Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
FloatContactMatrix | 23 | 28 | 20 |
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 | public class FloatContactMatrix extends GroupSetHolder | |
24 | implements ContactMatrixI | |
25 | { | |
26 | ||
27 | int maxrow = 0, maxcol = 0; | |
28 | ||
29 | float[][] elements; | |
30 | ||
31 | float maxscore; | |
32 | ||
33 | 58 | public FloatContactMatrix(float[][] matrix) |
34 | { | |
35 | 58 | maxcol = 0; |
36 | 58 | for (float[] row : matrix) |
37 | { | |
38 | 10765 | if (row.length > maxcol) |
39 | { | |
40 | 58 | maxcol = row.length; |
41 | } | |
42 | 10765 | maxscore = row[0]; |
43 | 10765 | for (float f : row) |
44 | { | |
45 | 7897553 | if (maxscore < f) |
46 | { | |
47 | 21449 | maxscore = f; |
48 | } | |
49 | } | |
50 | } | |
51 | 58 | maxrow = matrix.length; |
52 | 58 | elements = matrix; |
53 | } | |
54 | ||
55 | 3 | public FloatContactMatrix(float[][] elements2, GroupSet grps2) |
56 | { | |
57 | 3 | this(elements2); |
58 | 3 | setGroupSet(grps2); |
59 | } | |
60 | ||
61 | /** | |
62 | * getContactList(column) @returns the vector of predicted alignment errors | |
63 | * for reference position given by column | |
64 | */ | |
65 | 3917 | @Override |
66 | public ContactListI getContactList(final int column) | |
67 | { | |
68 | 3917 | if (column < 0 || column >= elements.length) |
69 | { | |
70 | 0 | return null; |
71 | } | |
72 | ||
73 | 3917 | return new ContactListImpl(new ContactListProviderI() |
74 | { | |
75 | 0 | @Override |
76 | public int getPosition() | |
77 | { | |
78 | 0 | return column; |
79 | } | |
80 | ||
81 | 4002539 | @Override |
82 | public int getContactHeight() | |
83 | { | |
84 | 4002539 | return maxcol - 1; |
85 | } | |
86 | ||
87 | 4210778 | @Override |
88 | public double getContactAt(int mcolumn) | |
89 | { | |
90 | 4210778 | if (mcolumn < 0 || mcolumn >= elements[column].length) |
91 | { | |
92 | 0 | return -1; |
93 | } | |
94 | 4210778 | return elements[column][mcolumn]; |
95 | } | |
96 | }); | |
97 | } | |
98 | ||
99 | /** | |
100 | * getElementAt(column, i) @returns the predicted superposition error for the | |
101 | * ith position when column is used as reference | |
102 | */ | |
103 | 435479 | @Override |
104 | public double getElementAt(int _column, int i) | |
105 | { | |
106 | 435492 | return elements[_column][i]; |
107 | } | |
108 | ||
109 | 120 | @Override |
110 | public float getMin() | |
111 | { | |
112 | 120 | return 0; |
113 | } | |
114 | ||
115 | 127 | @Override |
116 | public float getMax() | |
117 | { | |
118 | 127 | return maxscore; |
119 | } | |
120 | ||
121 | 0 | @Override |
122 | public String getAnnotDescr() | |
123 | { | |
124 | // TODO Auto-generated method stub | |
125 | 0 | return null; |
126 | } | |
127 | ||
128 | 0 | @Override |
129 | public String getAnnotLabel() | |
130 | { | |
131 | // TODO Auto-generated method stub | |
132 | 0 | return null; |
133 | } | |
134 | ||
135 | 0 | @Override |
136 | public String getType() | |
137 | { | |
138 | 0 | return null; |
139 | } | |
140 | ||
141 | 2142 | @Override |
142 | public int getWidth() | |
143 | { | |
144 | 2142 | return maxcol; |
145 | } | |
146 | ||
147 | 103448 | @Override |
148 | public int getHeight() | |
149 | { | |
150 | 103448 | return maxrow; |
151 | } | |
152 | } |