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
|
/*
* Copyright (C) 2014-2021 Brian L. Browning
*
* This file is part of Beagle
*
* Beagle is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Beagle is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package vcf;
import java.io.Closeable;
import java.util.Optional;
import java.util.concurrent.BlockingQueue;
import main.Pedigree;
/**
* <p>Interface {@code SlidingWindow} represents a sliding window of VCF
* records.</p>
*
* <p>Instances of class {@code SlidingWindow} are not thread-safe.</p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public interface SlidingWindow extends Closeable {
/**
* Returns the target samples.
* @return the target samples
*/
Samples targSamples();
/**
* Returns the target sample pedigree data.
* @return the target sample pedigree data
*/
Pedigree ped();
/**
* Returns the genetic map.
* @return the genetic map
*/
GeneticMap genMap();
/**
* Returns the number of distinct target markers returned in
* preceding {@code this.nextWindow()} method calls.
* @return the number of distinct target markers returned in
* preceding {@code this.nextWindow()} method calls
*/
int cumTargMarkers();
/**
* Returns the number of distinct markers returned in
* preceding {@code this.nextWindow()} method calls.
* @return the number of distinct markers returned in
* preceding {@code this.nextWindow()} method calls
*/
int cumMarkers();
/**
* Returns the next sliding window of VCF records.
*
* @return the next sliding window of VCF records or
* <code>Optional.empty()</code> if there are no additional windows.
*
* @throws IllegalArgumentException if a format error in the input data
* is detected
*/
public Optional<Window> nextWindow();
/**
* Releases any I/O resources controlled by this object.
*/
@Override
void close();
/**
* Takes and returns an element from the specified queue.
* @param <E> the element type
* @param q the queue
* @return an element from the specified queue
* @throws NullPointerException if {@code q == null}
* @throws RuntimeException if an {@code InterruptedException} is
* thrown while waiting to take an element
*/
public static <E> E takeFromQ(BlockingQueue<E> q) {
E e = null;
try {
e = q.take();
} catch (InterruptedException ex) {
throw new RuntimeException(ex);
}
return e;
}
/**
* Adds the specified element to the specified queue.
* @param <E> the element type
* @param q the queue
* @param e the element to be added
* @throws NullPointerException if {@code q == null}
* @throws RuntimeException if an {@code InterruptedException} is
* thrown while waiting to add the element
*/
public static <E> void addToQ(BlockingQueue<E> q, E e) {
try {
q.put(e);
} catch (InterruptedException ex) {
throw new RuntimeException(ex);
}
}
}
|
