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.schemes;
23 import jalview.api.AlignViewportI;
24 import jalview.datamodel.AnnotatedCollectionI;
25 import jalview.datamodel.SequenceCollectionI;
26 import jalview.datamodel.SequenceI;
28 import java.awt.Color;
32 * shade sequences using the colour shown in the ID panel. Useful to map
33 * sequence groupings onto residue data (eg tree subgroups visualised on
34 * structures or overview window)
38 public class IdColourScheme implements ColourSchemeI
40 AlignViewportI view = null;
42 public IdColourScheme()
46 public IdColourScheme(AlignViewportI view, AnnotatedCollectionI coll)
53 public String getSchemeName()
55 return JalviewColourScheme.IdColour.toString();
59 * Returns a new instance of this colour scheme with which the given data may
63 public ColourSchemeI getInstance(AlignViewportI view,
64 AnnotatedCollectionI coll)
66 return new IdColourScheme(view, coll);
70 public void alignmentChanged(AnnotatedCollectionI alignment,
71 Map<SequenceI, SequenceCollectionI> hiddenReps)
76 public Color findColour(char symbol, int position, SequenceI seq,
77 String consensusResidue, float pid)
79 // rather than testing if coll is a sequence group, and if so looking at
80 // ((SequenceGroup)coll).idColour
81 // we always return the sequence ID colour, in case the user has customised
82 // the displayed Id colour by right-clicking an internal node in the tree.
87 Color col = view.getSequenceColour(seq);
88 return Color.WHITE.equals(col) ? Color.WHITE : col.darker();
92 public boolean hasGapColour()
98 public boolean isApplicableTo(AnnotatedCollectionI ac)
104 public boolean isSimple()