remove .value from positioned trait

quinlan-lab · Sep 25, 2023 · 2a995f2 · 2a995f2
1 parent 90247ce
commit 2a995f2
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Showing 3 changed files with 15 additions and 29 deletions.
diff --git a/src/bedder_bed.rs b/src/bedder_bed.rs
@@ -1,6 +1,6 @@
 #![allow(clippy::useless_conversion)] // these are needed to support e.g. smartstring
 
-use crate::position::{Field, FieldError, Position, Positioned, Value};
+use crate::position::{Field, FieldError, Position, Positioned, Value, Valued};
 use crate::string::String;
 pub use bed::record::Record;
 pub use noodles::bed;
@@ -23,7 +23,9 @@ impl crate::position::Positioned for bed::record::Record<3> {
     fn stop(&self) -> u64 {
         self.end_position().get() as u64
     }
+}
 
+impl Valued for bed::record::Record<3> {
     fn value(&self, v: crate::position::Field) -> result::Result<Value, FieldError> {
         match v {
             Field::String(s) => Ok(Value::Strings(vec![s])),

diff --git a/src/bedder_vcf.rs b/src/bedder_vcf.rs
@@ -30,14 +30,7 @@ where
     }
 }
 
-/*
-pub fn _from_reader<R: Read>(r: Box<R>) -> io::Result<BedderVCF<R>> {
-    let reader = xvcf::Reader::from_reader(r, None)?;
-    BedderVCF::new(reader)
-}
-*/
-
-fn match_info_value(info: &vcf::record::Info, name: &str) -> result::Result<Value, FieldError> {
+pub fn match_info_value(info: &vcf::record::Info, name: &str) -> result::Result<Value, FieldError> {
     //let info = record.info();
     let key: vcf::record::info::field::Key = name
         .parse()
@@ -76,7 +69,7 @@ fn match_info_value(info: &vcf::record::Info, name: &str) -> result::Result<Valu
     }
 }
 
-fn match_value(record: &vcf::record::Record, f: Field) -> result::Result<Value, FieldError> {
+pub fn match_value(record: &vcf::record::Record, f: Field) -> result::Result<Value, FieldError> {
     match f {
         Field::String(s) => match s.as_str() {
             "chrom" => Ok(Value::Strings(vec![String::from(Positioned::chrom(
@@ -131,10 +124,6 @@ impl Positioned for vcf::record::Record {
     fn stop(&self) -> u64 {
         usize::from(self.end().expect("error getting end from vcf record")) as u64
     }
-
-    fn value(&self, f: crate::position::Field) -> result::Result<Value, FieldError> {
-        match_value(self, f)
-    }
 }
 
 impl<R> crate::position::PositionedIterator for BedderVCF<R>

diff --git a/src/position.rs b/src/position.rs
@@ -47,13 +47,15 @@ pub trait Positioned: Debug {
     /// non-inclusive end;
     fn stop(&self) -> u64;
 
-    // extract a value from the Positioned object Col
-    fn value(&self, b: Field) -> result::Result<Value, FieldError>;
-
     // get back the original line?
     //fn line(&self) -> &'a str;
 }
 
+pub trait Valued {
+    // extract a value from the Positioned object Col
+    fn value(&self, b: Field) -> result::Result<Value, FieldError>;
+}
+
 #[derive(Debug)]
 pub enum Position {
     Bed(crate::bedder_bed::Record<3>),
@@ -98,16 +100,13 @@ impl Position {
             Position::Other(o) => o.stop(),
         }
     }
+}
 
+#[cfg(feature = "dyn_positioned")]
+impl Valued for Box<dyn Positioned> {
     #[inline]
-    pub fn value(&self, f: Field) -> result::Result<Value, FieldError> {
-        match self {
-            Position::Bed(b) => b.value(f),
-            Position::Vcf(v) => v.value(f),
-            Position::Interval(i) => i.value(f),
-            #[cfg(feature = "dyn_positioned")]
-            Position::Other(o) => o.value(f),
-        }
+    fn value(&self, f: Field) -> result::Result<Value, FieldError> {
+        self.value(f)
     }
 }
 
@@ -124,10 +123,6 @@ impl Positioned for Box<dyn Positioned> {
     fn stop(&self) -> u64 {
         self.as_ref().stop()
     }
-
-    fn value(&self, b: Field) -> result::Result<Value, FieldError> {
-        self.as_ref().value(b)
-    }
 }
 
 impl PartialEq for dyn Positioned {