Updated docs.

Author: kcleal

docs/docs/api/gw-init.md

@@ -6,12 +6,13 @@ parent: API Reference
 nav_order: 1
 ---
 
-# Gw Class
+## Gw Class
+
+`Gw(reference, **kwargs)`
 
 The `Gw` class is the main interface to libgw (GW). Initialise the GW object 
 with a reference genome and optional parameters.
 
-### `Gw(reference, **kwargs)`
 
 **Parameters:**
 - `reference` (str): Path to reference genome file or genome tag
@@ -25,8 +26,9 @@ gw = Gw("reference.fa", theme="dark", threads=4,
 ```
 ---
 
+## onlineGenomeTags
 
-### `onlineGenomeTags()`
+`onlineGenomeTags()`
 
 Returns a dictionary of available online reference genome tags. Use a local genome 
 for much better performance.

docs/docs/api/gw-interactive.md

@@ -8,6 +8,7 @@ nav_order: 7
 ---
 
 # Interactive Controls
+{: .no_toc .text-delta }
 
 ## Table of contents
 {: .no_toc .text-delta }
@@ -17,7 +18,8 @@ nav_order: 7
 
 ---
 
-### `apply_command(command)`
+### apply_command
+`apply_command(command)`
 
 Apply a GW command string.
 
@@ -26,7 +28,8 @@ Apply a GW command string.
 
 ---
 
-### `key_press(key, scancode, action, mods)`
+### key_press
+`key_press(key, scancode, action, mods)`
 
 Process a key press event.
 
@@ -38,7 +41,8 @@ Process a key press event.
 
 ---
 
-### `mouse_event(x_pos, y_pos, button, action)`
+### mouse_event
+`mouse_event(x_pos, y_pos, button, action)`
 
 Process a mouse event.
 

docs/docs/api/gw-loading-data.md

@@ -6,6 +6,7 @@ nav_order: 2
 ---
 
 ## Loading Data
+{: .no_toc .text-delta }
 
 ## Table of contents
 {: .no_toc .text-delta }
@@ -15,7 +16,8 @@ nav_order: 2
 
 ---
 
-### `add_bam(path)`
+### add_bam
+`add_bam(path)`
 
 Add a BAM file to the visualisation.
 
@@ -31,7 +33,8 @@ gw.add_bam("sample.bam")
 ```
 ---
 
-### `remove_bam(index)`
+### remove_bam
+`remove_bam(index)`
 
 Remove a BAM file from the visualisation.
 
@@ -43,7 +46,8 @@ Remove a BAM file from the visualisation.
 
 ---
 
-### `add_track(path, vcf_as_track=True, bed_as_track=True)`
+### add_track
+`add_track(path, vcf_as_track=True, bed_as_track=True)`
 
