algbio · sebschmi · Jun 2, 2025 · Jun 2, 2025 · Jun 2, 2025
diff --git a/lib_tsshow/src/svg.rs b/lib_tsshow/src/svg.rs
@@ -768,6 +768,7 @@ fn render_source_char(
         SourceChar::Gap { copy_depth } => {
             Character::new_char('-', CharacterData::new_colored(copy_color(copy_depth)))
         }
+        SourceChar::Separator => Character::new_char_with_default('|'),
         SourceChar::Hidden { .. } | SourceChar::Spacer | SourceChar::Blank => {
             Character::new_char_with_default(' ')
         }

diff --git a/lib_tsshow/src/svg/font/sans_serif_mono.rs b/lib_tsshow/src/svg/font/sans_serif_mono.rs
@@ -2,6 +2,7 @@ use std::sync::LazyLock;
 
 use super::Font;
 
+/// Font: monospace
 pub static FONT: LazyLock<Font> = LazyLock::new(|| {
     Font::new(
         [

diff --git a/lib_tsshow/src/svg/font/typewriter.rs b/lib_tsshow/src/svg/font/typewriter.rs
@@ -2,6 +2,7 @@ use std::sync::LazyLock;
 
 use super::Font;
 
+/// Font: Courier New
 pub static FONT: LazyLock<Font> = LazyLock::new(|| {
     Font::new(
         [
@@ -68,6 +69,7 @@ pub static FONT: LazyLock<Font> = LazyLock::new(|| {
             ('8', "m 0.86196288,-1.0557495 q 0.16278072,0.0790649 0.24494632,0.20928955 0.083716,0.12867432 0.083716,0.27750244 0,0.23099365 -0.1736328,0.39997558 Q 0.84335936,0 0.59531249,0 0.34726562,0 0.17363281,-0.16898193 0,-0.33796386 0,-0.56895751 0,-0.71623534 0.08216553,-0.84490966 0.16588135,-0.97513426 0.3302124,-1.0557495 0.18758545,-1.137915 0.12247314,-1.2262817 0.03255615,-1.3518554 0.03255615,-1.5037842 q 0,-0.2139404 0.16433105,-0.3736206 0.16588135,-0.1612304 0.39842529,-0.1612304 0.23409424,0 0.39842529,0.1612304 0.16433102,0.1596802 0.16433102,0.3736206 0,0.1519288 -0.089917,0.2759522 -0.063562,0.089917 -0.20618892,0.1720825 z M 1.0247436,-1.4991333 q 0,-0.1674316 -0.12557369,-0.2868042 -0.12402344,-0.1209228 -0.30540771,-0.1209228 -0.17983398,0 -0.30540771,0.1209228 -0.12402344,0.1209229 -0.12402344,0.2852539 0,0.1519287 0.12247315,0.2666504 0.12402343,0.1131714 0.306958,0.1131714 0.18448486,0 0.306958,-0.1131714 0.1240234,-0.1147217 0.1240234,-0.2651001 z m 0.035657,0.93327637 q 0,-0.17208251 -0.13332522,-0.29920653 -0.13332519,-0.12712403 -0.33176269,-0.12712403 -0.1984375,0 -0.33176269,0.12712403 -0.13332519,0.12712402 -0.13332519,0.29765624 0,0.1767334 0.13332519,0.306958 0.13487549,0.13022461 0.33176269,0.13022461 0.19688721,0 0.3302124,-0.13022461 0.13487551,-0.1302246 0.13487551,-0.30540771 z"),
             ('9', "m 1.0604004,-1.1472168 q -0.10076907,0.17828371 -0.24029544,0.2682007 -0.13797607,0.089917 -0.28370361,0.089917 -0.13487548,0 -0.26199951,-0.0775147 Q 0.14882812,-0.9441284 0.07441405,-1.0929565 0,-1.2433349 0,-1.407666 q 0,-0.2387451 0.14727782,-0.434082 0.14882813,-0.1968872 0.396875,-0.1968872 0.17673339,0 0.32246093,0.1100708 0.14572755,0.1100708 0.22634275,0.3193603 0.1038696,0.2682007 0.1038696,0.62321779 0,0.27595214 -0.088367,0.45888671 -0.058911,0.12402343 -0.17363276,0.2402954 Q 0.82165525,-0.17053222 0.6790283,-0.09766846 0.48369139,0 0.27285155,0 0.13332519,0 0.04495849,-0.05270996 0.00465087,-0.07751465 0.00465087,-0.11472168 q 0,-0.026355 0.01860352,-0.0434082 0.01860351,-0.0186035 0.04495849,-0.0186035 0.01860352,0 0.05426026,0.0170532 0.0604614,0.0294556 0.13952636,0.0294556 0.3302124,0 0.56740722,-0.23719482 0.23719478,-0.23874511 0.23719478,-0.59686278 0,-0.0651123 -0.0062,-0.18293459 z m -0.024805,-0.217041 Q 0.95343016,-1.6789673 0.83095701,-1.7921386 0.71003416,-1.9068603 0.5472534,-1.9068603 q -0.16588134,0 -0.29145507,0.1395263 -0.12557373,0.1395264 -0.12557373,0.3581177 0,0.2123901 0.12557373,0.3519165 0.12557373,0.13797608 0.28370361,0.13797608 0.0914673,0 0.17983398,-0.0496094 0.089917,-0.0496094 0.16898193,-0.14882811 0.0511597,-0.066663 0.14727785,-0.2464966 z"),
             ('-', "m 1.6169555,-0.99063719 v 0.18603515 H 0.28835449 v -0.18603515 z"),
+            ('|', "m 1.0185425,-1.8572509 -0.00155,2.17196037 q 0,0.0465088 -0.0186035,0.0666626 -0.0170532,0.0201538 -0.0465088,0.0201538 -0.0279053,0 -0.0465088,-0.0201538 -0.0186035,-0.0201538 -0.0186035,-0.0666626 V -1.8572509 q 0,-0.048059 0.0186035,-0.068213 0.0186035,-0.020154 0.0465088,-0.020154 0.0294556,0 0.0480591,0.020154 0.0186035,0.020154 0.0186035,0.068213 z"),
             (' ', ""),
         ].into_iter().map(|(c, value)| (c, value.to_string())).collect(),
         2.0,

