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
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
|
package hmm;
import shared.Parse;
import shared.Tools;
import structures.ByteBuilder;
public class HMMSearchLine {
public HMMSearchLine(byte[] line_){
line=line_;
Tools.FORCE_JAVA_PARSE_DOUBLE=true; //TODO: put this somewhere else
int a=0, b=0;
// System.err.println("1: a="+a+", b="+b);
//These are for parsing multi-space-delimited lines
while(b<line.length && line[b]!=' '){b++;}
// System.err.println("2: a="+a+", b="+b);
assert(b>a) : "Missing field 0: "+new String(line);
name=new String(line, a, b-a);
while(b<line.length && line[b]==' '){b++;}
a=b;
// System.err.println("3: a="+a+", b="+b);
while(b<line.length && line[b]!=' '){b++;}
// System.err.println("4: a="+a+", b="+b);
assert(b>a) : "Missing field 1: "+new String(line);
field1=new String(line, a, b-a);
while(b<line.length && line[b]==' '){b++;}
a=b;
// System.err.println("5: a="+a+", b="+b);
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 2: "+new String(line);
length=Parse.parseInt(line, a, b);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 3: "+new String(line);
hmmName=new String(line, a, b-a);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 4: "+new String(line);
accession=new String(line, a, b-a);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 5: "+new String(line);
field5=Parse.parseInt(line, a, b);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 6: "+new String(line);
field6=Parse.parseDouble(line, a, b);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 7: "+new String(line);
field7=Parse.parseFloat(line, a, b);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 8: "+new String(line);
field8=Parse.parseFloat(line, a, b);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 9: "+new String(line);
field9=Parse.parseFloat(line, a, b);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 10: "+new String(line);
field10=Parse.parseFloat(line, a, b);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 11: "+new String(line);
field11=Parse.parseDouble(line, a, b);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 12: "+new String(line);
field12=Parse.parseDouble(line, a, b);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 13: "+new String(line);
field13=Parse.parseFloat(line, a, b);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 14: "+new String(line);
field14=Parse.parseFloat(line, a, b);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 15: "+new String(line);
field15=Parse.parseInt(line, a, b);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 16: "+new String(line);
field16=Parse.parseInt(line, a, b);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 17: "+new String(line);
field17=Parse.parseInt(line, a, b);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 18: "+new String(line);
field18=Parse.parseInt(line, a, b);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 19: "+new String(line);
field19=Parse.parseInt(line, a, b);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 20: "+new String(line);
field20=Parse.parseInt(line, a, b);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 21: "+new String(line);
field21=Parse.parseFloat(line, a, b);
while(b<line.length && line[b]==' '){b++;}
a=b;
while(b<line.length && line[b]!=' '){b++;}
assert(b>a) : "Missing field 22: "+new String(line);
field22=new String(line, a, b-a);
while(b<line.length && line[b]==' '){b++;}
a=b;
}
public ByteBuilder toText(){
ByteBuilder bb=new ByteBuilder();
bb.append(name).tab();
bb.append(length).tab();
bb.append(hmmName);
return bb;
}
public String toString(){
return toText().toString();
}
public final byte[] line;
//protein_1 - 257 ATP-synt_A PF00119.18 211
//1.9e-49 159.6 27.5
//1 1 7.3e-51 2.5e-49 159.2 27.5
//3 210 41 250 38 251 0.87 -
//field0 - protein_1
String name;
//field1 - -
String field1;
//field2 - 257
int length; //length?
//field3 - ATP-synt_A
String hmmName;
//field4 - PF00119.18
String accession;
//field5 - 211
int field5;
//field6 - 1.9e-49
double field6;
//field7 - 159.6
float field7;
//field8 - 27.5
float field8;
//field9 - 1
float field9;
//field10 - 1
float field10;
//field11 - 7.3e-51
double field11;
//field12 - 2.5e-49
double field12;
//field13 - 159.2
float field13;
//field14 - 27.5
float field14;
//field15 - 3
int field15;
//field16 - 210
int field16;
//field17 - 41
int field17;
//field18 - 250
int field18;
//field19 - 38
int field19;
//field20 - 251
int field20;
//field21 - 0.87
float field21;
//field22 - -
String field22;
}
|
