}
/*
- * Find the RGB value of the colour of a sequence at a specified column position
+ * Returns the RGB value of the colour of a sequence at a specified column position
*
* @param seq
* sequence to get colour for
{
return (seq == null || icol >= seq.getLength()
? resColFinder.gapColourInt
- : resColFinder.getResidueColour(true, shader, allGroups, seq,
- icol, finder).getRGB());
+ : resColFinder.getResidueColourInt(true, shader, allGroups, seq,
+ icol, finder));
}
/**
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.util.Comparison;
import java.awt.Color;
final Color gapColour; // colour to use for gaps
- final int gapColourInt; // RGB value of gapColour
+ final int gapColourInt;
final Color residueColour; // colour to use for uncoloured residues
+ final int residueColourInt;
+
final Color hiddenColour; // colour for hidden regions
boolean useLegacy = false;
residueColour = Color.WHITE;
}
gapColourInt = gapColour.getRGB();
+ residueColourInt = residueColour.getRGB();
hiddenColour = hiddenCol;
}
- /**
- * Overrides the method to return the currently configured Overview colours
- * for gaps, or residues with no colour scheme set. A custom colour scheme
- * which specifies a colour for gaps overrides the normal gap colour.
- */
@Override
public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
{
+ return new Color(getBoxColourInt(shader, seq, i));
+ }
+
+ public int getBoxColourInt(ResidueShaderI shader, SequenceI seq, int i)
+ {
char currentChar = seq.getCharAt(i);
+ // In the overview window, gaps are coloured grey, unless the colour scheme
+ // specifies a gap colour, in which case gaps honour the colour scheme
+ // settings
boolean isGap = Comparison.isGap(currentChar);
if (shader.getColourScheme() == null)
{
- return (isGap ? gapColour : residueColour);
+ return (isGap ? gapColourInt : residueColourInt);
}
- return (isGap && !shader.getColourScheme().hasGapColour() ? gapColour
- : shader.findColour(currentChar, i, seq));
+ return (isGap && !shader.getColourScheme().hasGapColour() ? gapColourInt
+ : shader.findColourInt(currentChar, i, seq));
+ }
+
+ @Override
+ public Color getResidueColour(boolean showBoxes, ResidueShaderI shader,
+ SequenceGroup[] allGroups, final SequenceI seq, int i,
+ FeatureColourFinder finder)
+ {
+ Color col = getResidueBoxColour(showBoxes, shader, allGroups, seq, i);
+
+ // if there's a FeatureColourFinder we might override the residue colour
+ // here with feature colouring
+ col = finder == null || finder.noFeaturesDisplayed() ? col
+ : finder.findFeatureColour(col, seq, i);
+ return col;
+ }
+
+ public int getResidueColourInt(boolean showBoxes, ResidueShaderI shader,
+ SequenceGroup[] allGroups, final SequenceI seq, int i,
+ FeatureColourFinder finder)
+ {
+ int col = getResidueBoxColourInt(showBoxes, shader, allGroups, seq, i);
+
+ // if there's a FeatureColourFinder we might override the residue colour
+ // here with feature colouring
+ col = finder == null || finder.noFeaturesDisplayed() ? col
+ : finder.findFeatureColourInt(col, seq, i);
+ return col;
+ }
+
+ @Override
+ protected Color getResidueBoxColour(boolean showBoxes,
+ ResidueShaderI shader, SequenceGroup[] allGroups, SequenceI seq,
+ int i)
+ {
+ return new Color(
+ getResidueBoxColourInt(showBoxes, shader, allGroups, seq, i));
}
/**
* In the overview, the showBoxes setting is ignored, as the overview displays
- * the colours regardless
+ * the colours regardless.
