add missing parameter

rust-bio · Jun 13, 2023 · d1f21c4 · d1f21c4
1 parent 8157330
commit d1f21c4
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Showing 3 changed files with 19 additions and 19 deletions.
diff --git a/src/alignment/pairwise/banded.rs b/src/alignment/pairwise/banded.rs
@@ -68,7 +68,7 @@
 //! let y = b"AAAAACGTACGTACGTGTGCATCATCATGTGCGTATCATAGATAGATGTAGATGATCCACAGTAAAA";
 //! let mut aligner = Aligner::with_capacity_and_scoring(x.len(), y.len(), scoring, k, w);
 //! let alignment = aligner.custom(x, y);
-//! println!("{}", alignment.pretty(x, y));
+//! println!("{}", alignment.pretty(x, y, 80));
 //! assert_eq!(alignment.score, 49);
 //! let mut correct_ops = Vec::new();
 //! correct_ops.push(Yclip(4));
@@ -1795,7 +1795,7 @@ mod banded {
         let mut aligner = banded::Aligner::with_capacity(x.len(), y.len(), -5, -1, &score, 10, 10);
         let alignment = aligner.global(x, y);
 
-        println!("aln:\n{}", alignment.pretty(x, y));
+        println!("aln:\n{}", alignment.pretty(x, y, 80));
         assert_eq!(
             alignment.operations,
             [Match, Match, Match, Ins, Ins, Ins, Match, Match, Match]
@@ -1810,7 +1810,7 @@ mod banded {
         let mut aligner = banded::Aligner::with_capacity(x.len(), y.len(), -5, -1, &score, 10, 10);
         let alignment = aligner.local(x, y);
 
-        println!("aln:\n{}", alignment.pretty(x, y));
+        println!("aln:\n{}", alignment.pretty(x, y, 80));
         assert_eq!(alignment.x_aln_len(), 0);
         assert_eq!(alignment.y_aln_len(), 0);
     }
@@ -1823,7 +1823,7 @@ mod banded {
         let mut aligner = banded::Aligner::with_capacity(x.len(), y.len(), -5, -1, &score, 10, 10);
         let alignment = aligner.global(x, y);
 
-        println!("aln:\n{}", alignment.pretty(x, y));
+        println!("aln:\n{}", alignment.pretty(x, y, 80));
 
         let mut correct = Vec::new();
         correct.extend(repeat(Match).take(11));
@@ -1867,7 +1867,7 @@ mod banded {
         let mut aligner = banded::Aligner::with_capacity(x.len(), y.len(), -5, -1, &score, 10, 10);
         let alignment = aligner.global(x, y);
 
-        println!("\naln:\n{}", alignment.pretty(x, y));
+        println!("\naln:\n{}", alignment.pretty(x, y, 80));
         assert_eq!(alignment.ystart, 0);
         assert_eq!(alignment.xstart, 0);
         assert_eq!(
@@ -1969,7 +1969,7 @@ mod banded {
         let score = |a: u8, b: u8| if a == b { 1i32 } else { -1i32 };
         let mut aligner = banded::Aligner::with_capacity(x.len(), y.len(), -5, -1, &score, 10, 10);
         let alignment = aligner.global(x, y);
-        println!("\naln:\n{}", alignment.pretty(x, y));
+        println!("\naln:\n{}", alignment.pretty(x, y, 80));
 
         assert_eq!(alignment.ystart, 0);
         assert_eq!(alignment.xstart, 0);
@@ -1993,7 +1993,7 @@ mod banded {
         let mut aligner = banded::Aligner::with_capacity(x.len(), y.len(), -5, -1, &score, 10, 10);
         let alignment = aligner.global(x, y);
 
-        println!("\naln:\n{}", alignment.pretty(x, y));
+        println!("\naln:\n{}", alignment.pretty(x, y, 80));
 
         println!("score:{}", alignment.score);
         assert_eq!(alignment.score, -9);
@@ -2015,7 +2015,7 @@ mod banded {
         let score = |a: u8, b: u8| if a == b { 1i32 } else { -1i32 };
         let mut aligner = banded::Aligner::with_capacity(x.len(), y.len(), -5, -1, &score, 10, 10);
         let alignment = aligner.global(x, y);
-        println!("\naln:\n{}", alignment.pretty(x, y));
+        println!("\naln:\n{}", alignment.pretty(x, y, 80));
 
         assert_eq!(alignment.ystart, 0);
         assert_eq!(alignment.xstart, 0);
@@ -2169,7 +2169,7 @@ mod banded {
         let mut aligner = banded::Aligner::with_scoring(scoring, 10, 10);
         let alignment = aligner.custom(x, y);
 
