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PfamFile | 32 | 61 | 25 |
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 | import jalview.util.Format; | |
26 | import jalview.util.MessageManager; | |
27 | ||
28 | import java.io.IOException; | |
29 | import java.util.ArrayList; | |
30 | import java.util.HashMap; | |
31 | ||
32 | public class PfamFile extends AlignFile | |
33 | { | |
34 | ||
35 | 3 | public PfamFile() |
36 | { | |
37 | } | |
38 | ||
39 | 0 | public PfamFile(String inFile, DataSourceType sourceType) |
40 | throws IOException | |
41 | { | |
42 | 0 | super(inFile, sourceType); |
43 | } | |
44 | ||
45 | 11 | public PfamFile(FileParse source) throws IOException |
46 | { | |
47 | 11 | super(source); |
48 | } | |
49 | ||
50 | 14 | @Override |
51 | public void initData() | |
52 | { | |
53 | 14 | super.initData(); |
54 | } | |
55 | ||
56 | 11 | @Override |
57 | public void parse() throws IOException | |
58 | { | |
59 | 11 | int i = 0; |
60 | 11 | String line; |
61 | ||
62 | 11 | HashMap<String, StringBuffer> seqhash = new HashMap<String, StringBuffer>(); |
63 | 11 | ArrayList<String> headers = new ArrayList<String>(); |
64 | 11 | boolean useTabs = false; |
65 | 11 | int spces; |
66 | ? | while ((line = nextLine()) != null) |
67 | { | |
68 | 43 | if (line.indexOf("#") == 0) |
69 | { | |
70 | // skip comment lines | |
71 | 0 | continue; |
72 | } | |
73 | // locate first space or (if already checked), tab | |
74 | 43 | if (useTabs) |
75 | { | |
76 | 0 | spces = line.indexOf("\t"); |
77 | } | |
78 | else | |
79 | { | |
80 | 43 | spces = line.indexOf(" "); |
81 | // check to see if we ought to split on tabs instead. | |
82 | 43 | if (!useTabs && spces == -1) |
83 | { | |
84 | 4 | useTabs = true; |
85 | 4 | spces = line.indexOf("\t"); |
86 | } | |
87 | } | |
88 | 43 | if (spces <= 0) |
89 | { | |
90 | // no sequence data to split on | |
91 | 1 | continue; |
92 | } | |
93 | 42 | String id = line.substring(0, spces); |
94 | 42 | StringBuffer tempseq; |
95 | ||
96 | 42 | if (seqhash.containsKey(id)) |
97 | { | |
98 | 0 | tempseq = seqhash.get(id); |
99 | } | |
100 | else | |
101 | { | |
102 | 42 | tempseq = new StringBuffer(); |
103 | 42 | seqhash.put(id, tempseq); |
104 | } | |
105 | ||
106 | 42 | if (!(headers.contains(id))) |
107 | { | |
108 | 42 | headers.add(id); |
109 | } | |
110 | 42 | if (spces + 1 < line.length()) |
111 | { | |
112 | 42 | tempseq.append(line.substring(spces + 1).trim()); |
113 | } | |
114 | } | |
115 | ||
116 | 11 | this.noSeqs = headers.size(); |
117 | ||
118 | 11 | if (noSeqs < 1) |
119 | { | |
120 | 0 | throw new IOException(MessageManager |
121 | .getString("exception.pfam_no_sequences_found")); | |
122 | } | |
123 | ||
124 | 53 | for (i = 0; i < headers.size(); i++) |
125 | { | |
126 | 42 | if (seqhash.get(headers.get(i)) != null) |
127 | { | |
128 | 42 | if (maxLength < seqhash.get(headers.get(i)).toString().length()) |
129 | { | |
130 | 11 | maxLength = seqhash.get(headers.get(i)).toString().length(); |
131 | } | |
132 | ||
133 | 42 | Sequence newSeq = parseId(headers.get(i).toString()); |
134 | 42 | newSeq.setSequence( |
135 | seqhash.get(headers.get(i).toString()).toString()); | |
136 | 42 | seqs.addElement(newSeq); |
137 | } | |
138 | else | |
139 | { | |
140 | 0 | jalview.bin.Console |
141 | .errPrintln("PFAM File reader: Can't find sequence for " | |
142 | + headers.get(i)); | |
143 | } | |
144 | } | |
145 | } | |
146 | ||
147 | 3 | @Override |
148 | public String print(SequenceI[] s, boolean jvsuffix) | |
149 | { | |
150 | 3 | StringBuffer out = new StringBuffer(""); |
151 | ||
152 | 3 | int max = 0; |
153 | 3 | int maxid = 0; |
154 | ||
155 | 3 | int i = 0; |
156 | ||
157 | 48 | while ((i < s.length) && (s[i] != null)) |
158 | { | |
159 | 45 | String tmp = printId(s[i], jvsuffix); |
160 | ||
161 | 45 | max = Math.max(max, s[i].getLength()); |
162 | ||
163 | 45 | if (tmp.length() > maxid) |
164 | { | |
165 | 11 | maxid = tmp.length(); |
166 | } | |
167 | ||
168 | 45 | i++; |
169 | } | |
170 | ||
171 | 3 | if (maxid < 15) |
172 | { | |
173 | 1 | maxid = 15; |
174 | } | |
175 | ||
176 | 3 | int j = 0; |
177 | ||
178 | 48 | while ((j < s.length) && (s[j] != null)) |
179 | { | |
180 | 45 | out.append(new Format("%-" + maxid + "s") |
181 | .form(printId(s[j], jvsuffix) + " ")); | |
182 | ||
183 | 45 | out.append(s[j].getSequenceAsString()); |
184 | 45 | out.append(newline); |
185 | 45 | j++; |
186 | } | |
187 | ||
188 | 3 | out.append(newline); |
189 | ||
190 | 3 | return out.toString(); |
191 | } | |
192 | } |