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ContactListImpl | 33 | 35 | 17 |
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.awt.Color; | |
24 | ||
25 | import jalview.renderer.ContactGeometry.contactInterval; | |
26 | ||
27 | /** | |
28 | * helper class to compute min/max/mean for a range on a contact list | |
29 | * | |
30 | * @author jprocter | |
31 | * | |
32 | */ | |
33 | public class ContactListImpl implements ContactListI | |
34 | { | |
35 | ContactListProviderI clist; | |
36 | ||
37 | 0 | public static ContactListI newContactList(ContactListProviderI list) |
38 | { | |
39 | 0 | return new ContactListImpl(list); |
40 | } | |
41 | ||
42 | 7587 | public ContactListImpl(ContactListProviderI list) |
43 | { | |
44 | 7587 | clist = list; |
45 | } | |
46 | ||
47 | 0 | @Override |
48 | public int getPosition() | |
49 | { | |
50 | 0 | return clist.getPosition(); |
51 | } | |
52 | ||
53 | 4646236 | @Override |
54 | public double getContactAt(int column) | |
55 | { | |
56 | 4646236 | return clist.getContactAt(column); |
57 | } | |
58 | ||
59 | 4289630 | @Override |
60 | public int getContactHeight() | |
61 | { | |
62 | 4289629 | return clist.getContactHeight(); |
63 | } | |
64 | ||
65 | 142159 | @Override |
66 | public ContactRange getRangeFor(int from_column, int to_column) | |
67 | { | |
68 | // TODO: consider caching ContactRange for a particular call ? | |
69 | 142159 | if (clist instanceof ContactListI) |
70 | { | |
71 | // clist may implement getRangeFor in a more efficient way, so use theirs | |
72 | 0 | return ((ContactListI) clist).getRangeFor(from_column, to_column); |
73 | } | |
74 | 142159 | if (from_column < 0) |
75 | { | |
76 | 0 | from_column = 0; |
77 | } | |
78 | 142159 | if (to_column >= getContactHeight()) |
79 | { | |
80 | 0 | to_column = getContactHeight() - 1; |
81 | } | |
82 | 142159 | ContactRange cr = new ContactRange(); |
83 | 142155 | cr.setFrom_column(from_column); |
84 | 142155 | cr.setTo_column(to_column); |
85 | 142155 | double tot = 0; |
86 | 577560 | for (int i = from_column; i <= to_column; i++) |
87 | { | |
88 | 435408 | double contact = getContactAt(i); |
89 | 435524 | tot += contact; |
90 | 435527 | if (i == from_column) |
91 | { | |
92 | 142154 | cr.setMin(contact); |
93 | 142154 | cr.setMax(contact); |
94 | 142153 | cr.setMinPos(i); |
95 | 142153 | cr.setMaxPos(i); |
96 | } | |
97 | else | |
98 | { | |
99 | 293371 | if (cr.getMax() < contact) |
100 | { | |
101 | 67821 | cr.setMax(contact); |
102 | 67818 | cr.setMaxPos(i); |
103 | } | |
104 | 293367 | if (cr.getMin() < contact) |
105 | { | |
106 | 67818 | cr.setMin(contact); |
107 | 67818 | cr.setMinPos(i); |
108 | } | |
109 | } | |
110 | } | |
111 | 142155 | if (tot > 0 && to_column > from_column) |
112 | { | |
113 | 120083 | cr.setMean(tot / (1 + to_column - from_column)); |
114 | } | |
115 | else | |
116 | { | |
117 | 22072 | cr.setMean(tot); |
118 | } | |
119 | 142156 | return cr; |
120 | } | |
121 | ||
122 | 142113 | @Override |
123 | public int[] getMappedPositionsFor(int cStart, int cEnd) | |
124 | { | |
125 | 142113 | return clist.getMappedPositionsFor(cStart, cEnd); |
126 | } | |
127 | ||
128 | 3552 | @Override |
129 | public Color getColourForGroup() | |
130 | { | |
131 | 3552 | return clist.getColourForGroup(); |
132 | } | |
133 | } |