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Merged
sebschmi merged 8 commits into from
May 11, 2026
Merged

162 visualise uncertainties in some way #179

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eae5393
Make equal cost range available to TS inner renderer.
sebschmi May 11, 2026
0486bec
Consider inner arrangement separately for intersting range.
sebschmi May 11, 2026
2508368
Visualise uncertainties completely in inners.
sebschmi May 11, 2026
b83942a
Silence new clippy warning.
sebschmi May 11, 2026
5ea58ec
Fix nightly clippy lints.
sebschmi May 11, 2026
7f02085
Make uncertainty visualisation optional.
sebschmi May 11, 2026
01bb3c6
Explain uncertainty colours in legend.
sebschmi May 11, 2026
fb636bf
Fix a bunch of stuff.
sebschmi May 11, 2026
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76 changes: 65 additions & 11 deletions lib_tsshow/src/svg.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,8 @@ mod numbers;

const SVG_PADDING: f32 = 10.0;
const COPY_COLORS: &[&str] = &["#00CC00", "#009900", "#006600", "#003300"];
const OPTIONAL_COPY_COLORS: &[&str] = &["#88CC88", "#669966", "#446644", "#223322"];
const OPTIONAL_SOURCE_COLOR: &str = "blue";
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const COMPLEMENT_SOURCE_HIDDEN_COLOR: &str = "grey";
const TS_RUNNING_NUMBER: &str = "ABCDEFGHIJKLMNOPQRSTUVWXYZ";

Expand All @@ -61,6 +63,7 @@ pub struct SvgConfig {
/// Restrict the context around the template switches to this many characters on each side.
/// If `None`, the full sequences will be rendered.
pub restrict_context: Option<usize>,
pub visualise_equal_cost_ranges: bool,
}

pub fn create_ts_svg(
Expand Down Expand Up @@ -92,6 +95,7 @@ pub fn create_ts_svg(
reference.len(),
query.len(),
alignment.iter_flat_cloned(),
config.visualise_equal_cost_ranges,
)?;

if config.render_more_complement {
Expand Down Expand Up @@ -274,8 +278,8 @@ pub fn create_ts_svg(
)
.skip(primary_sp4_minus_one.unwrap_or(0.into()).into())
.find(|(_, c)| !c.is_blank())
.unwrap()
.0,
.map(|(column, _)| column)
.unwrap_or(ts_arrangement.query().len().into()),
TsArrangementRow::Query,
),
};
Expand Down Expand Up @@ -801,11 +805,12 @@ fn render_source_char(
c
};

Character::new_char(c, CharacterData::new_colored(copy_color(copy_depth)))
}
SourceChar::Gap { copy_depth } => {
Character::new_char('-', CharacterData::new_colored(copy_color(copy_depth)))
Character::new_char(c, CharacterData::new_colored(copy_color(copy_depth, false)))
}
SourceChar::Gap { copy_depth } => Character::new_char(
'-',
CharacterData::new_colored(copy_color(copy_depth, false)),
),
SourceChar::Separator => Character::new_char_with_default('|'),
SourceChar::Hidden { .. } | SourceChar::Spacer | SourceChar::Blank => {
Character::new_char_with_default(' ')
Expand Down Expand Up @@ -867,11 +872,25 @@ fn render_inner_char(
} else {
c
};
Character::new_char(c, CharacterData::new_colored(copy_color(copy_depth)))
Character::new_char(c, CharacterData::new_colored(copy_color(copy_depth, false)))
}
InnerChar::Gap { copy_depth } => {
Character::new_char('-', CharacterData::new_colored(copy_color(copy_depth)))
InnerChar::OptionalInner {
column,
lower_case,
copy_depth,
} => {
let c = source_sequence.char_at(column.into());
let c = if *lower_case {
c.to_ascii_lowercase()
} else {
c
};
Character::new_char(c, CharacterData::new_colored(copy_color(copy_depth, true)))
}
InnerChar::Gap { copy_depth } => Character::new_char(
'-',
CharacterData::new_colored(copy_color(copy_depth, false)),
),
InnerChar::Blank => Character::new_char(' ', Default::default()),
}
}
Expand All @@ -880,9 +899,15 @@ fn render_label_char(c: char) -> Character<CharacterData> {
Character::new_char(c, CharacterData::new_colored("#555555"))
}

fn copy_color(copy_depth: &Option<usize>) -> impl ToString {
fn copy_color(copy_depth: &Option<usize>, is_optional: bool) -> impl ToString {
if let Some(copy_depth) = copy_depth {
COPY_COLORS[copy_depth % COPY_COLORS.len()]
if is_optional {
OPTIONAL_COPY_COLORS[copy_depth % OPTIONAL_COPY_COLORS.len()]
} else {
COPY_COLORS[copy_depth % COPY_COLORS.len()]
}
} else if is_optional {
OPTIONAL_SOURCE_COLOR
} else {
"black"
}
Expand Down Expand Up @@ -946,6 +971,20 @@ fn legend(reference_name: &str, query_name: &str, scale: f32) -> (Group, f32, f3
));
label_width =
label_width.max(copy_label.chars().count() as f32 * typewriter::FONT.character_width);
y += typewriter::FONT
.character_height
.max(sans_serif_mono::FONT.character_height);

