1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179

//! FASTA record sequence.

pub mod complement;

pub use self::complement::Complement;

use std::ops::Index;

use bytes::Bytes;
use noodles_core::{position::SequenceIndex, region::Interval};

/// A FASTA record sequence.
#[derive(Clone, Debug, Default, Eq, PartialEq)]
pub struct Sequence(Bytes);

impl Sequence {
    /// Returns the length of the sequence.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_fasta::record::Sequence;
    /// let sequence = Sequence::default();
    /// assert_eq!(sequence.len(), 0);
    /// ```
    pub fn len(&self) -> usize {
        self.0.len()
    }

    /// Returns whether the sequence is empty.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_fasta::record::Sequence;
    /// let sequence = Sequence::default();
    /// assert!(sequence.is_empty());
    /// ```
    pub fn is_empty(&self) -> bool {
        self.0.is_empty()
    }

    /// Returns a reference to a base at or slice of bases between the given index.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_core::Position;
    /// use noodles_fasta::record::Sequence;
    ///
    /// let sequence = Sequence::from(b"ACGT".to_vec());
    ///
    /// let start = Position::try_from(2)?;
    /// assert_eq!(sequence.get(start), Some(&b'C'));
    ///
    /// assert_eq!(sequence.get(start..), Some(&b"CGT"[..]));
    ///
    /// let end = Position::try_from(3)?;
    /// assert_eq!(sequence.get(start..=end), Some(&b"CG"[..]));
    /// # Ok::<_, noodles_core::position::TryFromIntError>(())
    /// ```
    pub fn get<I>(&self, index: I) -> Option<&I::Output>
    where
        I: SequenceIndex<u8>,
    {
        index.get(self.as_ref())
    }

    /// Returns a subset of the sequence within the given range.
    ///
    /// Unlike [`Self::get`], this returns the slice as a [`Sequence`].
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_core::Position;
    /// use noodles_fasta::record::Sequence;
    ///
    /// let sequence = Sequence::from(b"ACGT".to_vec());
    ///
    /// let start = Position::try_from(2)?;
    /// let end = Position::try_from(3)?;
    /// let actual = sequence.slice(start..=end);
    ///
    /// let expected = Sequence::from(b"CG".to_vec());
    ///
    /// assert_eq!(actual, Some(expected));
    /// # Ok::<_, noodles_core::position::TryFromIntError>(())
    /// ```
    pub fn slice<I>(&self, interval: I) -> Option<Self>
    where
        I: Into<Interval>,
    {
        let interval = interval.into();

        let start = interval
            .start()
            .map(|position| usize::from(position) - 1)
            .unwrap_or(usize::MIN);

        let end = interval.end().map(usize::from).unwrap_or(self.len());

        if start <= end && end <= self.len() {
            let buf = self.0.slice(start..end);
            Some(Self::from(buf))
        } else {
            None
        }
    }

    /// Returns an iterator that complements the sequence.
    ///
    /// # Examples
    ///
    /// ## Complement a sequence
    ///
    /// ```
    /// use noodles_fasta::record::Sequence;
    /// let sequence = Sequence::from(b"ACGT".to_vec());
    /// let actual: Sequence = sequence.complement().collect::<Result<_, _>>()?;
    /// let expected = Sequence::from(b"TGCA".to_vec());
    /// assert_eq!(actual, expected);
    /// # Ok::<_, noodles_fasta::record::sequence::complement::ComplementError>(())
    /// ```
    ///
    /// ## Reverse complement a sequence
    ///
    /// ```
    /// use noodles_fasta::record::Sequence;
    /// let sequence = Sequence::from(b"ACGT".to_vec());
    /// let actual: Sequence = sequence.complement().rev().collect::<Result<_, _>>()?;
    /// let expected = sequence.clone();
    /// assert_eq!(actual, expected);
    /// # Ok::<_, noodles_fasta::record::sequence::complement::ComplementError>(())
    /// ```
    pub fn complement(&self) -> Complement<'_> {
        Complement::new(self.0.iter())
    }
}

impl AsRef<[u8]> for Sequence {
    fn as_ref(&self) -> &[u8] {
        &self.0
    }
}

impl From<Vec<u8>> for Sequence {
    fn from(data: Vec<u8>) -> Self {
        Self(Bytes::from(data))
    }
}

impl From<Bytes> for Sequence {
    fn from(data: Bytes) -> Self {
        Self(data)
    }
}

impl FromIterator<u8> for Sequence {
    fn from_iter<T>(iter: T) -> Self
    where
        T: IntoIterator<Item = u8>,
    {
        let mut buf = Vec::new();
        buf.extend(iter);
        Self::from(buf)
    }
}

impl<I> Index<I> for Sequence
where
    I: SequenceIndex<u8>,
{
    type Output = I::Output;

    fn index(&self, index: I) -> &Self::Output {
        index.index(self.as_ref())
    }
}