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

// Copyright 2024 WHERE TRUE Technologies.
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
//     http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.

use std::sync::Arc;

use arrow::{
    array::{ArrayRef, GenericStringBuilder, Int64Builder},
    datatypes::SchemaRef,
};
use exon_common::ExonArrayBuilder;

use super::bed_record_builder::BEDRecord;

pub struct BEDArrayBuilder {
    reference_sequence_names: GenericStringBuilder<i32>,
    starts: Int64Builder,
    ends: Int64Builder,
    names: GenericStringBuilder<i32>,
    scores: Int64Builder,
    strands: GenericStringBuilder<i32>,
    thick_starts: Int64Builder,
    thick_ends: Int64Builder,
    colors: GenericStringBuilder<i32>,
    block_counts: Int64Builder,
    block_sizes: GenericStringBuilder<i32>,
    block_starts: GenericStringBuilder<i32>,

    projection: Vec<usize>,

    rows: usize,
}

impl BEDArrayBuilder {
    pub fn create(schema: SchemaRef, projection: Option<Vec<usize>>) -> Self {
        let projection = match projection {
            Some(p) => p,
            None => (0..schema.fields().len()).collect(),
        };

        Self {
            reference_sequence_names: GenericStringBuilder::<i32>::new(),
            starts: Int64Builder::new(),
            ends: Int64Builder::new(),
            names: GenericStringBuilder::<i32>::new(),
            scores: Int64Builder::new(),
            strands: GenericStringBuilder::<i32>::new(),
            thick_starts: Int64Builder::new(),
            thick_ends: Int64Builder::new(),
            colors: GenericStringBuilder::<i32>::new(),
            block_counts: Int64Builder::new(),
            block_sizes: GenericStringBuilder::<i32>::new(),
            block_starts: GenericStringBuilder::<i32>::new(),
            projection,
            rows: 0,
        }
    }

    pub fn append(&mut self, record: BEDRecord) -> std::io::Result<()> {
        self.rows += 1;

        for col_idx in self.projection.iter() {
            match col_idx {
                0 => self
                    .reference_sequence_names
                    .append_value(record.reference_sequence_name()),
                1 => self.starts.append_value(record.start() as i64),
                2 => self.ends.append_value(record.end() as i64),
                3 => self.names.append_option(record.name()),
                4 => self.scores.append_option(record.score()),
                5 => self.strands.append_option(record.strand()),
                6 => self
                    .thick_starts
                    .append_option(record.thick_start().map(|x| x as i64)),
                7 => self
                    .thick_ends
                    .append_option(record.thick_end().map(|x| x as i64)),
                8 => self.colors.append_option(record.color()),
                9 => self
                    .block_counts
                    .append_option(record.block_count().map(|x| x as i64)),
                10 => self.block_sizes.append_option(record.block_sizes()),
                11 => self.block_starts.append_option(record.block_starts()),
                _ => panic!("Invalid column index"),
            }
        }

        Ok(())
    }

    pub fn finish(&mut self) -> Vec<ArrayRef> {
        let mut arrays: Vec<ArrayRef> = vec![];

        for col_idx in self.projection.iter() {
            match col_idx {
                0 => arrays.push(Arc::new(self.reference_sequence_names.finish())),
                1 => arrays.push(Arc::new(self.starts.finish())),
                2 => arrays.push(Arc::new(self.ends.finish())),
                3 => arrays.push(Arc::new(self.names.finish())),
                4 => arrays.push(Arc::new(self.scores.finish())),
                5 => arrays.push(Arc::new(self.strands.finish())),
                6 => arrays.push(Arc::new(self.thick_starts.finish())),
                7 => arrays.push(Arc::new(self.thick_ends.finish())),
                8 => arrays.push(Arc::new(self.colors.finish())),
                9 => arrays.push(Arc::new(self.block_counts.finish())),
                10 => arrays.push(Arc::new(self.block_sizes.finish())),
                11 => arrays.push(Arc::new(self.block_starts.finish())),
                _ => panic!("Invalid column index"),
            }
        }

        arrays
    }
}

impl ExonArrayBuilder for BEDArrayBuilder {
    fn finish(&mut self) -> Vec<ArrayRef> {
        self.finish()
    }

    fn len(&self) -> usize {
        self.rows
    }
}