let uncertainty_label = "BLUE CHARACTERS";
result = result.add(svg_string(
uncertainty_label
.chars()
.map(|c| Character::new_char(c, CharacterData::new_colored(OPTIONAL_SOURCE_COLOR))),
&SvgLocation { x: 0.0, y },
&typewriter::FONT,
));
label_width = label_width
.max(uncertainty_label.chars().count() as f32 * typewriter::FONT.character_width);

// Explanations.
let label_width = label_width + typewriter::FONT.character_width;
Expand Down Expand Up @@ -979,6 +1018,21 @@ fn legend(reference_name: &str, query_name: &str, scale: f32) -> (Group, f32, f3
.character_height
.max(sans_serif_mono::FONT.character_height);

let uncertainty_explanation = "Equal-cost range of the TSM";
result = result.add(svg_string(
uncertainty_explanation
.chars()
.map(Character::<CharacterData>::new_char_with_default),
&SvgLocation { x: label_width, y },
&sans_serif_mono::FONT,
));
explanation_width = explanation_width.max(
uncertainty_explanation.chars().count() as f32 * sans_serif_mono::FONT.character_width,
);
y += typewriter::FONT
.character_height
.max(sans_serif_mono::FONT.character_height);

result = result.set("transform", format!("scale({scale})"));
let legend_width = headline_width.max(label_width + explanation_width) * scale;
let legend_height = y * scale;
Expand Down
50 changes: 42 additions & 8 deletions lib_tsshow/src/ts_arrangement.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@ impl TsArrangement {
reference_length: usize,
query_length: usize,
alignment: impl IntoIterator<Item = AlignmentType>,
visualise_equal_cost_ranges: bool,
) -> Result<Self> {
let mut template_switches = Vec::new();
let mut source = TsSourceArrangement::new(
Expand All @@ -49,7 +50,12 @@ impl TsArrangement {
&mut template_switches,
)?;
let mut complement = TsComplementArrangement::new(&source);
let inner = TsInnerArrangement::new(&mut source, &mut complement, template_switches);
let inner = TsInnerArrangement::new(
&mut source,
&mut complement,
template_switches,
visualise_equal_cost_ranges,
);

Ok(Self {
source,
Expand Down Expand Up @@ -333,6 +339,18 @@ impl TsArrangement {
inner.template_switch().sp4_reference,
),
self.query_arrangement_char_to_source_column(inner.template_switch().sp4_query),
inner
.sequence()
.iter_values()
.filter_map(|c| {
if c.is_gap_or_blank() {
None
} else {
Some(c.source_column())
}
})
.next()
.unwrap(),
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]
.into_iter()
.min()
Expand All @@ -350,14 +368,31 @@ impl TsArrangement {
[
self.reference_arrangement_char_to_source_column(
inner.template_switch().sp1_reference,
),
self.query_arrangement_char_to_source_column(inner.template_switch().sp1_query),
inner.template_switch().sp2_secondary,
inner.template_switch().sp3_secondary,
)
.saturating_sub(1),
self.query_arrangement_char_to_source_column(inner.template_switch().sp1_query)
.saturating_sub(1),
inner.template_switch().sp2_secondary.saturating_sub(1),
inner.template_switch().sp3_secondary.saturating_sub(1),
self.reference_arrangement_char_to_source_column(
inner.template_switch().sp4_reference,
),
self.query_arrangement_char_to_source_column(inner.template_switch().sp4_query),
)
.saturating_sub(1),
self.query_arrangement_char_to_source_column(inner.template_switch().sp4_query)
.saturating_sub(1),
inner
.sequence()
.iter_values()
.rev()
.filter_map(|c| {
if c.is_gap_or_blank() {
None
} else {
Some(c.source_column())
}
})
.next()
.unwrap(),
]
Comment thread
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.into_iter()
.max()
Expand All @@ -370,6 +405,5 @@ impl TsArrangement {
.max(self.source.query_length())
.into(),
)
.saturating_sub(1)
}
}
10 changes: 10 additions & 0 deletions lib_tsshow/src/ts_arrangement/index_types.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -82,6 +82,16 @@ macro_rules! index_type_ops {
}
}

impl std::ops::Sub<$signed_inner> for $name {
type Output = Self;

fn sub(self, other: $signed_inner) -> Self::Output {
Self(
<$inner>::try_from(<$signed_inner>::try_from(self.0).unwrap() - other).unwrap(),
)
}
}

impl std::ops::AddAssign<$inner> for $name {
fn add_assign(&mut self, other: $inner) {
self.0 += other
Expand Down
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