tskit 0.15.0

rust interface to tskit
Documentation 
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

use std::ffi::c_char;
use std::ptr::NonNull;

use super::bindings::tsk_size_t;
use super::newtypes::Position;
use super::newtypes::SiteId;

use super::bindings::tsk_id_t;
use super::bindings::tsk_site_table_add_row;
use super::bindings::tsk_site_table_clear;
use super::bindings::tsk_site_table_init;
use super::bindings::tsk_site_table_t;
use super::tskbox::TskBox;
use super::TskitError;

#[derive(Debug)]
pub struct SiteTable(TskBox<tsk_site_table_t>);

impl SiteTable {
    pub fn new(options: u32) -> Result<Self, TskitError> {
        let tsk =
            TskBox::new(|e: *mut tsk_site_table_t| unsafe { tsk_site_table_init(e, options) })?;
        Ok(Self(tsk))
    }

    pub unsafe fn new_borrowed(ptr: NonNull<tsk_site_table_t>) -> Self {
        let tsk = TskBox::new_init_from_ptr(ptr);
        Self(tsk)
    }

    pub fn as_ref(&self) -> &tsk_site_table_t {
        self.0.as_ref()
    }

    pub fn as_mut(&mut self) -> &mut tsk_site_table_t {
        self.0.as_mut()
    }

    pub fn clear(&mut self) -> i32 {
        unsafe { tsk_site_table_clear(self.as_mut()) }
    }

    pub fn add_row(
        &mut self,
        position: f64,
        ancestral_state: Option<&[u8]>,
    ) -> Result<tsk_id_t, TskitError> {
        self.add_row_with_metadata(position, ancestral_state, &[])
    }

    pub fn add_row_with_metadata(
        &mut self,
        position: f64,
        ancestral_state: Option<&[u8]>,
        metadata: &[u8],
    ) -> Result<tsk_id_t, TskitError> {
        unsafe {
            Ok(tsk_site_table_add_row(
                self.as_mut(),
                position,
                match ancestral_state {
                    Some(d) => d.as_ptr() as *const c_char,
                    None => std::ptr::null(),
                },
                match ancestral_state {
                    Some(d) => d.len() as u64,
                    None => 0,
                },
                metadata.as_ptr().cast::<c_char>(),
                metadata.len() as u64,
            ))
        }
    }

    pub fn position(&self, row: SiteId) -> Option<Position> {
        safe_tsk_column_access!(self, row, Position, position)
    }

    raw_metadata_getter_for_tables!(SiteId);

    fn ancestral_state_column(&self) -> &[u8] {
        unsafe {
            std::slice::from_raw_parts(
                self.as_ref().ancestral_state.cast::<u8>(),
                self.as_ref().ancestral_state_length as usize,
            )
        }
    }

    fn ancestral_state_offset_raw(&self) -> &[tsk_size_t] {
        unsafe {
            std::slice::from_raw_parts(
                self.as_ref().ancestral_state_offset,
                self.as_ref().num_rows as usize,
            )
        }
    }

    pub fn ancestral_state(&self, row: SiteId) -> Option<&[u8]> {
        super::tsk_ragged_column_access(
            row,
            self.ancestral_state_column(),
            self.ancestral_state_offset_raw(),
        )
    }
}

impl Default for SiteTable {
    fn default() -> Self {
        Self::new(0).unwrap()
    }
}