hiddenReps)
+ {
+ if (colourScheme != null)
+ {
+ colourScheme.alignmentChanged(alignment, hiddenReps);
+ }
+ }
+
+ /**
+ * @see jalview.renderer.ResidueShaderI#setThreshold(int, boolean)
+ */
+ @Override
+ public void setThreshold(int consensusThreshold, boolean ignoreGaps)
+ {
+ pidThreshold = consensusThreshold;
+ this.ignoreGaps = ignoreGaps;
+ }
+
+ /**
+ * @see jalview.renderer.ResidueShaderI#setConservationInc(int)
+ */
+ @Override
+ public void setConservationInc(int i)
+ {
+ conservationIncrement = i;
+ }
+
+ /**
+ * @see jalview.renderer.ResidueShaderI#getConservationInc()
+ */
+ @Override
+ public int getConservationInc()
+ {
+ return conservationIncrement;
+ }
+
+ /**
+ * @see jalview.renderer.ResidueShaderI#getThreshold()
+ */
+ @Override
+ public int getThreshold()
+ {
+ return pidThreshold;
+ }
+
+ /**
+ * @see jalview.renderer.ResidueShaderI#findColour(char, int,
+ * jalview.datamodel.SequenceI)
+ */
+ @Override
+ public Color findColour(char symbol, int position, SequenceI seq)
+ {
+ /*
+ * 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);
+ Color colour = colourScheme == null ? Color.white
+ : colourScheme.findColour(symbol, position, seq, modalResidue,
+ pid);
+
+ /*
+ * apply PID threshold and consensus fading if in force
+ */
+ colour = adjustColour(symbol, position, colour);
+
+ return colour;
+ }
+
+ /**
+ * Adjusts colour by applying thresholding or conservation shading, if in
+ * force. That is
+ *
+ * - if there is a threshold set for colouring, and the residue doesn't
+ * match the consensus (or a joint consensus) residue, or the consensus score
+ * is not above the threshold, then the colour is set to white
+ * - if conservation colouring is selected, the colour is faded by an amount
+ * depending on the conservation score for the column, and the conservation
+ * colour threshold
+ *
+ *
+ * @param symbol
+ * @param column
+ * @param colour
+ * @return
+ */
+ protected Color adjustColour(char symbol, int column, Color colour)
+ {
+ if (!aboveThreshold(symbol, column))
+ {
+ colour = Color.white;
+ }
+
+ if (conservationColouring)
+ {
+ colour = applyConservation(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
+ * the column, and the percentage identity for the profile is equal to or
+ * greater than the current threshold; else answers false. The percentage
+ * calculation depends on whether or not we are ignoring gapped sequences.
+ *
+ * @param residue
+ * @param column
+ * (index into consensus profiles)
+ *
+ * @return
+ * @see #setThreshold(int, boolean)
+ */
+ protected boolean aboveThreshold(char residue, int column)
+ {
+ if (pidThreshold == 0)
+ {
+ return true;
+ }
+ if ('a' <= residue && residue <= 'z')
+ {
+ // TO UPPERCASE !!!
+ // Faster than toUpperCase
+ residue -= ('a' - 'A');
+ }
+
+ if (consensus == null)
+ {
+ return false;
+ }
+
+ ProfileI profile = consensus.get(column);
+
+ /*
+ * test whether this is the consensus (or joint consensus) residue
+ */
+ if (profile != null
+ && profile.getModalResidue().contains(String.valueOf(residue)))
+ {
+ if (profile.getPercentageIdentity(ignoreGaps) >= pidThreshold)
+ {
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * Applies a combination of column conservation score, and conservation
+ * percentage slider, to 'bleach' out the residue colours towards white.
+ *
+ * If a column is fully conserved (identical residues, conservation score 11,
+ * shown as *), or all 10 physico-chemical properties are conserved
+ * (conservation score 10, shown as +), then the colour is left unchanged.
+ *
+ * Otherwise a 'bleaching' factor is computed and applied to the colour. This
+ * is designed to fade colours for scores of 0-9 completely to white at slider
+ * positions ranging from 18% - 100% respectively.
+ *
+ * @param currentColour
+ * @param column
+ *
+ * @return bleached (or unmodified) colour
+ */
+ protected Color applyConservation(Color 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 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.bleachColour(currentColour, bleachFactor);
+ }
+
+ /**
+ * @see jalview.renderer.ResidueShaderI#getColourScheme()
+ */
+ @Override
+ public ColourSchemeI getColourScheme()
+ {
+ return this.colourScheme;
+ }
+
+ /**
+ * @see jalview.renderer.ResidueShaderI#setColourScheme(jalview.schemes.ColourSchemeI)
+ */
+ @Override
+ public void setColourScheme(ColourSchemeI cs)
+ {
+ colourScheme = cs;
+ }
+}