Coverage Report
File FloatContactMatrix.java
Coverage histogram
21% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| FloatContactMatrix | 23 | 28 | 20 |
Contributing tests
This file is covered by 37 tests.
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Source view
| 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 | } |