-
Notifications
You must be signed in to change notification settings - Fork 379
/
MafChunk.java
121 lines (104 loc) · 3.93 KB
/
MafChunk.java
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
/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.maf;
import java.util.*;
/**
* @author jrobinso
* Date: 2/19/13
* Time: 1:09 AM
*/
public class MafChunk {
String chr;
int start;
int end;
LinkedHashMap<String, MultipleAlignmentBlock> blocks;
public MafChunk(String chr, int start, int end, List<MultipleAlignmentBlock> blockList) {
this.chr = chr;
this.start = start;
this.end = end;
this.blocks = new LinkedHashMap<String, MultipleAlignmentBlock>();
for (MultipleAlignmentBlock b : blockList) {
blocks.put(b.getKey(), b);
}
}
public boolean overlaps(String chr, int start, int end) {
if(!chr.equals(this.chr)) return false;
return end >= this.start && start <= this.end;
}
public boolean contains(String chr, int start, int end) {
if(!chr.equals(this.chr)) return false;
return start >= this.start && end <= this.end;
}
public void addBlocks(int start, int end, List<MultipleAlignmentBlock> blockList) {
// Can only add blocks if interval is contiguous with current extent. Otherwise start over.
if (start > this.end || end < this.start) {
blocks.clear();
for (MultipleAlignmentBlock b : blockList) {
blocks.put(b.getKey(), b);
}
} else if (start < this.start) {
// Add to left
LinkedHashMap<String, MultipleAlignmentBlock> tmp = this.blocks;
this.blocks = new LinkedHashMap<String, MultipleAlignmentBlock>();
for (MultipleAlignmentBlock b : blockList) {
String key = b.getKey();
if(blocks.containsKey(key)) {
// Done
break;
}
blocks.put(key, b);
}
this.blocks.putAll(tmp);
this.start = start;
} else {
// Add to right
for (MultipleAlignmentBlock b : blockList) {
String key = b.getKey();
if(blocks.containsKey(key)) {
continue;
}
blocks.put(b.getKey(), b);
}
this.end = end;
}
}
public void trimTo(int start, int end) {
LinkedHashMap<String, MultipleAlignmentBlock> tmp = blocks;
blocks = new LinkedHashMap<String, MultipleAlignmentBlock>();
for(Map.Entry<String, MultipleAlignmentBlock> entry : tmp.entrySet()) {
String key = entry.getKey();
MultipleAlignmentBlock block = entry.getValue();
if(block.getEnd() < start) {
continue;
}
else if(block.getStart() > end) {
break;
}
else {
blocks.put(key, block);
}
}
}
}