diff --git a/lib_tsshow/src/ts_arrangement/complement.rs b/lib_tsshow/src/ts_arrangement/complement.rs
@@ -64,6 +64,7 @@ impl TsComplementArrangement {
                         ..
                     }
                     | SourceChar::Gap { .. }
+                    | SourceChar::Separator
                     | SourceChar::Spacer
                     | SourceChar::Blank => {
                         sequence_c.push(ComplementChar::Blank);
@@ -75,6 +76,11 @@ impl TsComplementArrangement {
         result
     }
 
+    pub fn width(&self) -> usize {
+        debug_assert_eq!(self.reference_c.len(), self.query_c.len());
+        self.reference_c.len()
+    }
+
     pub fn secondary_complement(
         &self,
         secondary: TemplateSwitchSecondary,

diff --git a/lib_tsshow/src/ts_arrangement/inner.rs b/lib_tsshow/src/ts_arrangement/inner.rs
@@ -49,6 +49,12 @@ impl TsInnerArrangement {
             inners: Default::default(),
         };
 
+        trace!(
+            "source width: {}; complement width: {}",
+            source_arrangement.width(),
+            complement_arrangement.width(),
+        );
+
         for ts in template_switches {
             trace!("source_inner: {:?}", ts.inner);
 
@@ -63,6 +69,12 @@ impl TsInnerArrangement {
                 ),
             };
             let forward = sp2_secondary < sp3_secondary;
+            trace!(
+                "sp2_secondary: {} -> {sp2_secondary}; sp3_secondary: {} -> {sp3_secondary}; {}",
+                ts.sp2_secondary,
+                ts.sp3_secondary,
+                if forward { "forward" } else { "reverse" }
+            );
 
             let mut source_inner = ts.inner.iter().copied();
             let mut inner = TaggedVec::<ArrangementColumn, _>::default();
@@ -395,7 +407,7 @@ impl From<SourceChar> for InnerChar {
                 panic!("Cannot be translated into InnerChar")
             }
             SourceChar::Gap { copy_depth } => Self::Gap { copy_depth },
-            SourceChar::Spacer | SourceChar::Blank => Self::Blank,
+            SourceChar::Separator | SourceChar::Spacer | SourceChar::Blank => Self::Blank,
         }
     }
 }