-        println!("{}", alignment.pretty(x, y));
+        println!("{}", alignment.pretty(x, y, 80));
         assert_eq!(alignment.score, 7);
     }
 

diff --git a/src/alignment/pairwise/mod.rs b/src/alignment/pairwise/mod.rs
@@ -126,7 +126,7 @@
 //! let y = b"AAAAACGTACGTACGTAAAA";
 //! let mut aligner = Aligner::with_capacity_and_scoring(x.len(), y.len(), scoring);
 //! let alignment = aligner.custom(x, y);
-//! println!("{}", alignment.pretty(x, y));
+//! println!("{}", alignment.pretty(x, y, 80));
 //! assert_eq!(alignment.score, 2);
 //! assert_eq!(
 //!     alignment.operations,
@@ -1231,7 +1231,7 @@ mod tests {
         let mut aligner = Aligner::with_capacity(x.len(), y.len(), -5, -1, score);
         let alignment = aligner.global(x, y);
 
-        println!("aln:\n{}", alignment.pretty(x, y));
+        println!("aln:\n{}", alignment.pretty(x, y, 80));
         assert_eq!(
             alignment.operations,
             [Match, Match, Match, Ins, Ins, Ins, Match, Match, Match]
@@ -1246,7 +1246,7 @@ mod tests {
         let mut aligner = Aligner::with_capacity(x.len(), y.len(), -5, -1, score);
         let alignment = aligner.global(x, y);
 
-        println!("aln:\n{}", alignment.pretty(x, y));
+        println!("aln:\n{}", alignment.pretty(x, y, 80));
 
         let mut correct = Vec::new();
         correct.extend(repeat(Match).take(11));
@@ -1290,7 +1290,7 @@ mod tests {
         let mut aligner = Aligner::with_capacity(x.len(), y.len(), -5, -1, score);
         let alignment = aligner.global(x, y);
 
-        println!("\naln:\n{}", alignment.pretty(x, y));
+        println!("\naln:\n{}", alignment.pretty(x, y, 80));
         assert_eq!(alignment.ystart, 0);
         assert_eq!(alignment.xstart, 0);
         assert_eq!(
@@ -1409,7 +1409,7 @@ mod tests {
         let score = |a: u8, b: u8| if a == b { 1i32 } else { -1i32 };
         let mut aligner = Aligner::with_capacity(x.len(), y.len(), -5, -1, &score);
         let alignment = aligner.global(x, y);
-        println!("\naln:\n{}", alignment.pretty(x, y));
+        println!("\naln:\n{}", alignment.pretty(x, y, 80));
 
         assert_eq!(alignment.ystart, 0);
         assert_eq!(alignment.xstart, 0);
@@ -1433,7 +1433,7 @@ mod tests {
         let mut aligner = Aligner::with_capacity(x.len(), y.len(), -5, -1, &score);
         let alignment = aligner.global(x, y);
 
-        println!("\naln:\n{}", alignment.pretty(x, y));
+        println!("\naln:\n{}", alignment.pretty(x, y, 80));
 
         println!("score:{}", alignment.score);
         assert_eq!(alignment.score, -9);
@@ -1455,7 +1455,7 @@ mod tests {
         let score = |a: u8, b: u8| if a == b { 1i32 } else { -1i32 };
         let mut aligner = Aligner::with_capacity(x.len(), y.len(), -5, -1, &score);
         let alignment = aligner.global(x, y);
-        println!("\naln:\n{}", alignment.pretty(x, y));
+        println!("\naln:\n{}", alignment.pretty(x, y, 80));
 
         assert_eq!(alignment.ystart, 0);
         assert_eq!(alignment.xstart, 0);
@@ -1633,7 +1633,7 @@ mod tests {
         let mut aligner = Aligner::with_scoring(scoring);
         let alignment = aligner.custom(x, y);
 
-        println!("{}", alignment.pretty(x, y));
+        println!("{}", alignment.pretty(x, y, 80));
         assert_eq!(alignment.score, 7);
     }
 

diff --git a/src/pattern_matching/myers/mod.rs b/src/pattern_matching/myers/mod.rs
@@ -122,7 +122,7 @@
 //! let mut matches = myers.find_all(text, 3);
 //! while matches.next_alignment(&mut aln) {
 //!     //println!("Hit fond in range: {}..{} (distance: {})", aln.ystart, aln.yend, aln.score);
-//!     //println!("{}", aln.pretty(pattern, text));
+//!     //println!("{}", aln.pretty(pattern, text, 80));
 //! }
 //! # }
 //! ```
@@ -192,7 +192,7 @@
 //!     "Best alignment at {}..{} (distance: {})",
 //!     aln.ystart, aln.yend, aln.score
 //! );
-//! println!("{}", aln.pretty(pattern, text));
+//! println!("{}", aln.pretty(pattern, text, 80));
 //! # }
 //! ```
 //!