2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.renderer;
23 import jalview.datamodel.SequenceGroup;
24 import jalview.datamodel.SequenceI;
25 import jalview.util.Comparison;
27 import java.awt.Color;
29 public class OverviewResColourFinder extends ResidueColourFinder
31 public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray;
33 public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white;
35 public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
38 final Color gapColour; // colour to use for gaps
40 final int gapColourInt; // RGB value of gapColour
42 final Color residueColour; // colour to use for uncoloured residues
44 final Color hiddenColour; // colour for hidden regions
46 boolean useLegacy = false;
49 * Constructor without colour settings (used by applet)
51 public OverviewResColourFinder()
53 this(false, OVERVIEW_DEFAULT_GAP, OVERVIEW_DEFAULT_HIDDEN);
57 * Constructor with colour settings
59 * @param useLegacyColouring
60 * whether to use legacy gap colouring (white gaps, grey residues)
62 * gap colour if not legacy
64 * hidden region colour (transparency applied by rendering code)
66 public OverviewResColourFinder(boolean useLegacyColouring, Color gapCol,
69 if (useLegacyColouring)
71 gapColour = Color.white;
72 residueColour = Color.lightGray;
77 residueColour = Color.WHITE;
79 gapColourInt = gapColour.getRGB();
80 hiddenColour = hiddenCol;
84 * Overrides the method to return the currently configured Overview colours
85 * for gaps, or residues with no colour scheme set. A custom colour scheme
86 * which specifies a colour for gaps overrides the normal gap colour.
89 public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
91 char currentChar = seq.getCharAt(i);
92 boolean isGap = Comparison.isGap(currentChar);
93 if (shader.getColourScheme() == null)
95 return (isGap ? gapColour : residueColour);
97 return (isGap && !shader.getColourScheme().hasGapColour() ? gapColour
98 : shader.findColour(currentChar, i, seq));
102 * In the overview, the showBoxes setting is ignored, as the overview displays
103 * the colours regardless
106 protected Color getResidueBoxColour(boolean showBoxes,
107 ResidueShaderI shader, SequenceGroup[] allGroups, SequenceI seq,
110 SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
112 ResidueShaderI currentShader = (currentSequenceGroup == null ? shader
113 : currentSequenceGroup.getGroupColourScheme());
114 return getBoxColour(currentShader, seq, i);
118 * Returns the coloured configured for hidden regions in the Overview
122 protected Color getHiddenColour()