diff --git a/lib_tsshow/src/ts_arrangement/source.rs b/lib_tsshow/src/ts_arrangement/source.rs
@@ -40,6 +40,10 @@ pub enum SourceChar {
     Gap {
         copy_depth: Option<usize>,
     },
+    /// Separates the aligned section of the sequences from the unaligned section.
+    ///
+    /// This is used when the alignment is only computed on a substring of the reference and the query.
+    Separator,
     /// Like a blank, but not treated as an empty column.
     Spacer,
     Blank,
@@ -56,13 +60,42 @@ impl TsSourceArrangement {
     ) -> Result<Self> {
         let mut ts_index = 0;
         let mut alignment = alignment.into_iter();
+
+        // Insert the source sequences with blanks to the left to make sure their alignments start at the same arrangement column.
+        let reference_left_blank_count =
+            query_alignment_offset.saturating_sub(reference_alignment_offset);
+        let query_left_blank_count =
+            reference_alignment_offset.saturating_sub(query_alignment_offset);
         let mut result = Self {
-            reference: FromIterator::from_iter((0..reference_length).map(SourceChar::new_source)),
-            query: FromIterator::from_iter((0..query_length).map(SourceChar::new_source)),
+            reference: FromIterator::from_iter(
+                iter::repeat_n(SourceChar::Blank, reference_left_blank_count)
+                    .chain((0..reference_length).map(SourceChar::new_source)),
+            ),
+            query: FromIterator::from_iter(
+                iter::repeat_n(SourceChar::Blank, query_left_blank_count)
+                    .chain((0..query_length).map(SourceChar::new_source)),
+            ),
         };
 
-        let mut current_reference_index = ArrangementColumn::from(reference_alignment_offset);
-        let mut current_query_index = ArrangementColumn::from(query_alignment_offset);
+        let mut current_reference_index =
+            ArrangementColumn::from(reference_left_blank_count + reference_alignment_offset);
+        let mut current_query_index =
+            ArrangementColumn::from(query_left_blank_count + query_alignment_offset);
+        debug_assert_eq!(current_reference_index, current_query_index);
+
+        // If there are further characters to the left of the alignment, we insert a separator into both sequences.
+        if reference_alignment_offset > 0 || query_alignment_offset > 0 {
+            result
+                .reference
+                .insert(current_reference_index, SourceChar::Separator);
+            current_reference_index += 1;
+
+            result
+                .query
+                .insert(current_query_index, SourceChar::Separator);
+            current_query_index += 1;
+        }
+        debug_assert_eq!(current_reference_index, current_query_index);
 
         while let Some(alignment_type) = alignment.next() {
             match alignment_type {
@@ -127,6 +160,36 @@ impl TsSourceArrangement {
             }
         }
 
+        debug_assert_eq!(current_reference_index, current_query_index);
+
+        // If there are further source chars right of the alignment, we insert a separator into both sequences.
+        if result.reference_arrangement_to_source_column(current_reference_index)
+            < SourceColumn::new(reference_length - 1)
+            || result.query_arrangement_to_source_column(current_query_index)
+                < SourceColumn::new(query_length - 1)
+        {
+            result
+                .reference
+                .insert(current_reference_index, SourceChar::Separator);
+            current_reference_index += 1;
+
+            result
+                .query
+                .insert(current_query_index, SourceChar::Separator);
+            current_query_index += 1;
+        }
+
+        debug_assert_eq!(current_reference_index, current_query_index);
+
+        // Fill the back with blanks to ensure equal length.
+        while result.reference.len() < result.query.len() {
+            result.reference.push(SourceChar::Blank);
+        }
+        while result.query.len() < result.reference.len() {
+            result.query.push(SourceChar::Blank);
+        }
+
+        debug_assert_eq!(result.reference.len(), result.query.len());
         Ok(result)
     }
 
@@ -147,12 +210,24 @@ impl TsSourceArrangement {
         let sp1_query = self.query_arrangement_to_arrangement_char_column(*current_query_index);
         let sp2_secondary = match ts_secondary {
             TemplateSwitchSecondary::Reference => {
-                self.reference_arrangement_to_source_column(*current_reference_index)
+                let source_current_reference_index =
+                    self.reference_arrangement_to_source_column(*current_reference_index);
+                trace!(
+                    "current_reference_index: {current_reference_index} -> {source_current_reference_index}"
+                );
+                source_current_reference_index
             }
             TemplateSwitchSecondary::Query => {
-                self.query_arrangement_to_source_column(*current_query_index)
+                let source_current_query_index =
+                    self.query_arrangement_to_source_column(*current_query_index);
+                trace!(
+                    "current_query_index: {current_query_index} -> {source_current_query_index}"
+                );
+                source_current_query_index
             }
         } + first_offset;
+        trace!("first_offset: {first_offset}");
+        trace!("sp2_secondary: {sp2_secondary}");
 
         let mut sp3_secondary = sp2_secondary;
         let mut primary_inner_length = 0;
@@ -333,6 +408,7 @@ impl TsSourceArrangement {
     }
 
     pub fn width(&self) -> usize {
+        debug_assert_eq!(self.reference.len(), self.query.len());
         self.reference.len()
     }
 
