factor common behavior out into a library

5 files changed, 109 insertions, 0 deletions

diff --git a/rosalind/dna.rs b/rosalind/dna.rs
new file mode 100644
index 0000000..a2ee73d
--- /dev/null
+++ b/rosalind/dna.rs
@@ -0,0 +1,30 @@
+use str = core::str;
+
+pure fn gc_content(dna: ~str) -> float {
+    let mut content = 0;
+    for str::each_char(dna) |ch| {
+        match ch {
+            'C' | 'G' => content += 1,
+            _         => (),
+        }
+    }
+    (content as float) / (str::len(dna) as float)
+}
+
+pure fn complement(base: char) -> char {
+    match base {
+        'A' => 'T',
+        'C' => 'G',
+        'G' => 'C',
+        'T' => 'A',
+        _   => fail ~"Unknown character found",
+    }
+}
+
+pure fn transcribe(base: char) -> char {
+    match base {
+        'T'             => 'U',
+        'A' | 'C' | 'G' => base,
+        _               => fail ~"Unknown character found",
+    }
+}
diff --git a/rosalind/fasta.rs b/rosalind/fasta.rs
new file mode 100644
index 0000000..9cd80a1
--- /dev/null
+++ b/rosalind/fasta.rs
@@ -0,0 +1,45 @@
+use core::io::{stdin,Reader,ReaderUtil};
+use str = core::str;
+
+const EOF: char = -1 as char;
+
+struct FASTAReader {
+    in:              Reader,
+    priv mut peeked: char,
+}
+
+impl FASTAReader {
+    static fn new() -> FASTAReader {
+        FASTAReader { in: stdin(), peeked: EOF }
+    }
+
+    priv fn read_line(&self) -> ~str {
+        let mut line = self.in.read_line();
+        if self.peeked != '>' {
+            str::unshift_char(&mut line, self.peeked);
+        }
+        self.peeked = self.in.read_char();
+        line
+    }
+
+    priv fn read_sequence(&self) -> (~str, ~str) {
+        if self.peeked == EOF {
+            self.peeked = self.in.read_char();
+        }
+
+        let name = self.read_line();
+        let mut dna = ~"";
+        while !self.in.eof() && self.peeked != '>' {
+            let line = self.read_line();
+            str::push_str(&mut dna, line);
+        }
+        (name, dna)
+    }
+
+    fn each_sequence(&self, cb: fn(~str, ~str) -> bool) {
+        while !self.in.eof() {
+            let (name, dna) = self.read_sequence();
+            cb(name, dna);
+        }
+    }
+}
diff --git a/rosalind/io.rs b/rosalind/io.rs
new file mode 100644
index 0000000..86abe3f
--- /dev/null
+++ b/rosalind/io.rs
@@ -0,0 +1,5 @@
+use core::io::{stdin,ReaderUtil};
+
+fn input_line() -> ~str {
+    stdin().read_line()
+}
diff --git a/rosalind/mod.rc b/rosalind/mod.rc
new file mode 100644
index 0000000..3908b83
--- /dev/null
+++ b/rosalind/mod.rc
@@ -0,0 +1,8 @@
+#[link(name = "rosalind", vers = "0.0.1", author = "doy")];
+
+#[crate_type = "lib"];
+
+mod dna;
+mod fasta;
+mod io;
+mod str;
diff --git a/rosalind/str.rs b/rosalind/str.rs
new file mode 100644
index 0000000..0fac1cd
--- /dev/null
+++ b/rosalind/str.rs
@@ -0,0 +1,21 @@
+use str = core::str;
+
+/* really feels like there should be a more efficient way to do this */
+fn reverse(s: &str) -> ~str {
+    let mut r = ~"";
+    str::reserve(&mut r, str::len(s));
+    for str::each_char(s) |ch| {
+        str::unshift_char(&mut r, ch)
+    }
+    r
+}
+
+pure fn hamming(string1: ~str, string2: ~str) -> int {
+    let mut hamming = 0;
+    for str::each_chari(string1) |i, ch| {
+        if ch != str::char_at(string2, i) {
+            hamming += 1;
+        }
+    }
+    hamming
+}