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

use std::{
    cmp,
    io::{self, Write},
};

use super::{record::Sequence, Record};

const LINE_BASES: u64 = 80;

/// A FASTA writer.
pub struct Writer<W> {
    inner: W,
}

impl<W> Writer<W>
where
    W: Write,
{
    /// Creates a FASTA writer.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_fasta as fasta;
    /// let writer = fasta::Writer::new(Vec::new());
    /// ```
    pub fn new(inner: W) -> Self {
        Self { inner }
    }

    /// Returns a reference to the underlying writer.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_fasta as fasta;
    /// let writer = fasta::Writer::new(Vec::new());
    /// assert!(writer.get_ref().is_empty());
    /// ```
    pub fn get_ref(&self) -> &W {
        &self.inner
    }

    /// Writes a FASTA record.
    ///
    /// Sequence lines are hard wrapped at 80 bases.
    ///
    /// # Examples
    ///
    /// ```
    /// # use std::io;
    /// use noodles_fasta::{self as fasta, record::{Definition, Sequence}};
    ///
    /// let mut writer = fasta::Writer::new(Vec::new());
    ///
    /// let definition = Definition::new("sq0", None);
    /// let sequence = Sequence::from(b"ACGT".to_vec());
    /// let record = fasta::Record::new(definition, sequence);
    ///
    /// writer.write_record(&record)?;
    ///
    /// assert_eq!(writer.get_ref(), b">sq0\nACGT\n");
    /// # Ok::<(), io::Error>(())
    /// ```
    pub fn write_record(&mut self, record: &Record) -> io::Result<()> {
        writeln!(self.inner, "{}", record.definition())?;
        write_record_sequence(&mut self.inner, record.sequence(), LINE_BASES as usize)?;
        Ok(())
    }
}

fn write_record_sequence<W>(
    writer: &mut W,
    sequence: &Sequence,
    line_bases: usize,
) -> io::Result<()>
where
    W: Write,
{
    let mut start = 0;
    let raw_sequence = sequence.as_ref();

    while start < sequence.len() {
        let end = cmp::min(start + line_bases, sequence.len());
        let line = &raw_sequence[start..end];

        writer.write_all(line)?;
        writeln!(writer)?;

        start = end;
    }

    Ok(())
}

#[cfg(test)]
mod tests {
    use super::*;

    #[test]
    fn test_write_record_sequence() -> io::Result<()> {
        let mut writer = Vec::new();
        let sequence = Sequence::from(b"AC".to_vec());
        write_record_sequence(&mut writer, &sequence, 4)?;
        assert_eq!(writer, b"AC\n");

        writer.clear();
        let sequence = Sequence::from(b"ACGT".to_vec());
        write_record_sequence(&mut writer, &sequence, 4)?;
        assert_eq!(writer, b"ACGT\n");

        writer.clear();
        let sequence = Sequence::from(b"ACGTACGT".to_vec());
        write_record_sequence(&mut writer, &sequence, 4)?;
        assert_eq!(writer, b"ACGT\nACGT\n");

        writer.clear();
        let sequence = Sequence::from(b"ACGTACGTAC".to_vec());
        write_record_sequence(&mut writer, &sequence, 4)?;
        assert_eq!(writer, b"ACGT\nACGT\nAC\n");

        Ok(())
    }
}