allow preliminary enzyme numbers (x.x.x.nx)

fa-compression/src/algorithm1/decode.rs

@@ -82,39 +82,39 @@ mod tests {
 
     #[test]
     fn test_decode_single_ec() {
-        assert_eq!(decode(&[44, 44, 44, 189, 208]), "EC:1.1.1.-")
+        assert_eq!(decode(&[44, 44, 44, 190, 224]), "EC:1.1.1.-")
     }
 
     #[test]
     fn test_decode_single_go() {
-        assert_eq!(decode(&[209, 17, 163, 138, 208]), "GO:0009279")
+        assert_eq!(decode(&[225, 17, 163, 138, 224]), "GO:0009279")
     }
 
     #[test]
     fn test_decode_single_ipr() {
-        assert_eq!(decode(&[221, 18, 116, 117]), "IPR:IPR016364")
+        assert_eq!(decode(&[238, 18, 116, 117]), "IPR:IPR016364")
     }
 
     #[test]
     fn test_decode_no_ec() {
         assert_eq!(
-            decode(&[209, 17, 163, 138, 209, 39, 71, 94, 17, 153, 39]),
+            decode(&[225, 17, 163, 138, 225, 39, 71, 95, 17, 153, 39]),
             "GO:0009279;IPR:IPR016364;IPR:IPR008816"
         )
     }
 
     #[test]
     fn test_decode_no_go() {
         assert_eq!(
-            decode(&[44, 44, 44, 190, 44, 60, 44, 141, 209, 39, 71, 80]),
+            decode(&[44, 44, 44, 191, 44, 60, 44, 142, 225, 39, 71, 80]),
             "EC:1.1.1.-;EC:1.2.1.7;IPR:IPR016364"
         )
     }
 
     #[test]
     fn test_decode_no_ipr() {
         assert_eq!(
-            decode(&[44, 44, 44, 189, 17, 26, 56, 174, 17, 26, 56, 173]),
+            decode(&[44, 44, 44, 190, 17, 26, 56, 175, 17, 26, 56, 174]),
             "EC:1.1.1.-;GO:0009279;GO:0009279"
         )
     }
@@ -123,7 +123,7 @@ mod tests {
     fn test_decode_all() {
         assert_eq!(
             decode(&[
-                44, 44, 44, 189, 17, 26, 56, 173, 18, 116, 117, 225, 67, 116, 110, 17, 153, 39
+                44, 44, 44, 190, 17, 26, 56, 174, 18, 116, 117, 241, 67, 116, 111, 17, 153, 39
             ]),
             "EC:1.1.1.-;GO:0009279;IPR:IPR016364;IPR:IPR032635;IPR:IPR008816"
         )

fa-compression/src/algorithm1/encode.rs

@@ -94,48 +94,48 @@ mod tests {
 
     #[test]
     fn test_encode_single_ec() {
-        assert_eq!(encode("EC:1.1.1.-"), vec![44, 44, 44, 189, 208])
+        assert_eq!(encode("EC:1.1.1.-"), vec![44, 44, 44, 190, 224])
     }
 
     #[test]
     fn test_encode_single_go() {
-        assert_eq!(encode("GO:0009279"), vec![209, 17, 163, 138, 208])
+        assert_eq!(encode("GO:0009279"), vec![225, 17, 163, 138, 224])
     }
 
     #[test]
     fn test_encode_single_ipr() {
-        assert_eq!(encode("IPR:IPR016364"), vec![221, 18, 116, 117])
+        assert_eq!(encode("IPR:IPR016364"), vec![238, 18, 116, 117])
     }
 
     #[test]
     fn test_encode_no_ec() {
         assert_eq!(
             encode("IPR:IPR016364;GO:0009279;IPR:IPR008816"),
-            vec![209, 17, 163, 138, 209, 39, 71, 94, 17, 153, 39]
+            vec![225, 17, 163, 138, 225, 39, 71, 95, 17, 153, 39]
         )
     }
 
     #[test]
     fn test_encode_no_go() {
         assert_eq!(
             encode("IPR:IPR016364;EC:1.1.1.-;EC:1.2.1.7"),
-            vec![44, 44, 44, 190, 44, 60, 44, 141, 209, 39, 71, 80]
+            vec![44, 44, 44, 191, 44, 60, 44, 142, 225, 39, 71, 80]
         )
     }
 
     #[test]
     fn test_encode_no_ipr() {
         assert_eq!(
             encode("EC:1.1.1.-;GO:0009279;GO:0009279"),
-            vec![44, 44, 44, 189, 17, 26, 56, 174, 17, 26, 56, 173]
+            vec![44, 44, 44, 190, 17, 26, 56, 175, 17, 26, 56, 174]
         )
     }
 
     #[test]
     fn test_encode_all() {
         assert_eq!(
             encode("IPR:IPR016364;EC:1.1.1.-;IPR:IPR032635;GO:0009279;IPR:IPR008816"),
-            vec![44, 44, 44, 189, 17, 26, 56, 173, 18, 116, 117, 225, 67, 116, 110, 17, 153, 39]
+            vec![44, 44, 44, 190, 17, 26, 56, 174, 18, 116, 117, 241, 67, 116, 111, 17, 153, 39]
         )
     }
 }

fa-compression/src/algorithm1/mod.rs

@@ -73,6 +73,7 @@ enum CharacterSet {
     /// Special Enzyme Commission characters
     Dash,
     Point,
+    Preliminary,
 
     /// Different annotation type separator
     Comma,
@@ -106,6 +107,7 @@ impl Encode for CharacterSet {
             b'9' => CharacterSet::Nine,
             b'-' => CharacterSet::Dash,
             b'.' => CharacterSet::Point,
+            b'n' => CharacterSet::Preliminary,
             b',' => CharacterSet::Comma,
             b';' => CharacterSet::Semicolon,
             _ => panic!("Invalid character")
@@ -138,8 +140,9 @@ impl Decode for CharacterSet {
             10 => '9',
             11 => '-',
             12 => '.',
-            13 => ',',
-            14 => ';',
+            13 => 'n',
+            14 => ',',
+            15 => ';',
             _ => panic!("Invalid character")
         }
     }
@@ -167,10 +170,10 @@ impl BitOr for CharacterSet {
 mod tests {
     use super::*;
 
-    static CHARACTERS: [u8; 15] =
-        [b'$', b'0', b'1', b'2', b'3', b'4', b'5', b'6', b'7', b'8', b'9', b'-', b'.', b',', b';'];
+    static CHARACTERS: [u8; 16] =
+        [b'$', b'0', b'1', b'2', b'3', b'4', b'5', b'6', b'7', b'8', b'9', b'-', b'.', b'n', b',', b';'];
 
-    static CHARACTER_SETS: [CharacterSet; 15] = [
+    static CHARACTER_SETS: [CharacterSet; 16] = [
         CharacterSet::Empty,
         CharacterSet::Zero,
         CharacterSet::One,
@@ -184,6 +187,7 @@ mod tests {
         CharacterSet::Nine,
         CharacterSet::Dash,
         CharacterSet::Point,
+        CharacterSet::Preliminary,
         CharacterSet::Comma,
         CharacterSet::Semicolon
     ];
@@ -233,13 +237,7 @@ mod tests {
     #[test]
     #[should_panic]
     fn test_decode_invalid() {
-        CharacterSet::decode(15);
-    }
-
-    #[test]
-    #[should_panic]
-    fn test_decode_pair_invalid() {
-        CharacterSet::decode_pair(0b11111111);
+        CharacterSet::decode(16);
     }
 
     #[test]