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.analysis.Conservation;
24 import jalview.api.ViewStyleI;
25 import jalview.datamodel.AnnotatedCollectionI;
26 import jalview.datamodel.ProfileI;
27 import jalview.datamodel.ProfilesI;
28 import jalview.datamodel.SequenceCollectionI;
29 import jalview.datamodel.SequenceI;
30 import jalview.schemes.ColourSchemeI;
31 import jalview.util.ColorUtils;
32 import jalview.util.Comparison;
34 import java.awt.Color;
38 * A class that computes the colouring of an alignment (or subgroup). Currently
39 * the factors that may influence residue colouring are
41 * <li>the colour scheme that provides a colour for each aligned residue</li>
42 * <li>any threshold for colour, based on percentage identity with
44 * <li>any graduation based on conservation of physico-chemical properties</li>
50 public class ResidueShader implements ResidueShaderI
52 private static final int INITIAL_CONSERVATION = 30;
55 * the colour scheme that gives the colour of each residue
56 * before applying any conservation or PID shading
58 private ColourSchemeI colourScheme;
61 * the consensus data for each column
63 private ProfilesI consensus;
66 * the consensus data for each column
68 private ProfilesI ssConsensus;
71 public ProfilesI getSsConsensus()
76 public void setSsConsensus(ProfilesI ssConsensus)
78 this.ssConsensus = ssConsensus;
82 * if true, apply shading of colour by conservation
84 private boolean conservationColouring;
87 * the physico-chemical property conservation scores for columns, with values
88 * 0-9, '+' (all properties conserved), '*' (residue fully conserved) or '-' (gap)
89 * (may be null if colour by conservation is not selected)
91 private char[] conservation;
94 * minimum percentage identity for colour to be applied;
95 * if above zero, residue must match consensus (or joint consensus)
96 * and column have >= pidThreshold identity with the residue
98 private int pidThreshold;
101 * if true, ignore gaps in percentage identity calculation
103 private boolean ignoreGaps;
106 * setting of the By Conservation slider
108 private int conservationIncrement = INITIAL_CONSERVATION;
110 public ResidueShader(ColourSchemeI cs)
116 * Default constructor
118 public ResidueShader()
123 * Constructor given view style settings
127 public ResidueShader(ViewStyleI viewStyle)
129 // TODO remove duplicated storing of conservation / pid thresholds?
131 setConservationApplied(viewStyle.isConservationColourSelected());
132 // setThreshold(viewStyle.getThreshold());
138 public ResidueShader(ResidueShader rs)
140 this.colourScheme = rs.colourScheme;
141 this.consensus = rs.consensus;
142 this.conservation = rs.conservation;
143 this.conservationColouring = rs.conservationColouring;
144 this.conservationIncrement = rs.conservationIncrement;
145 this.ignoreGaps = rs.ignoreGaps;
146 this.pidThreshold = rs.pidThreshold;
147 this.ssConsensus = rs.ssConsensus;
151 * @see jalview.renderer.ResidueShaderI#setConsensus(jalview.datamodel.ProfilesI)
154 public void setConsensus(ProfilesI cons)
161 * @see jalview.renderer.ResidueShaderI#conservationApplied()
164 public boolean conservationApplied()
166 return conservationColouring;
170 * @see jalview.renderer.ResidueShaderI#setConservationApplied(boolean)
173 public void setConservationApplied(boolean conservationApplied)
175 conservationColouring = conservationApplied;
179 * @see jalview.renderer.ResidueShaderI#setConservation(jalview.analysis.Conservation)
182 public void setConservation(Conservation cons)
186 conservationColouring = false;
191 conservationColouring = true;
192 conservation = cons.getConsSequence().getSequenceAsString()
199 * @see jalview.renderer.ResidueShaderI#alignmentChanged(jalview.datamodel.AnnotatedCollectionI,
203 public void alignmentChanged(AnnotatedCollectionI alignment,
204 Map<SequenceI, SequenceCollectionI> hiddenReps)
206 if (colourScheme != null)
208 colourScheme.alignmentChanged(alignment, hiddenReps);
213 * @see jalview.renderer.ResidueShaderI#setThreshold(int, boolean)
216 public void setThreshold(int consensusThreshold, boolean ignoreGaps)
218 pidThreshold = consensusThreshold;
219 this.ignoreGaps = ignoreGaps;
223 * @see jalview.renderer.ResidueShaderI#setConservationInc(int)
226 public void setConservationInc(int i)
228 conservationIncrement = i;
232 * @see jalview.renderer.ResidueShaderI#getConservationInc()
235 public int getConservationInc()
237 return conservationIncrement;
241 * @see jalview.renderer.ResidueShaderI#getThreshold()
244 public int getThreshold()
250 * @see jalview.renderer.ResidueShaderI#findColour(char, int,
251 * jalview.datamodel.SequenceI)
254 public Color findColour(char symbol, int position, SequenceI seq)
