-
Notifications
You must be signed in to change notification settings - Fork 0
/
alignment1.js
202 lines (182 loc) · 5.92 KB
/
alignment1.js
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
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
//seq-id alignment-start alignment-end
const alignment = [
['evm.model.1.10740', 632, 681, 'PTCB-BRCT'],
['evm.model.1.10808', 265, 338, 'BRCT_2'],
['evm.model.1.3990', 47, 108, 'BRCT'],
['evm.model.1.7034', 150, 224, 'BRCT'],
['evm.model.2.613', 109, 180, 'BRCT'],
['evm.model.2.613', 917, 981, 'BRCT'],
['evm.model.3.1134', 595, 704, 'BRCT_2'],
['evm.model.3.1134', 485, 560, 'BRCT'],
['evm.model.3.1204', 413, 482, 'BRCT'],
['evm.model.3.1486', 7, 66, 'BRCT'],
['evm.model.3.1486', 104, 181, 'BRCT'],
['evm.model.3.1541', 358, 419, 'BRCT'],
['evm.model.3.1648', 564, 641, 'BRCT'],
['evm.model.3.1840', 358, 419, 'PTCB-BRCT'],
['evm.model.3.2233', 667, 728, 'PTCB-BRCT'],
['evm.model.3.2233', 563, 646, 'BTCT_2'],
['evm.model.3.2233', 103, 172, 'BRCT'],
['evm.model.4.1000', 319, 389, 'BRCT'],
['evm.model.4.27', 78, 139, 'PTCB-BRCT'],
['evm.model.4.282', 78, 139, 'PTCB-BRCT'],
['evm.model.4.372', 661, 706, 'PTCB-BRCT'],
['evm.model.4.4602', 279, 350, 'BRCT'],
// ['evm.model.6.575', 541, 667, 'BRCA-2_OB1'],
// ['evm.model.6.575', 463, 537, 'BRCA-2_helical'],
// ['evm.model.6.575', 92, 119, 'BRCA2'],
// ['evm.model.6.575', 197, 224, 'BRCA2'],
['evm.model.8.2802', 968, 1064, 'BRCT_3'],
['evm.model.8.777', 9, 71, 'BRCT'],
// ['evm.model.8.806', 9, 71, 'BRCT'],
]
const names= {
'evm.model.1.10740':'BRCT3',
'evm.model.1.10808':'BRCT4',
'evm.model.1.3990':'BRCT1',
'evm.model.1.7034':'BRCT2',
'evm.model.2.613':'BRCT5',
'evm.model.3.1134':'BRCT6',
'evm.model.3.1204':'BRCT7',
'evm.model.3.1486':'BRCT8',
'evm.model.3.1541':'BRCT9',
'evm.model.3.1648':'BRCT10',
'evm.model.3.1840':'BRCT11',
'evm.model.3.2233':'BRCT12',
'evm.model.4.1000':'BRCT17',
'evm.model.4.27':'BRCT13',
'evm.model.4.282':'BRCT15',
'evm.model.4.372':'BRCT16',
'evm.model.4.4602':'BRCT18',
'evm.model.4.72':'BRCT14',
'evm.model.6.575':'BRCT19',
'evm.model.8.2802':'BRCT21',
'evm.model.8.777':'BRCT20'
}
function brctNames(alignment) {
let namesWithNum = [];
let i = 1;
alignment.map((item, index) => {
let key = item[0]
let suffix = ''
if(index<alignment.length-1 && key=== alignment[index+1][0]
|| index>2 && key=== alignment[index-1][0]){
suffix = "_" + (i++)
}
if(index<alignment.length-1 && key !== alignment[index+1][0]){
i = 1;
}
// debugger
namesWithNum.push( names[key] + suffix)
})
return namesWithNum;
}
//output 'key', 'start', 'end', 'before', 'brct', 'after','name'
// where name is hmm-name, key is protein sequence id
// brct is BRCT domain
function calcTableData(alignment, brct, cutLength) {
let data = [];
let i = 1;
alignment.map((item, index) => {
let key = item[0]
let start = item[1]
let end = item[2]
let name = item[3]
let value = brct[key]
if (!value) return
let v = value.replaceAll('\n', '').replaceAll('\r', '')
let brctCut = v.substr(start, end - start)
let before = v.substr(start - cutLength, cutLength)
let after = v.substr(end, cutLength)
let suffix = ''
if(index<alignment.length-1 && key=== alignment[index+1][0]
|| index>2 && key=== alignment[index-1][0]){
suffix = "_" + (i++)
}
if(index<alignment.length-1 && key !== alignment[index+1][0]){
i = 1;
}
data.push({ No: index+1, key: names[key] + suffix, start, end, before, 'brct': brctCut, after, name })
})
return data;
}
/**
* 链接：https://leetcode-cn.com/problems/longest-common-subsequence/solution/js-dian-xing-de-dong-tai-gui-hua-by-hblvsjtu/
* @param {string} text1
* @param {string} text2
* @return {string} // {number}
*/
var longestCommonSubsequence = function (text1, text2) {
const dp = [];
for (let i = 0; i <= text1.length; i++) {
dp[i] = [];
for (let j = 0; j <= text2.length; j++) {
if (!i || !j) dp[i][j] = 0;
else if (text1[i - 1] === text2[j - 1]) {
dp[i][j] = dp[i - 1][j - 1] + 1;
}
else {
dp[i][j] = Math.max(dp[i - 1][j], dp[i][j - 1]);
}
}
}
let i = text1.length
let j = text2.length
let res = ''
while (i > 0 && j > 0) {
if (dp[i][j] == dp[i - 1][j]) {
i--
} else if (dp[i][j] == dp[i][j - 1]) {
j--
} else if (dp[i][j] > dp[i - 1][j - 1]) {
res = text2.charAt(j - 1) + res
i--
j--
}
}
return res;
};
function createArray(m, n) {
return Array(m).fill([]).map(() => Array(n).fill(0))
}
function longest_substring(s1, s2) {
let t = createArray(s1.length + 1, s2.length + 1)
let l = 0, xl = 0
for (let x = 1; x < 1 + s1.length; x++) {
for (let y = 1; y < 1 + s2.length; y++) {
if (s1.charAt(x - 1) == s2.charAt(y - 1)) {
t[x][y] = t[x - 1][y - 1] + 1
if (t[x][y] > l) {
l = t[x][y]
xl = x
}
}
else
t[x][y] = 0
}
}
return s1.substr(xl - l, l)
}
/**
* v minV~maxV
*/
const scale = (num, in_min, in_max, out_min, out_max) => {
return Math.round((num - in_min) * (out_max - out_min) / (in_max - in_min) + out_min);
}
function mapColor(v, minV, maxV) {
let cmin = [0x01,0x74,0x2f] //[198, 255, 221]
let cmid = [251, 215, 134]
let cmax = [247, 121, 125]
let midV = (minV + maxV) / 2;
let res = []
if (v > midV) {
res = [scale(v, midV, maxV, cmid[0], cmax[0]),
scale(v, midV, maxV, cmid[1], cmax[1]),
scale(v, midV, maxV, cmid[2], cmax[2])]
} else {
res = [scale(v, minV, midV, cmin[0], cmid[0]),
scale(v, minV, midV, cmin[1], cmid[1]),
scale(v, minV, midV, cmin[2], cmid[2])]
}
return res
}