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ContactMatrix | 29 | 77 | 39 |
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.datamodel; | |
22 | ||
23 | import java.util.ArrayList; | |
24 | import java.util.List; | |
25 | import java.util.StringTokenizer; | |
26 | ||
27 | import jalview.bin.Console; | |
28 | ||
29 | public abstract class ContactMatrix extends GroupSetHolder | |
30 | implements ContactMatrixI | |
31 | { | |
32 | /** | |
33 | * are contacts reflexive ? | |
34 | */ | |
35 | boolean symmetric = true; | |
36 | ||
37 | 0 | public ContactMatrix(boolean symmetric) |
38 | { | |
39 | 0 | this.symmetric = symmetric; |
40 | } | |
41 | ||
42 | List<List<Float>> contacts = null; | |
43 | ||
44 | int width = 0, numcontacts = 0; | |
45 | ||
46 | float min = 0f, max = 0f; | |
47 | ||
48 | 0 | public void addContact(int left, int right, float strength) |
49 | { | |
50 | 0 | if (left < 0 || right < 0) |
51 | { | |
52 | 0 | throw new Error(new RuntimeException( |
53 | "Cannot have negative indices for contact left=" + left | |
54 | + " right=" + right + " strength=" + strength)); | |
55 | } | |
56 | 0 | if (symmetric) |
57 | { | |
58 | 0 | if (left > right) |
59 | { | |
60 | // swap | |
61 | 0 | int r = right; |
62 | 0 | right = left; |
63 | 0 | left = r; |
64 | } | |
65 | } | |
66 | 0 | if (contacts == null) |
67 | { | |
68 | // TODO: use sparse list for efficiency ? | |
69 | 0 | contacts = new ArrayList<List<Float>>(); |
70 | } | |
71 | 0 | List<Float> clist = contacts.get(left); |
72 | 0 | if (clist == null) |
73 | { | |
74 | 0 | clist = new ArrayList<Float>(); |
75 | 0 | contacts.set(left, clist); |
76 | } | |
77 | 0 | Float last = clist.set(right, strength); |
78 | // TODO: if last is non null, may need to recompute range | |
79 | 0 | checkBounds(strength); |
80 | 0 | if (last == null) |
81 | { | |
82 | 0 | numcontacts++; |
83 | } | |
84 | } | |
85 | ||
86 | 0 | private void checkBounds(float strength) |
87 | { | |
88 | 0 | if (min > strength) |
89 | { | |
90 | 0 | min = strength; |
91 | } | |
92 | 0 | if (max < strength) |
93 | { | |
94 | 0 | max = strength; |
95 | } | |
96 | } | |
97 | ||
98 | 0 | @Override |
99 | public ContactListI getContactList(final int column) | |
100 | { | |
101 | 0 | if (column < 0 || column >= width) |
102 | { | |
103 | 0 | return null; |
104 | } | |
105 | ||
106 | 0 | return new ContactListImpl(new ContactListProviderI() |
107 | { | |
108 | int p = column; | |
109 | ||
110 | 0 | @Override |
111 | public int getPosition() | |
112 | { | |
113 | 0 | return p; |
114 | } | |
115 | ||
116 | 0 | @Override |
117 | public int getContactHeight() | |
118 | { | |
119 | 0 | return width; |
120 | ||
121 | } | |
122 | ||
123 | 0 | @Override |
124 | public double getContactAt(int column) | |
125 | { | |
126 | 0 | Float cl = getFloatElementAt(column, p); |
127 | 0 | if (cl == null) |
128 | { | |
129 | // return 0 not NaN ? | |
130 | 0 | return Double.NaN; |
131 | } | |
132 | 0 | return cl.doubleValue(); |
133 | } | |
134 | }); | |
135 | } | |
136 | ||
137 | 0 | private Float getFloatElementAt(int column, int p) |