 
 Add a genomic data track to the visualisation.
@@ -66,7 +70,8 @@ gw.add_track("features.bed")
 ```
 ---
 
-### `remove_track(index)`
+### remove_track
+`remove_track(index)`
 
 Remove a data track from the visualisation.
 

docs/docs/api/gw-managing-regions.md

@@ -6,6 +6,7 @@ nav_order: 3
 ---
 
 ## Managing Regions
+{: .no_toc .text-delta }
 
 ## Table of contents
 {: .no_toc .text-delta }
@@ -15,7 +16,8 @@ nav_order: 3
 
 ---
 
-### `add_region(chrom, start, end, marker_start=-1, marker_end=-1)`
+### add_region
+`add_region(chrom, start, end, marker_start=-1, marker_end=-1)`
 
 Add a genomic region for visualisation. Setting the markers will result in a small triangle being drawn at
 the genomic position.
@@ -38,7 +40,8 @@ gw.add_region("chr1", 1000000, 1100000, 1050000, 1060000)
 
 ---
 
-### `remove_region(index)`
+### remove_region
+`remove_region(index)`
 
 Remove a genomic region from the visualisation.
 
@@ -50,7 +53,8 @@ Remove a genomic region from the visualisation.
 
 ---
 
-### `view_region(chrom, start, end)`
+### view_region
+`view_region(chrom, start, end)`
 
 Clear existing regions and view a specific genomic region.
 
@@ -70,7 +74,8 @@ gw.view_region("chr1", 1000000, 1100000)
 
 ---
 
-### `set_active_region_index(index)`
+### set_active_region_index
+`set_active_region_index(index)`
 
 Set the currently active region for dynamic visualisation.
 
@@ -82,19 +87,22 @@ Set the currently active region for dynamic visualisation.
 
 ---
 
-### `clear()`
+### clear
+`clear()`
 
 Remove all data.
 
 ---
 
-### `clear_regions()`
+### clear_regions
+`clear_regions()`
 
 Remove all defined genomic regions.
 
 ---
 
-### `clear_alignments()`
+### clear_alignments
+`clear_alignments()`
 
 Remove all loaded alignment data.
 

docs/docs/api/gw-palette.md

@@ -7,6 +7,7 @@ nav_order: 8
 
 
 # GwPalette Class
+{: .no_toc .text-delta }
 
 ## Table of contents
 {: .no_toc .text-delta }

docs/docs/api/gw-saving-images.md

@@ -6,6 +6,7 @@ nav_order: 5
 ---
 
 ## Saving images
+{: .no_toc .text-delta }
 
 ## Table of contents
 {: .no_toc .text-delta }
@@ -15,7 +16,8 @@ nav_order: 5
 
 ---
 
-### `save_png(path)`
+### save_png
+`save_png(path)`
 
 Save the current raster image to a PNG file.
 
@@ -32,7 +34,8 @@ gw.save_png("visualisation.png")
 
 ---
 
-### `save_pdf(path)`
+### save_pdf
+`save_pdf(path)`
 
 Save the plot to a PDF file.
 
@@ -49,7 +52,8 @@ gw.save_pdf("visualization.pdf")
 
 ---
 
-### `save_svg(path)`
+### save_svg
+`save_svg(path)`
 
 Save the plot to a SVG file.
 
@@ -66,7 +70,8 @@ gw.save_svg("visualization.svg")
 
 ---
 
-### `encode_as_png(compression_level=6)`
+### encode_as_png
+`encode_as_png(compression_level=6)`
 
 Encode the current canvas as PNG and return the binary data.
 
@@ -76,7 +81,8 @@ Encode the current canvas as PNG and return the binary data.
 **Returns:**
 - `bytes`: PNG encoded image data
 
-### `encode_as_jpeg(quality=80)`
+### encode_as_jpeg
+`encode_as_jpeg(quality=80)`
 
 Encode the current canvas as JPEG and return the binary data.
 
@@ -88,7 +94,8 @@ Encode the current canvas as JPEG and return the binary data.
 
 ---
 
-### `array()`
+### array
+`array()`
 
 Convert the raster image to a numpy array.
 

docs/docs/api/gw-settings.md

@@ -6,6 +6,7 @@ nav_order: 6
 ---
 
 ### Display Settings
+{: .no_toc .text-delta }
 
 ## Table of contents
 {: .no_toc .text-delta }
@@ -15,7 +16,8 @@ nav_order: 6
 
 ---
 
-## `set_canvas_width(width)`
+## set_canvas_width
+`set_canvas_width(width)`
 
 Set the canvas width and recreate the raster surface.
 
@@ -27,7 +29,8 @@ Set the canvas width and recreate the raster surface.
 
 ---
 
-### `set_canvas_height(height)`
+### set_canvas_height
+`set_canvas_height(height)`
 
 Set the canvas height and recreate the raster surface.
 
@@ -39,7 +42,8 @@ Set the canvas height and recreate the raster surface.
 
 ---
 
-### `set_canvas_size(width, height)`
+### set_canvas_size
+`set_canvas_size(width, height)`
 
 Set both canvas width and height and recreate the raster surface.
 
@@ -52,7 +56,8 @@ Set both canvas width and height and recreate the raster surface.
 
 ---
 
-### `set_theme(theme_name)`
+### set_theme
+`set_theme(theme_name)`
 
 Set a predefined visualisation theme.
 
@@ -70,7 +75,8 @@ gw.set_theme("dark")
 
 ---
 
-### `set_paint_ARBG(paint_enum, a, r, g, b)`
+### set_paint_ARBG
+`set_paint_ARBG(paint_enum, a, r, g, b)`
 
 Set the ARGB color for a specific paint type.
 
@@ -89,7 +95,8 @@ gw.set_paint_ARBG(GwPalette.NORMAL_READ, 255, 0, 0, 128)
 
 ---
 
-### `apply_theme(theme_dict)`
+### apply_theme
+`apply_theme(theme_dict)`
 
 Apply a custom theme using a dictionary of paint types and colors.
 
@@ -111,7 +118,8 @@ gw.apply_theme(custom_theme)
 
 ---
 
-### `load_theme_from_json(filepath)`
+### load_theme_from_json
+`load_theme_from_json(filepath)`
 
 Load and apply a theme from a JSON file.
 
@@ -128,7 +136,8 @@ gw.load_theme_from_json("custom_theme.json")
 
 ---
 
-### `save_theme_to_json(filepath)`
+### save_theme_to_json
+`save_theme_to_json(filepath)`
 
 Save the current theme settings to a JSON file.
 
@@ -146,7 +155,8 @@ gw.save_theme_to_json("my_theme.json")
 
 ---
 
-### `set_font_size(size)`
+### set_font_size
+`set_font_size(size)`
 
 Set the font size.
 
@@ -156,7 +166,8 @@ Set the font size.
 **Returns:**
 - `Gw`: Self for method chaining
 
-## `set_font_name(name)`
+## set_font_name
+`set_font_name(name)`
 
 Set the font name.