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BLCFile | 35 | 81 | 34 |
1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
7 | * Jalview is free software: you can redistribute it and/or | |
8 | * modify it under the terms of the GNU General Public License | |
9 | * as published by the Free Software Foundation, either version 3 | |
10 | * of the License, or (at your option) any later version. | |
11 | * | |
12 | * Jalview is distributed in the hope that it will be useful, but | |
13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
15 | * PURPOSE. See the GNU General Public License for more details. | |
16 | * | |
17 | * You should have received a copy of the GNU General Public License | |
18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
20 | */ | |
21 | package jalview.io; | |
22 | ||
23 | import jalview.datamodel.Sequence; | |
24 | import jalview.datamodel.SequenceI; | |
25 | ||
26 | import java.io.IOException; | |
27 | import java.util.Vector; | |
28 | ||
29 | /** | |
30 | * DOCUMENT ME! | |
31 | * | |
32 | * @author $author$ | |
33 | * @version $Revision$ | |
34 | */ | |
35 | public class BLCFile extends AlignFile | |
36 | { | |
37 | Vector titles; | |
38 | ||
39 | /** | |
40 | * Creates a new BLCFile object. | |
41 | */ | |
42 | 6 | public BLCFile() |
43 | { | |
44 | } | |
45 | ||
46 | /** | |
47 | * Creates a new BLCFile object. | |
48 | * | |
49 | * @param inFile | |
50 | * DOCUMENT ME! | |
51 | * @param sourceType | |
52 | * DOCUMENT ME! | |
53 | * | |
54 | * @throws IOException | |
55 | * DOCUMENT ME! | |
56 | */ | |
57 | 0 | public BLCFile(String inFile, DataSourceType sourceType) |
58 | throws IOException | |
59 | { | |
60 | 0 | super(inFile, sourceType); |
61 | } | |
62 | ||
63 | 1 | public BLCFile(FileParse source) throws IOException |
64 | { | |
65 | 1 | super(source); |
66 | } | |
67 | ||
68 | /** | |
69 | * DOCUMENT ME! | |
70 | */ | |
71 | 7 | @Override |
72 | public void initData() | |
73 | { | |
74 | 7 | super.initData(); |
75 | 7 | titles = new Vector(); |
76 | } | |
77 | ||
78 | /** | |
79 | * Control the number of block iterations to skip before returning. set to 0 | |
80 | * to read first block file entry only set to -1 to read last block file entry | |
81 | * only set to greater than zero to skip at most that many entries before | |
82 | * parsing | |
83 | */ | |
84 | int iterationSkips = 0; | |
85 | ||
86 | /** | |
87 | * The iteration number for the alignment actually parsed from the blc file | |
88 | */ | |
89 | int iterationCount = 0; | |
90 | ||
91 | /** | |
92 | * DOCUMENT ME! | |
93 | */ | |
94 | 1 | @Override |
95 | public void parse() throws IOException | |
96 | { | |
97 | 1 | StringBuffer headerLines = new StringBuffer(); |
98 | 1 | int numHeaderLines = 0; // number of lines appended. |
99 | 1 | StringBuffer[] seqstrings = null; |
100 | 1 | if (suffix != null) |
101 | { | |
102 | 0 | try |
103 | { | |
104 | 0 | iterationSkips = Integer.parseInt(suffix); |
105 | } catch (NumberFormatException e) | |
106 | { | |
107 | 0 | iterationSkips = 0; // first |
108 | } | |
109 | } | |
110 | ||
111 | 1 | String line = null; |
112 | ||
113 | 1 | do |
114 | { | |
115 | 1 | boolean idsFound = false; |
116 | 1 | boolean newids = false; |
117 | // search for ID header. | |
118 | 1 | do |
119 | { | |
120 | 16 | line = nextLine(); |
121 | 16 | if (line == null) |
122 | { | |
123 | 0 | break; |
124 | } | |
125 | // seek end of ids | |
126 | 16 | if (line.indexOf("*") > -1) |
127 | { | |
128 | 1 | idsFound = true; |
129 | ||
130 | 1 | break; |
131 | } | |
132 | ||
133 | 15 | int abracket = line.indexOf(">"); |
134 | ||
135 | 15 | if (abracket > -1) |
136 | { | |
137 | ||
138 | 15 | if (iterationCount > 0 && !newids) |
139 | { | |
140 | // we have a new set of IDs to record. | |
