feat: strand: Use +/- rather than (+)/(-) for str (#39)

Change the string representation of Strand to "+", "-", ".". The current string representation is "(+)", "(-)", and "".
rust-bio · Jun 6, 2023 · 45f518e · 45f518e
1 parent cf89188
commit 45f518e
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Showing 4 changed files with 29 additions and 22 deletions.
diff --git a/src/annot/contig.rs b/src/annot/contig.rs
@@ -287,17 +287,21 @@ impl<R, S> Loc for Contig<R, S> {
 impl<R, S> Display for Contig<R, S>
 where
     R: Display,
-    S: Display,
+    S: Display + Clone + Into<Strand>,
 {
     fn fmt(&self, f: &mut Formatter) -> fmt::Result {
         write!(
             f,
-            "{}:{}-{}{}",
+            "{}:{}-{}",
             self.refid,
             self.start,
-            self.start + self.length as isize,
-            self.strand
-        )
+            self.start + self.length as isize
+        )?;
+        let strand: Strand = self.strand.clone().into();
+        if !strand.is_unknown() {
+            write!(f, "({})", strand)?;
+        }
+        Ok(())
     }
 }
 

diff --git a/src/annot/pos.rs b/src/annot/pos.rs
@@ -227,10 +227,15 @@ where
 impl<R, S> Display for Pos<R, S>
 where
     R: Display,
-    S: Display,
+    S: Display + Clone + Into<Strand>,
 {
     fn fmt(&self, f: &mut Formatter) -> fmt::Result {
-        write!(f, "{}:{}{}", self.refid, self.pos, self.strand)
+        let strand: Strand = self.strand.clone().into();
+        if strand.is_unknown() {
+            write!(f, "{}:{}", self.refid, self.pos)
+        } else {
+            write!(f, "{}:{}({})", self.refid, self.pos, strand)
+        }
     }
 }
 

diff --git a/src/annot/spliced.rs b/src/annot/spliced.rs
@@ -545,7 +545,7 @@ impl<R, S> Loc for Spliced<R, S> {
 impl<R, S> Display for Spliced<R, S>
 where
     R: Display,
-    S: Display,
+    S: Display + Clone + Into<Strand>,
 {
     fn fmt(&self, f: &mut Formatter) -> fmt::Result {
         write!(f, "{}:", self.refid)?;
@@ -562,7 +562,11 @@ where
             )?;
             sep = true;
         }
-        write!(f, "{}", self.strand)
+        let strand: Strand = self.strand.clone().into();
+        if !strand.is_unknown() {
+            write!(f, "({})", self.strand)?;
+        }
+        Ok(())
     }
 }
 

diff --git a/src/strand.rs b/src/strand.rs
@@ -91,20 +91,17 @@ impl Same for Strand {
 
 impl Display for Strand {
     fn fmt(&self, f: &mut Formatter) -> fmt::Result {
-        match *self {
-            Strand::Unknown => Ok(()),
-            _ => write!(f, "({})", self.strand_symbol()),
-        }
+        f.write_str(self.strand_symbol())
     }
 }
 
 impl FromStr for Strand {
     type Err = StrandError;
     fn from_str(s: &str) -> Result<Self, Self::Err> {
         match s {
-            "" => Ok(Strand::Unknown),
-            "(+)" => Ok(Strand::Forward),
-            "(-)" => Ok(Strand::Reverse),
+            "+" | "(+)" => Ok(Strand::Forward),
+            "-" | "(-)" => Ok(Strand::Reverse),
+            "." | "" => Ok(Strand::Unknown),
             _ => Err(StrandError::ParseError),
         }
     }
@@ -200,19 +197,16 @@ impl Same for ReqStrand {
 
 impl Display for ReqStrand {
     fn fmt(&self, f: &mut Formatter) -> fmt::Result {
-        match self {
-            ReqStrand::Forward => write!(f, "(+)"),
-            ReqStrand::Reverse => write!(f, "(-)"),
-        }
+        f.write_str(self.strand_symbol())
     }
 }
 
 impl FromStr for ReqStrand {
     type Err = StrandError;
     fn from_str(s: &str) -> Result<Self, Self::Err> {
         match s {
-            "(+)" => Ok(ReqStrand::Forward),
-            "(-)" => Ok(ReqStrand::Reverse),
+            "+" | "(+)" => Ok(ReqStrand::Forward),
+            "-" | "(-)" => Ok(ReqStrand::Reverse),
             _ => Err(StrandError::ParseError),
         }
     }