@@ -574,22 +650,26 @@ impl SourceChar {
             Self::Source { copy_depth, .. }
             | Self::Hidden { copy_depth, .. }
             | Self::Gap { copy_depth } => copy_depth.is_some(),
-            Self::Spacer | Self::Blank => panic!("Blank has no copy property"),
+            Self::Separator | Self::Spacer | Self::Blank => panic!("Blank has no copy property"),
         }
     }
 
     pub fn copy_depth(&self) -> Option<usize> {
         match self {
             Self::Source { copy_depth, .. } | Self::Hidden { copy_depth, .. } => *copy_depth,
             Self::Gap { copy_depth } => *copy_depth,
-            Self::Spacer | Self::Blank => panic!("Blank has no copy property"),
+            Self::Separator | Self::Spacer | Self::Blank => panic!("Blank has no copy property"),
         }
     }
 
     pub fn to_lower_case(&mut self) {
         match self {
             Self::Source { lower_case, .. } => *lower_case = true,
-            Self::Hidden { .. } | Self::Gap { .. } | Self::Spacer | Self::Blank => {
+            Self::Hidden { .. }
+            | Self::Gap { .. }
+            | Self::Separator
+            | Self::Spacer
+            | Self::Blank => {
                 panic!("Not lowercasable: {self:?}")
             }
         }
@@ -598,7 +678,11 @@ impl SourceChar {
     pub fn to_upper_case(&mut self) {
         match self {
             Self::Source { lower_case, .. } => *lower_case = false,
-            Self::Hidden { .. } | Self::Gap { .. } | Self::Spacer | Self::Blank => {
+            Self::Hidden { .. }
+            | Self::Gap { .. }
+            | Self::Separator
+            | Self::Spacer
+            | Self::Blank => {
                 panic!("Not uppercasable: {self:?}")
             }
         }
@@ -618,7 +702,7 @@ impl SourceChar {
                 };
             }
             Self::Hidden { .. } => unreachable!("Already hidden"),
-            Self::Gap { .. } | Self::Spacer | Self::Blank => {
+            Self::Gap { .. } | Self::Separator | Self::Spacer | Self::Blank => {
                 unreachable!("Cannot be hidden: {self:?}")
             }
         }
@@ -637,7 +721,7 @@ impl SourceChar {
                 column: *column,
                 copy_depth: Some(copy_depth.map(|copy_depth| copy_depth + 1).unwrap_or(0)),
             },
-            Self::Gap { .. } | Self::Spacer | Self::Blank => {
+            Self::Gap { .. } | Self::Separator | Self::Spacer | Self::Blank => {
                 panic!("Should never be copied: {self:?}")
             }
         }
@@ -648,7 +732,7 @@ impl Char for SourceChar {
     fn source_column(&self) -> SourceColumn {
         match self {
             Self::Source { column, .. } | Self::Hidden { column, .. } => *column,
-            Self::Gap { .. } | Self::Spacer | Self::Blank => panic!("Not a char"),
+            Self::Gap { .. } | Self::Separator | Self::Spacer | Self::Blank => panic!("Not a char"),
         }
     }
 