141 | 0 | newids = true; |
142 | 0 | seqs.removeAllElements(); |
143 | } | |
144 | ||
145 | 15 | line = line.substring(abracket + 1); |
146 | ||
147 | 15 | Sequence seq = parseId(line); |
148 | 15 | seqs.addElement(seq); |
149 | } | |
150 | else | |
151 | { | |
152 | // header lines - keep them for the alignment comments. | |
153 | 0 | headerLines.append(line); |
154 | 0 | headerLines.append(newline); |
155 | 0 | numHeaderLines++; |
156 | } | |
157 | 15 | } while (!idsFound); |
158 | 1 | if (line == null) |
159 | { | |
160 | 0 | break; // end of file. |
161 | } | |
162 | 1 | int starCol = line.indexOf("*"); |
163 | 1 | seqstrings = new StringBuffer[seqs.size()]; |
164 | ||
165 | 16 | for (int i = 0; i < seqs.size(); i++) |
166 | { | |
167 | 15 | if (seqstrings[i] == null) |
168 | { | |
169 | 15 | seqstrings[i] = new StringBuffer(); |
170 | } | |
171 | } | |
172 | ||
173 | 1 | try |
174 | { | |
175 | 1 | line = nextLine(); |
176 | 158 | while (line != null && line.indexOf("*") == -1) |
177 | { | |
178 | 2512 | for (int i = 0; i < seqs.size(); i++) |
179 | { | |
180 | 2355 | if (line.length() > (i + starCol)) |
181 | { | |
182 | 2355 | seqstrings[i].append(line.charAt(i + starCol)); |
183 | } | |
184 | } | |
185 | 157 | line = nextLine(); |
186 | } | |
187 | } catch (IOException e) | |
188 | { | |
189 | 0 | if (iterationCount == 0) |
190 | { | |
191 | 0 | throw (e); // otherwise we've just run out of iterations. |
192 | } | |
193 | else | |
194 | { | |
195 | 0 | iterationSkips = 0; |
196 | } | |
197 | } | |
198 | 1 | iterationCount++; |
199 | 1 | } while (--iterationSkips != -1); |
200 | ||
201 | 16 | for (int i = 0; i < seqs.size(); i++) |
202 | { | |
203 | 15 | Sequence newSeq = (Sequence) seqs.elementAt(i); |
204 | ||
205 | 15 | newSeq.setSequence(seqstrings[i].toString()); |
206 | } | |
207 | 1 | if (seqs.size() > 0) |
208 | { | |
209 | 1 | if (headerLines.length() > 1 + numHeaderLines) |
210 | { | |
211 | // just whitespace or not. | |
212 | 0 | setAlignmentProperty("Comments", headerLines.toString()); |
213 | } | |
214 | 1 | setAlignmentProperty("iteration", "" + iterationCount); |
215 | } | |
216 | } | |
217 | ||
218 | /** | |
219 | * DOCUMENT ME! | |
220 | * | |
221 | * @param s | |
222 | * DOCUMENT ME! | |
223 | * | |
224 | * @return DOCUMENT ME! | |
225 | */ | |
226 | 6 | @Override |
227 | public String print(SequenceI[] s, boolean jvsuffix) | |
228 | { | |
229 | 6 | StringBuffer out = new StringBuffer(); |
230 | /** | |
231 | * A general parser for ids. Will look for dbrefs in Uniprot format | |
232 | * source|id And also Jalview /start-end | |
233 | * | |
234 | * @String id Id to be parsed | |
235 | */ | |
236 | 6 | int i = 0; |
237 | 6 | int max = -1; |
238 | ||
239 | 96 | while ((i < s.length) && (s[i] != null)) |
240 | { | |
241 | 90 | out.append(">" + printId(s[i], jvsuffix)); |
242 | 90 | if (s[i].getDescription() != null) |
243 | { | |
244 | 90 | out.append(" " + s[i].getDescription()); |
245 | } | |
246 | ||
247 | 90 | out.append(newline); |
248 | ||
249 | 90 | max = Math.max(max, s[i].getLength()); |
250 | ||
251 | 90 | i++; |
252 | } | |
253 | ||
254 | 6 | out.append("* iteration 1"); |
255 | 6 | out.append(newline); |
256 | ||
257 | 948 | for (int j = 0; j < max; j++) |
258 | { | |
259 | 942 | i = 0; |
260 | ||
261 | 15072 | while ((i < s.length) && (s[i] != null)) |
262 | { | |
263 | 14130 | if (s[i].getSequence().length > j) |
264 | { | |
265 | 14130 | out.append(s[i].getSequenceAsString(j, j + 1)); |
266 | } | |
267 | else | |
268 | { | |
269 | 0 | out.append("-"); |
270 | } | |
271 | ||
272 | 14130 | i++; |
273 | } | |
274 | ||
275 | 942 | out.append(newline); |
276 | } | |
277 | ||
278 | 6 | out.append("*"); |
279 | 6 | out.append(newline); |
280 | ||
281 | 6 | return out.toString(); |
282 | } | |
283 | } |