138 | { | |
139 | ||
140 | 0 | List<Float> clist; |
141 | 0 | Float cl = null; |
142 | 0 | if (symmetric) |
143 | { | |
144 | 0 | if (p < column) |
145 | { | |
146 | 0 | clist = contacts.get(p); |
147 | 0 | cl = clist.get(column); |
148 | } | |
149 | else | |
150 | { | |
151 | 0 | clist = contacts.get(column); |
152 | 0 | cl = clist.get(p); |
153 | } | |
154 | } | |
155 | else | |
156 | { | |
157 | 0 | clist = contacts.get(p); |
158 | 0 | cl = clist.get(column); |
159 | } | |
160 | 0 | return cl; |
161 | } | |
162 | ||
163 | 0 | @Override |
164 | public double getElementAt(int column, int row) | |
165 | { | |
166 | 0 | Float cl = getFloatElementAt(column, row); |
167 | 0 | if (cl != null) |
168 | { | |
169 | 0 | return cl; |
170 | } | |
171 | 0 | throw (new RuntimeException("Out of Bounds " + column + "," + row)); |
172 | } | |
173 | ||
174 | 0 | @Override |
175 | public float getMin() | |
176 | { | |
177 | 0 | return min; |
178 | } | |
179 | ||
180 | 0 | @Override |
181 | public float getMax() | |
182 | { | |
183 | 0 | return max; |
184 | } | |
185 | ||
186 | 0 | @Override |
187 | public String getAnnotLabel() | |
188 | { | |
189 | 0 | return "Contact Matrix"; |
190 | } | |
191 | ||
192 | 0 | @Override |
193 | public String getAnnotDescr() | |
194 | { | |
195 | 0 | return "Contact Matrix"; |
196 | } | |
197 | ||
198 | 5 | public static String contactToFloatString(ContactMatrixI cm) |
199 | { | |
200 | 5 | StringBuilder sb = new StringBuilder(); |
201 | 2049 | for (int c = 0; c < cm.getWidth(); c++) |
202 | { | |
203 | 2044 | ContactListI cl = cm.getContactList(c); |
204 | 2044 | long lastsb = -1; |
205 | 2044 | if (cl != null) |
206 | { | |
207 | 4002528 | for (int h = 0; h <= cl.getContactHeight(); h++) |
208 | { | |
209 | 4000484 | if (sb.length() > 0) |
210 | { | |
211 | 4000479 | if (sb.length() - lastsb > 320) |
212 | { | |
213 | // newline | |
214 | 56466 | sb.append('\n'); |
215 | 56466 | lastsb = sb.length(); |
216 | } | |
217 | else | |
218 | { | |
219 | 3944013 | sb.append('\t'); |
220 | } | |
221 | } | |
222 | 4000484 | sb.append(cl.getContactAt(h)); |
223 | } | |
224 | } | |
225 | } | |
226 | 5 | return sb.toString(); |
227 | } | |
228 | ||
229 | 4 | public static float[][] fromFloatStringToContacts(String values, int cols, |
230 | int rows) | |
231 | { | |
232 | 4 | float[][] vals = new float[cols][rows]; |
233 | 4 | StringTokenizer tabsep = new StringTokenizer(values, "" + '\t' + '\n'); |
234 | 4 | int c = 0, r = 0; |
235 | 4000363 | while (tabsep.hasMoreTokens()) |
236 | { | |
237 | 4000363 | double elem = Double.valueOf(tabsep.nextToken()); |
238 | 4000363 | vals[c][r++] = (float) elem; |
239 | 4000363 | if (r >= vals[c].length) |
240 | { | |
241 | 2033 | r = 0; |
242 | 2033 | c++; |
243 | } | |
244 | 4000363 | if (c >= vals.length) |
245 | { | |
246 | 4 | break; |
247 | } | |
248 | } | |
249 | 4 | if (tabsep.hasMoreElements()) |
250 | { | |
251 | 0 | Console.warn( |
252 | "Ignoring additional elements for Float string to contact matrix parsing."); | |
253 | } | |
254 | 4 | return vals; |
255 | } | |
256 | } |