_segments([
+		{"start_bp": 0, "end_bp": 300}
+	])
+	controller._strip_pending_requests[4] = {"side": "right"}
+	controller._strip_right_pending = true
+	controller._visible_pending_requests[2] = {"serial": 2}
+	controller._latest_visible_serial = 2
+
+	controller.invalidate_read_strips()
+
+	assert_false(controller.detailed_read_target_ready(100, 200, 1.0))
+	assert_eq(controller._strip_pending_requests.size(), 0)
+	assert_false(controller._strip_right_pending)
+	assert_true(controller._visible_pending_requests.has(2))
+	assert_eq(controller._latest_visible_serial, 2)
+
+
 func test_stale_visible_error_is_ignored() -> void:
 	controller._visible_pending_requests[2] = {"serial": 2, "query_start": 0, "query_end": 100}
 	controller._latest_visible_serial = 3

tests/godot/test_track_settings_controller.gd

@@ -0,0 +1,230 @@
+extends "res://tests/godot/test_case.gd"
+
+const ReadTrackSettingsPanelScene = preload("res://scenes/ReadTrackSettingsPanel.tscn")
+const TrackSettingsControllerScript = preload("res://scripts/track_settings_controller.gd")
+
+var host: FakeHost
+var feature_content: VBoxContainer
+var controller: RefCounted
+
+
+class FakeHost:
+	extends Node
+
+	const CONTEXT_PANEL_TRACK_SETTINGS := 2
+	const TRACK_AA := "aa"
+	const TRACK_GC_PLOT := "gc_plot"
+	const TRACK_DEPTH_PLOT := "depth_plot"
+	const TRACK_VCF := "vcf"
+	const TRACK_GENOME := "genome"
+	const SEQ_VIEW_CONCAT := 0
+	const SEQ_VIEW_SINGLE := 1
+	const DEFAULT_READ_THICKNESS := 8.0
+	const DEFAULT_READ_MAX_ROWS := 500
+	const DEFAULT_READ_MIN_MAPQ := 0
+	const DEFAULT_READ_HIDDEN_FLAGS := 256 | 512 | 1024 | 2048
+	const ANNOT_MAX_ON_SCREEN_MIN := 200
+	const ANNOT_MAX_ON_SCREEN_MAX := 50000
+	const MIN_PLOT_HEIGHT := 50.0
+	const MAX_PLOT_HEIGHT := 360.0
+	const READ_FILTER_FLAG_LABELS := [
+		{"bit": 1, "label": "paired"},
+		{"bit": 2, "label": "proper pair"},
+		{"bit": 8, "label": "mate unmapped"},
+		{"bit": 16, "label": "reverse strand"}
+	]
+
+	var _track_settings_box: VBoxContainer
+	var _read_track_settings_panel: VBoxContainer
+	var _track_settings_open := false
+	var _active_track_settings_id := ""
+	var _feature_panel_open := false
+	var feature_name_label := Label.new()
+	var _bam_tracks: Array[Dictionary] = [
+		{
+			"track_id": "reads:1",
+			"label": "sample.bam",
+			"view_mode": 0,
+			"fragment_log": true,
+			"thickness": 8.0,
+			"auto_expand_snp_text": true,
+			"show_soft_clips": false,
+			"show_pileup_logo": false,
+			"color_by_mate_contig": false,
+			"max_rows": 500,
+			"min_mapq": 0,
+			"hidden_flags": 0
+		}
+	]
+	var _show_full_length_regions := false
+	var _show_stop_codons := false
+	var _annotation_max_on_screen := 4400
+	var _seq_view_mode := SEQ_VIEW_CONCAT
+	var _selected_seq_id := -1
+	var _seq_option := OptionButton.new()
+	var _concat_gap_bp := 50
+	var _axis_coords_with_commas := false
+	var _gc_window_bp := 200
+	var _gc_plot_height := 100.0
+	var _depth_plot_height := 100.0
+	var _has_bam_loaded := true
+	var _variant_controller: RefCounted = null
+	var prepared_title := ""
+	var close_count := 0
+	var save_count := 0
+	var sound_count := 0
+	var slide_count := 0
+	var fetch_count := 0
+	var filter_change_count := 0
+
+	func _track_label_for_id(track_id: String) -> String:
+		return "Reads" if track_id.begins_with("reads:") else track_id
+
+	func _prepare_context_panel(_mode: int, title: String, _show_detail_labels: bool) -> void:
+		prepared_title = title
+		_track_settings_open = false
+		_active_track_settings_id = ""
+
+	func _play_ui_sound(_sound_id: String) -> void:
+		sound_count += 1
+
+	func _close_feature_panel() -> void:
+		close_count += 1
+		_feature_panel_open = false
+
+	func _save_config() -> void:
+		save_count += 1
+
+	func _bam_track_for_id(track_id: String) -> Dictionary:
+		for track in _bam_tracks:
+			if str(track.get("track_id", "")) == track_id:
+				return track
+		return {}
+
+	func _play_toggle_sound(_enabled: bool) -> void:
+		sound_count += 1
+
+	func _schedule_fetch() -> void:
+		fetch_count += 1
+
+	func _on_read_track_filter_changed() -> void:
+		filter_change_count += 1
+
+	func _slide_feature_panel(_open: bool, _animated: bool) -> void:
+		slide_count += 1
+
+	func _on_active_read_track_view_selected(_index: int) -> void:
+		pass
+
+	func _on_active_read_track_fragment_log_toggled(_enabled: bool) -> void:
+		pass
+
+	func _on_active_read_track_thickness_changed(_value: float) -> void:
+		pass
+
+	func _on_active_read_track_auto_expand_snp_toggled(_enabled: bool) -> void:
+		pass
+
+	func _on_active_read_track_show_soft_clips_toggled(_enabled: bool) -> void:
+		pass
+
+	func _on_active_read_track_show_pileup_logo_toggled(_enabled: bool) -> void:
+		pass
+
+	func _on_active_read_track_mate_contig_color_toggled(_enabled: bool) -> void:
+		pass
+
+	func _on_active_read_track_max_rows_changed(_value: float) -> void:
+		pass
+
+	func _on_active_read_track_min_mapq_changed(_value: float) -> void:
+		pass
+
+	func _on_show_full_region_toggled(_enabled: bool) -> void:
+		pass
+
+	func _on_show_stop_codons_toggled(_enabled: bool) -> void:
+		pass
+
+	func _on_annotation_max_on_screen_changed(_value: float) -> void:
+		pass
+
+	func _on_axis_coords_commas_toggled(_enabled: bool) -> void:
+		pass
+
+	func _on_seq_view_selected(_index: int) -> void:
+		pass
+
+	func _on_seq_selected(_index: int) -> void:
+		pass
+
+	func _on_concat_gap_changed(_value: float) -> void:
+		pass
+
+	func _invalidate_cache() -> void:
+		pass
+
+	func _apply_gc_plot_height() -> void:
+		pass
+
+	func _apply_depth_plot_height() -> void:
+		pass
+
+	func _depth_plot_color_for_track(_track_id: String) -> Color:
+		return Color.WHITE
+
+
+func setup() -> void:
+	host = FakeHost.new()
+	host.add_child(host.feature_name_label)
+	host.add_child(host._seq_option)
+	feature_content = VBoxContainer.new()
+	host.add_child(feature_content)
+	controller = TrackSettingsControllerScript.new()
+	controller.configure(host)
+	controller.setup(feature_content, ReadTrackSettingsPanelScene)
+
+
+func teardown() -> void:
+	host.free()
+	host = null
+	feature_content = null
+	controller = null
+
+
+func test_setup_creates_read_track_panel() -> void:
+	assert_ne(host._track_settings_box, null)
+	assert_ne(host._read_track_settings_panel, null)
+	var view_option := host._read_track_settings_panel.get_node("ReadViewOption") as OptionButton
+	assert_eq(view_option.item_count, 4)
+
+
+func test_show_read_track_settings_populates_controls() -> void:
+	controller.show_track_settings("reads:1")
+
+	assert_true(host._track_settings_open)
+	assert_eq(host._active_track_settings_id, "reads:1")
+	assert_eq(host.prepared_title, "Reads track settings")
+	assert_true(host._read_track_settings_panel.visible)
+	var bam_label := host._read_track_settings_panel.get_node("BAMLabel") as Label
+	assert_eq(bam_label.text, "BAM: sample.bam")
+	var dynamic_options := host._read_track_settings_panel.get_node("DynamicOptions") as VBoxContainer
+	assert_true(dynamic_options.get_child_count() > 0)
+
+
+func test_read_filter_toggle_updates_track_and_fetches() -> void:
+	controller.show_track_settings("reads:1")
+	var dynamic_options := host._read_track_settings_panel.get_node("DynamicOptions") as VBoxContainer
+	var paired_cb := dynamic_options.get_child(0) as CheckBox
+
+	paired_cb.button_pressed = true
+
+	assert_true((int(host._bam_tracks[0].get("hidden_flags", 0)) & 1) != 0)
+	assert_eq(host.filter_change_count, 1)
+
+
+func test_reopening_same_track_closes_panel() -> void:
+	controller.show_track_settings("reads:1")
+	controller.show_track_settings("reads:1")
+
+	assert_eq(host.close_count, 1)

tests/godot/test_track_settings_controller.gd.uid

@@ -0,0 +1 @@
+uid://dqavbhui15a02