*/
- @Override
- protected Color getResidueBoxColour(boolean showBoxes,
+ protected int getResidueBoxColourInt(boolean showBoxes,
ResidueShaderI shader, SequenceGroup[] allGroups, SequenceI seq,
int i)
{
i);
ResidueShaderI currentShader = (currentSequenceGroup == null ? shader
: currentSequenceGroup.getGroupColourScheme());
- return getBoxColour(currentShader, seq, i);
+ return getBoxColourInt(currentShader, seq, i);
}
/**
- * Returns the coloured configured for hidden regions in the Overview
+ * Supply hidden colour
*
- * @return
+ * @return colour of hidden regions
*/
protected Color getHiddenColour()
{
return colour;
}
+ @Override
+ public int findColourInt(char symbol, int position, SequenceI seq)
+ {
+ if (colourScheme == null)
+ {
+ return -1;// Color.white; // Colour is 'None'
+ }
+
+ /*
+ * get 'base' colour
+ */
+ ProfileI profile = consensus == null ? null : consensus.get(position);
+ String modalResidue = profile == null ? null
+ : profile.getModalResidue();
+ float pid = profile == null ? 0f
+ : profile.getPercentageIdentity(ignoreGaps);
+ int colour = colourScheme
+ .findColour(symbol, position, seq, modalResidue, pid).getRGB();
+
+ /*
+ * apply PID threshold and consensus fading if in force
+ */
+ if (!Comparison.isGap(symbol))
+ {
+ colour = adjustColourInt(symbol, position, colour);
+ }
+
+ return colour;
+ }
+
/**
* Adjusts colour by applying thresholding or conservation shading, if in
* force. That is
return colour;
}
+ protected int adjustColourInt(char symbol, int column, int colour)
+ {
+ if (!aboveThreshold(symbol, column))
+ {
+ colour = -1;// Color.white;
+ }
+
+ if (conservationColouring)
+ {
+ colour = applyConservationInt(colour, column);
+ }
+ return colour;
+ }
+
/**
* Answers true if there is a consensus profile for the specified column, and
* the given residue matches the consensus (or joint consensus) residue for
return ColorUtils.bleachColour(currentColour, bleachFactor);
}
+ protected int applyConservationInt(int currentColour, int column)
+ {
+ if (conservation == null || conservation.length <= column)
+ {
+ return currentColour;
+ }
+ char conservationScore = conservation[column];
+
+ /*
+ * if residues are fully conserved (* or 11), or all properties
+ * are conserved (+ or 10), leave colour unchanged
+ */
+ if (conservationScore == '*' || conservationScore == '+'
+ || conservationScore == (char) 10
+ || conservationScore == (char) 11)
+ {
+ return currentColour;
+ }
+
+ if (Comparison.isGap(conservationScore))
+ {
+ return -1;// Color.white;
+ }
+
+ /*
+ * convert score 0-9 to a bleaching factor 1.1 - 0.2
+ */
+ float bleachFactor = (11 - (conservationScore - '0')) / 10f;
+
+ /*
+ * scale this up by 0-5 (percentage slider / 20)
+ * as a result, scores of: 0 1 2 3 4 5 6 7 8 9
+ * fade to white at slider value: 18 20 22 25 29 33 40 50 67 100%
+ */
+ bleachFactor *= (conservationIncrement / 20f);
+
+ return ColorUtils.bleachColourInt(currentColour, bleachFactor);
+ }
+
/**
* @see jalview.renderer.ResidueShaderI#getColourScheme()
*/
public abstract Color findColour(char symbol, int position,
SequenceI seq);
+ /**
+ * A variant of findColour that returns the rgb value of the colour rather
+ * than a Color object
+ *
+ * @param symbol
+ * @param position
+ * @param seq
+ * @return
+ */
+ public int findColourInt(char symbol, int position, SequenceI seq);
+
public abstract ColourSchemeI getColourScheme();
public abstract void setColourScheme(ColourSchemeI cs);
return c;
}
+ public int findFeatureColourInt(int defaultColour, SequenceI seq,
+ int column)
+ {
+ Graphics g = null;
+
+ /*
+ * if transparency applies, provide a notional 1x1 graphics context
+ * that has been primed with the default colour
+ */
+ if (featureRenderer.getTransparency() != 1f)
+ {
+ g = goff;
+ if (defaultColour != 0)
+ {
+ offscreenImage.setRGB(0, 0, defaultColour);
+ }
+ }
+
+ Color c = featureRenderer.findFeatureColour(seq, column + 1, g);
+ if (c == null)
+ {
+ return defaultColour;
+ }
+
+ if (g != null)
+ {
+ return offscreenImage.getRGB(0, 0);
+ }
+ return c.getRGB();
+ }
/**
* Answers true if feature display is turned off, or there are no features
* configured to be visible
}
}
+ public static int bleachColourInt(int colour, float bleachFactor)
+ {
+ if (bleachFactor >= 1f)
+ {
+ return -1;// Color.WHITE;
+ }
+ if (bleachFactor <= -1f)
+ {
+ return 0xFF000000;// Color.BLACK;
+ }
+ if (bleachFactor == 0f)
+ {
+ return colour;
+ }
+
+ int red = (colour >> 16) & 0xFF;// getRed();
+ int green = (colour >> 8) & 0xFF;// colour.getGreen();
+ int blue = colour & 0xFF;// .getBlue();
+
+ if (bleachFactor > 0)
+ {
+ red += (255 - red) * bleachFactor;
+ green += (255 - green) * bleachFactor;
+ blue += (255 - blue) * bleachFactor;
+ }
+ else
+ {
+ float factor = 1 + bleachFactor;
+ red *= factor;
+ green *= factor;
+ blue *= factor;
+ }
+ return 0xFF000000 | (red << 16) | (green << 8) | blue;// new Color(red,
+ // green, blue);
+ }
+
/**
* Parses a string into a Color, where the accepted formats are
* <ul>
git://source.jalview.org / jalview.git / commitdiff