256 if (colourScheme == null)
258 return Color.white; // Colour is 'None'
264 ProfileI profile = consensus == null ? null : consensus.get(position);
265 String modalResidue = profile == null ? null
266 : profile.getModalResidue();
267 float pid = profile == null ? 0f
268 : profile.getPercentageIdentity(ignoreGaps);
269 Color colour = colourScheme.findColour(symbol, position, seq,
273 * apply PID threshold and consensus fading if in force
275 if (!Comparison.isGap(symbol))
277 colour = adjustColour(symbol, position, colour);
284 public Color findSSColour(char symbol, int position, SequenceI seq)
286 if (colourScheme == null)
288 return Color.white; // Colour is 'None'
294 ProfileI profile = ssConsensus == null ? null : ssConsensus.get(position);
295 String modalSS = profile == null ? null
296 : profile.getModalSS();
297 float pid = profile == null ? 0f
298 : profile.getSSPercentageIdentity(ignoreGaps);
299 Color colour = colourScheme.findColour(symbol, position, seq,
303 * apply PID threshold and consensus fading if in force
305 if (!Comparison.isGap(symbol))
307 colour = adjustColour(symbol, position, colour);
314 * Adjusts colour by applying thresholding or conservation shading, if in
317 * <li>if there is a threshold set for colouring, and the residue doesn't
318 * match the consensus (or a joint consensus) residue, or the consensus score
319 * is not above the threshold, then the colour is set to white</li>
320 * <li>if conservation colouring is selected, the colour is faded by an amount
321 * depending on the conservation score for the column, and the conservation
322 * colour threshold</li>
330 protected Color adjustColour(char symbol, int column, Color colour)
332 if (!aboveThreshold(symbol, column))
334 colour = Color.white;
337 if (conservationColouring)
339 colour = applyConservation(colour, column);
345 * Answers true if there is a consensus profile for the specified column, and
346 * the given residue matches the consensus (or joint consensus) residue for
347 * the column, and the percentage identity for the profile is equal to or
348 * greater than the current threshold; else answers false. The percentage
349 * calculation depends on whether or not we are ignoring gapped sequences.
353 * (index into consensus profiles)
356 * @see #setThreshold(int, boolean)
358 protected boolean aboveThreshold(char residue, int column)
360 if (pidThreshold == 0)
364 if ('a' <= residue && residue <= 'z')
367 // Faster than toUpperCase
368 residue -= ('a' - 'A');
371 if (consensus == null)
376 ProfileI profile = consensus.get(column);
379 * test whether this is the consensus (or joint consensus) residue
382 && profile.getModalResidue().contains(String.valueOf(residue)))
384 if (profile.getPercentageIdentity(ignoreGaps) >= pidThreshold)
394 * Applies a combination of column conservation score, and conservation
395 * percentage slider, to 'bleach' out the residue colours towards white.
397 * If a column is fully conserved (identical residues, conservation score 11,
398 * shown as *), or all 10 physico-chemical properties are conserved
399 * (conservation score 10, shown as +), then the colour is left unchanged.
401 * Otherwise a 'bleaching' factor is computed and applied to the colour. This
402 * is designed to fade colours for scores of 0-9 completely to white at slider
403 * positions ranging from 18% - 100% respectively.
405 * @param currentColour
408 * @return bleached (or unmodified) colour
410 protected Color applyConservation(Color currentColour, int column)
412 if (conservation == null || conservation.length <= column)
414 return currentColour;
416 char conservationScore = conservation[column];
419 * if residues are fully conserved (* or 11), or all properties
420 * are conserved (+ or 10), leave colour unchanged
422 if (conservationScore == '*' || conservationScore == '+'
423 || conservationScore == (char) 10
424 || conservationScore == (char) 11)
426 return currentColour;
429 if (Comparison.isGap(conservationScore))
435 * convert score 0-9 to a bleaching factor 1.1 - 0.2
437 float bleachFactor = (11 - (conservationScore - '0')) / 10f;
440 * scale this up by 0-5 (percentage slider / 20)
441 * as a result, scores of: 0 1 2 3 4 5 6 7 8 9
442 * fade to white at slider value: 18 20 22 25 29 33 40 50 67 100%
444 bleachFactor *= (conservationIncrement / 20f);
446 return ColorUtils.bleachColour(currentColour, bleachFactor);
450 * @see jalview.renderer.ResidueShaderI#getColourScheme()
453 public ColourSchemeI getColourScheme()
455 return this.colourScheme;
459 * @see jalview.renderer.ResidueShaderI#setColourScheme(jalview.schemes.ColourSchemeI)
462 public void setColourScheme(ColourSchemeI cs)