tskit 0.16.0

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
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

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

use super::newtypes::MigrationId;
use super::newtypes::NodeId;
use super::newtypes::PopulationId;
use super::newtypes::Position;
use super::newtypes::Time;

use super::bindings::tsk_id_t;
use super::bindings::tsk_migration_table_add_row;
use super::bindings::tsk_migration_table_clear;
use super::bindings::tsk_migration_table_init;
use super::bindings::tsk_migration_table_t;
use super::tskbox::TskBox;
use super::TskitError;

#[derive(Debug)]
pub struct MigrationTable(TskBox<tsk_migration_table_t>);

pub struct MigrationTableIter<'table> {
    table: &'table MigrationTable,
    current_row: MigrationId,
}

impl<'table> Iterator for MigrationTableIter<'table> {
    type Item = super::Migration<'table>;

    fn next(&mut self) -> Option<Self::Item> {
        let c = self.current_row;
        self.current_row += 1;
        self.table.row(c)
    }
}

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

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

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

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

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

    pub fn add_row(
        &mut self,
        span: (f64, f64),
        node: tsk_id_t,
        source: tsk_id_t,
        dest: tsk_id_t,
        time: f64,
    ) -> Result<tsk_id_t, TskitError> {
        self.add_row_with_metadata(span, node, source, dest, time, &[])
    }

    pub fn add_row_with_metadata(
        &mut self,
        span: (f64, f64),
        node: tsk_id_t,
        source: tsk_id_t,
        dest: tsk_id_t,
        time: f64,
        metadata: &[u8],
    ) -> Result<tsk_id_t, TskitError> {
        unsafe {
            Ok(tsk_migration_table_add_row(
                self.as_mut(),
                span.0,
                span.1,
                node,
                source,
                dest,
                time,
                metadata.as_ptr().cast::<c_char>(),
                metadata.len() as u64,
            ))
        }
    }

    pub fn node(&self, row: MigrationId) -> Option<NodeId> {
        safe_tsk_column_access!(self, row, NodeId, node)
    }

    pub fn source(&self, row: MigrationId) -> Option<PopulationId> {
        safe_tsk_column_access!(self, row, PopulationId, source)
    }

    pub fn dest(&self, row: MigrationId) -> Option<PopulationId> {
        safe_tsk_column_access!(self, row, PopulationId, dest)
    }

    pub fn time(&self, row: MigrationId) -> Option<Time> {
        safe_tsk_column_access!(self, row, Time, time)
    }

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

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

    raw_metadata_getter_for_tables!(MigrationId);

    pub fn row<'table>(&self, row: MigrationId) -> Option<super::Migration<'table>> {
        let mut migration = unsafe {
            std::mem::MaybeUninit::<super::bindings::tsk_migration_t>::zeroed().assume_init()
        };
        let rv = unsafe {
            super::bindings::tsk_migration_table_get_row(
                self.as_ref(),
                row.into(),
                &mut migration as *mut super::bindings::tsk_migration_t,
            )
        };
        if rv == 0 {
            Some(super::Migration {
                row: migration,
                marker: std::marker::PhantomData,
            })
        } else {
            None
        }
    }

    pub fn iter(&self) -> impl Iterator<Item = super::Migration<'_>> {
        MigrationTableIter {
            table: self,
            current_row: 0.into(),
        }
    }
}

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