Coverage Report
File OverviewResColourFinder.java
Coverage histogram
0% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| OverviewResColourFinder | 29 | 22 | 12 |
Contributing tests
This file is covered by 10 tests.
.
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.renderer; | |
| 22 | ||
| 23 | import java.awt.Color; | |
| 24 | ||
| 25 | import jalview.datamodel.SequenceGroup; | |
| 26 | import jalview.datamodel.SequenceI; | |
| 27 | import jalview.util.Comparison; | |
| 28 | ||
| 29 | public class OverviewResColourFinder extends ResidueColourFinder | |
| 30 | { | |
| 31 | /* | |
| 32 | * colour for gaps (unless overridden by colour scheme) | |
| 33 | * - as set in Preferences, _or_ read from a project file | |
| 34 | */ | |
| 35 | Color gapColour; | |
| 36 | ||
| 37 | /* | |
| 38 | * colour for residues if no colour scheme set (before feature colouring) | |
| 39 | * - as set in Preferences, _or_ read from a project file | |
| 40 | */ | |
| 41 | Color residueColour; | |
| 42 | ||
| 43 | /* | |
| 44 | * colour for hidden regions | |
| 45 | * - as set in Preferences, _or_ read from a project file | |
| 46 | */ | |
| 47 | Color hiddenColour; | |
| 48 | ||
| 49 | /** | |
| 50 | * Constructor without colour settings (used by applet) | |
| 51 | * | |
| 52 | * @deprecated | |
| 53 | */ | |
| 54 | 3 |  @Deprecated |
| 55 | public OverviewResColourFinder() | |
| 56 | { | |
| 57 | 3 | this(Color.lightGray, Color.white, Color.darkGray.darker()); |
| 58 | } | |
| 59 | ||
| 60 | /** | |
| 61 | * Constructor given default colours for gaps, residues and hidden regions | |
| 62 | * | |
| 63 | * @param gaps | |
| 64 | * @param residues | |
| 65 | * @param hidden | |
| 66 | */ | |
| 67 | 57 | public OverviewResColourFinder(Color gaps, Color residues, Color hidden) |
| 68 | { | |
| 69 | 57 | gapColour = gaps; |
| 70 | 57 | residueColour = residues; |
| 71 | 57 | hiddenColour = hidden; |
| 72 | } | |
| 73 | ||
| 74 | 347639 | @Override |
| 75 | public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i) | |
| 76 | { | |
| 77 | 347666 | Color resBoxColour = residueColour; |
| 78 | 347700 | char currentChar = seq.getCharAt(i); |
| 79 | ||
| 80 | // In the overview window, gaps are coloured grey, unless the colour scheme | |
| 81 | // specifies a gap colour, in which case gaps honour the colour scheme | |
| 82 | // settings | |
| 83 | 347772 | if (shader.getColourScheme() != null) |
| 84 | { | |
| 85 | 126561 | if (Comparison.isGap(currentChar) |
| 86 | && (!shader.getColourScheme().hasGapColour())) | |
| 87 | { | |
| 88 | 8619 | resBoxColour = gapColour; |
| 89 | } | |
| 90 | else | |
| 91 | { | |
| 92 | 117944 | resBoxColour = shader.findColour(currentChar, i, seq); |
| 93 | } | |
| 94 | } | |
| 95 | 221214 | else if (Comparison.isGap(currentChar)) |
| 96 | { | |
| 97 | 37312 | resBoxColour = gapColour; |
| 98 | } | |
| 99 | ||
| 100 | 347579 | return resBoxColour; |
| 101 | } | |
| 102 | ||
| 103 | /** | |
| 104 | * {@inheritDoc} In the overview, the showBoxes setting is ignored, as the | |
| 105 | * overview displays the colours regardless. | |
| 106 | */ | |
| 107 | 347728 | @Override |
| 108 | protected Color getResidueBoxColour(boolean showBoxes, | |
| 109 | ResidueShaderI shader, SequenceGroup[] allGroups, SequenceI seq, | |
| 110 | int i) | |
| 111 | { | |
| 112 | 347740 | ResidueShaderI currentShader; |
| 113 | 347760 | SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups, |
| 114 | i); | |
| 115 | 347740 | if (currentSequenceGroup != null) |
| 116 | { | |
| 117 | 106023 | currentShader = currentSequenceGroup.getGroupColourScheme(); |
| 118 | } | |
| 119 | else | |
| 120 | { | |
| 121 | 241708 | currentShader = shader; |
| 122 | } | |
| 123 | ||
| 124 | 347636 | return getBoxColour(currentShader, seq, i); |
| 125 | } | |
| 126 | ||
| 127 | /** | |
| 128 | * Returns the colour used for hidden regions | |
| 129 | * | |
| 130 | * @return | |
| 131 | */ | |
| 132 | 16 | public Color getHiddenColour() |
| 133 | { | |
| 134 | 16 | return hiddenColour; |
| 135 | } | |
| 136 | ||
| 137 | /** | |
| 138 | * Returns the colour used for gaps, if not overridden by the alignment colour | |
| 139 | * scheme | |
| 140 | * | |
| 141 | * @return | |
| 142 | */ | |
| 143 | 16 | public Color getGapColour() |
| 144 | { | |
| 145 | 16 | return gapColour; |
| 146 | } | |
| 147 | ||
| 148 | /** | |
| 149 | * Returns the colour used for residues (before applying any feature | |
| 150 | * colouring) if there is no alignment colour scheme | |
| 151 | * | |
| 152 | * @return | |
| 153 | */ | |
| 154 | 16 | public Color getResidueColour() |
| 155 | { | |
| 156 | 16 | return residueColour; |
| 157 | } | |
| 158 | } |