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PContactPredictionFile | 46 | 27 | 12 |
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.ContactMatrix; | |
24 | import jalview.datamodel.SequenceI; | |
25 | ||
26 | import java.io.IOException; | |
27 | import java.util.ArrayList; | |
28 | import java.util.BitSet; | |
29 | import java.util.HashMap; | |
30 | import java.util.List; | |
31 | import java.util.Map; | |
32 | ||
33 | /** | |
34 | * A file parser for contact prediction files. | |
35 | * | |
36 | * An example file is the following | |
37 | * | |
38 | * <pre> | |
39 | * | |
40 | * </pre> | |
41 | * | |
42 | * | |
43 | * @author jim procter | |
44 | * | |
45 | */ | |
46 | public class PContactPredictionFile extends AlignFile | |
47 | { | |
48 | protected static final String CONTACT_PREDICTION = "CONTACT_PREDICTION"; | |
49 | ||
50 | 0 | public PContactPredictionFile(String inFile, |
51 | DataSourceType fileSourceType) throws IOException | |
52 | { | |
53 | 0 | super(inFile, fileSourceType); |
54 | ||
55 | } | |
56 | ||
57 | 0 | public PContactPredictionFile(FileParse source) throws IOException |
58 | { | |
59 | 0 | super(source); |
60 | } | |
61 | ||
62 | Integer fWidth; | |
63 | ||
64 | List<ContactMatrix> models = new ArrayList<ContactMatrix>(); | |
65 | ||
66 | 0 | public List<ContactMatrix> getContactMatrices() |
67 | { | |
68 | 0 | return models; |
69 | } | |
70 | ||
71 | /* | |
72 | * RaptorX pattern: | |
73 | * for a contact prediction | |
74 | * Target sequence | |
75 | * alignment for target sequence | |
76 | * contact matrix for sequence | |
77 | * models generated that fit matrix | |
78 | */ | |
79 | ||
80 | /* | |
81 | * TODO: create annotation rows from contact matrices. | |
82 | * (non-Javadoc) | |
83 | * @see jalview.io.AlignFile#parse() | |
84 | */ | |
85 | 0 | @Override |
86 | public void parse() throws IOException | |
87 | { | |
88 | 0 | String line; |
89 | /* | |
90 | * stash any header lines if we've been given a CASP-RR file | |
91 | */ | |
92 | 0 | Map<String, String> header = new HashMap<String, String>(); |
93 | 0 | ContactMatrix cm = null; |
94 | ||
95 | 0 | while ((line = nextLine()) != null) |
96 | { | |
97 | 0 | int left, right; |
98 | 0 | double strength = Float.NaN; |
99 | 0 | String parts[] = line.split("\\s+"); |
100 | ||
101 | // check for header tokens in parts[0] | |
102 | ||
103 | // others - stash details | |
104 | // MODEL - start a new matrix | |
105 | // skip comments ? | |
106 | ||
107 | 0 | if (parts.length == 3) // and all are integers |
108 | { | |
109 | ||
110 | 0 | if (cm == null) |
111 | { | |
112 | 0 | cm = new ContactMatrix(true) |
113 | { | |
114 | 0 | @Override |
115 | public String getType() | |
116 | { | |
117 | 0 | return CONTACT_PREDICTION; |
118 | } | |
119 | ||
120 | 0 | @Override |
121 | public int getHeight() | |
122 | { | |
123 | // TODO Auto-generated method stub | |
124 | // return maximum contact height | |
125 | 0 | return 0; |
126 | } | |
127 | ||
128 | 0 | @Override |
129 | public int getWidth() | |
130 | { | |
131 | // TODO Auto-generated method stub | |
132 | // return total number of residues with contacts | |
133 | 0 | return 0; |
134 | } | |
135 | }; | |
136 | 0 | models.add(cm); |
137 | } | |
138 | ||
139 | 0 | try |
140 | { | |
141 | 0 | left = Integer.parseInt(parts[0]); |
142 | 0 | right = Integer.parseInt(parts[1]); |
143 | 0 | strength = Double.parseDouble(parts[2]); |
144 | } catch (Exception x) | |
145 | { | |
146 | 0 | error = true; |
147 | 0 | errormessage = "Couldn't process line: " + x.getLocalizedMessage() |
148 | + "\n" + line; | |
149 | 0 | return; |
150 | } | |
151 | 0 | cm.addContact(left, right, (float) strength); |
152 | } | |
153 | } | |
154 | // TODO COMPLETE | |
155 | 0 | throw (new Error("Not Implemented yet.")); |
156 | } | |
157 | ||
158 | 0 | @Override |
159 | public String print(SequenceI[] sqs, boolean jvsuffix) | |
160 | { | |
161 | // TODO Auto-generated method stub | |
162 | 0 | return "Not valid."; |
163 | } | |
164 | } |