diff --git a/raw_svg/font.svg b/raw_svg/font.svg
diff --git a/raw_svg/label_font.svg b/raw_svg/label_font.svg
diff --git a/test_files/twin_heli_MDC1-AS1_10.toml b/test_files/twin_heli_MDC1-AS1_10.toml
@@ -0,0 +1,26 @@
+type = "WithTarget"
+alignment = [[1, "PrimarySubstitution"], [1, "PrimaryMatch"], [152, { TemplateSwitchEntrance = { first_offset = -151, equal_cost_range = { min_start = 0, max_start = 0, min_end = 0, max_end = 0 }, primary = "Reference", secondary = "Reference", direction = "Reverse" } }], [7, "SecondaryMatch"], [1, "SecondarySubstitution"], [2, "SecondaryMatch"], [69, { TemplateSwitchExit = { anti_primary_gap = 78 } }], [273, { TemplateSwitchEntrance = { first_offset = 272, equal_cost_range = { min_start = 0, max_start = 0, min_end = 0, max_end = 0 }, primary = "Query", secondary = "Reference", direction = "Reverse" } }], [5, "SecondaryMatch"], [1, "SecondaryInsertion"], [4, "SecondaryMatch"], [85, { TemplateSwitchExit = { anti_primary_gap = 94 } }], [2, "PrimaryMatch"], [1, "PrimarySubstitution"], [1, "PrimaryMatch"]]
+reference_offset = 200
+query_offset = 164
+cost = 24.0
+cost_per_base = 0.05263157894736842
+duration_seconds = 69.622919049
+opened_nodes = 50127278.0
+closed_nodes = 22733640.0
+suboptimal_opened_nodes = 4326095.0
+suboptimal_opened_nodes_ratio = 0.09445378299508116
+template_switch_amount = 2.0
+runtime = 0.0
+memory = 0.0
+
+[result]
+astar_result_type = "FoundTarget"
+cost = 24
+
+[sequences]
+reference_name = "Homo_sapiens "
+reference = "TCTTTACGGTGAACATCAGAGAAAACCCCCTCCTGTTGCAGTAACAGTTTTGAAATACACCAAGGGTGTTCCGGTCTCCCTAACAAAAACTTGCCTTCTCAGGGAAAATGCTTTGACAAAGTCTTCTCTGACCTAGGGGAAAAGCAGACACTCAACTCTGGCTGTATCTATCTGTCCTGTCTCCTTTGAAAGAGAAAGAAAAAAAACTGCTATGAAACAATTCTGGTCACAGGCCAGAAATTCAGCCTTATTTTAAAAATAGGACCTTACCAACATTCATCAACAGGGCTTCCATATAGTAAGAGTGGATTACAACTGAGAGAGCAGTAAGCCACAGACTCTATTTAGGAAATAGTTCTCAAGGAATCCCAGACAAGAGAGTGAAGAAACAACATCACAAGTCAACTACGGAAAACTAAAACCTGTGGCACTTACAGCTATAGCAAATACTAAACAAAACCCAGCTCATAGTCAGATTAACATAAAACCTCAC"
+reference_rc = "GTGAGGTTTTATGTTAATCTGACTATGAGCTGGGTTTTGTTTAGTATTTGCTATAGCTGTAAGTGCCACAGGTTTTAGTTTTCCGTAGTTGACTTGTGATGTTGTTTCTTCACTCTCTTGTCTGGGATTCCTTGAGAACTATTTCCTAAATAGAGTCTGTGGCTTACTGCTCTCTCAGTTGTAATCCACTCTTACTATATGGAAGCCCTGTTGATGAATGTTGGTAAGGTCCTATTTTTAAAATAAGGCTGAATTTCTGGCCTGTGACCAGAATTGTTTCATAGCAGTTTTTTTTCTTTCTCTTTCAAAGGAGACAGGACAGATAGATACAGCCAGAGTTGAGTGTCTGCTTTTCCCCTAGGTCAGAGAAGACTTTGTCAAAGCATTTTCCCTGAGAAGGCAAGTTTTTGTTAGGGAGACCGGAACACCCTTGGTGTATTTCAAAACTGTTACTGCAACAGGAGGGGGTTTTCTCTGATGTTCACCGTAAAGA"
+query_name = "PrimatesAnc069 "
+query = "CTCTCCTGCTTAAGAACAGCTGCAGCCCACTCTGCCCCAGCATCCCCTTCTGCTGGAAGCTGGCTCTTTCTTACATCTGCAACTACTGAGGCTGTTAGGGAGGTGCCCTCCTCTGCATCTGTTTCACAGTCCCCATGCAGAGGCCAGGCTTCCTCTAGAGATACCACAAGCAGCTTTGCTGGTCCCCCAACTGCTTTCACATCTGTTTGATTTGTCCCCTCCACAGACACCTGATGCTTCTTTATATGTATAATGGCTGACCCTGGCGGGACTTCCTTCTCCACTTGTGTGTTGATGTCCACTGTGGTGGAGGCTTGGCTTCTCTCCAGGTGGATCCCAGGTGAGCTCTTATCTGCTTCCACACTGTCATCACTGTCCCCAAAAGGAGGTTGGTCCTTTTCTGAATGTGCTCTAACAAG"
+query_rc = "CTTGTTAGAGCACATTCAGAAAAGGACCAACCTCCTTTTGGGGACAGTGATGACAGTGTGGAAGCAGATAAGAGCTCACCTGGGATCCACCTGGAGAGAAGCCAAGCCTCCACCACAGTGGACATCAACACACAAGTGGAGAAGGAAGTCCCGCCAGGGTCAGCCATTATACATATAAAGAAGCATCAGGTGTCTGTGGAGGGGACAAATCAAACAGATGTGAAAGCAGTTGGGGGACCAGCAAAGCTGCTTGTGGTATCTCTAGAGGAAGCCTGGCCTCTGCATGGGGACTGTGAAACAGATGCAGAGGAGGGCACCTCCCTAACAGCCTCAGTAGTTGCAGATGTAAGAAAGAGCCAGCTTCCAGCAGAAGGGGATGCTGGGGCAGAGTGGGCTGCAGCTGTTCTTAAGCAGGAGAG"