X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FResidueShader.java;h=73a5efdc71835e7e983a41b9674dbdb7efba2d8b;hb=0a94254977a8824ad154325a8ccb6d6d1d4e4dec;hp=8ecb2ad70669d3e6339cd211ebfe9a35a9ea8edf;hpb=331cd27699e0303dd42fd01e293f5fae9445e125;p=jalview.git
diff --git a/src/jalview/renderer/ResidueShader.java b/src/jalview/renderer/ResidueShader.java
index 8ecb2ad..73a5efd 100644
--- a/src/jalview/renderer/ResidueShader.java
+++ b/src/jalview/renderer/ResidueShader.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.renderer;
import jalview.analysis.Conservation;
@@ -19,7 +39,8 @@ import java.util.Map;
* the factors that may influence residue colouring are
*
* - the colour scheme that provides a colour for each aligned residue
- * - any threshold for colour, based on percentage identity with consensus
+ * - any threshold for colour, based on percentage identity with
+ * consensus
* - any graduation based on conservation of physico-chemical properties
*
*
@@ -153,7 +174,7 @@ public class ResidueShader implements ResidueShaderI
conservation = cons.getConsSequence().getSequenceAsString()
.toCharArray();
}
-
+
}
/**
@@ -214,21 +235,59 @@ public class ResidueShader implements ResidueShaderI
@Override
public Color findColour(char symbol, int position, SequenceI seq)
{
+ if (colourScheme == null)
+ {
+ return 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);
- Color colour = colourScheme == null ? Color.white : colourScheme
- .findColour(symbol, position, seq, modalResidue, pid);
+ String modalResidue = profile == null ? null
+ : profile.getModalResidue();
+ float pid = profile == null ? 0f
+ : profile.getPercentageIdentity(ignoreGaps);
+ Color colour = colourScheme.findColour(symbol, position, seq,
+ modalResidue, pid);
/*
* apply PID threshold and consensus fading if in force
*/
- colour = adjustColour(symbol, position, colour);
+ if (!Comparison.isGap(symbol))
+ {
+ colour = adjustColour(symbol, position, colour);
+ }
+
+ 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;
}
@@ -256,7 +315,7 @@ public class ResidueShader implements ResidueShaderI
{
colour = Color.white;
}
-
+
if (conservationColouring)
{
colour = applyConservation(colour, column);
@@ -264,6 +323,20 @@ public class ResidueShader implements ResidueShaderI
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
@@ -290,14 +363,14 @@ public class ResidueShader implements ResidueShaderI
// 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
*/
@@ -309,7 +382,7 @@ public class ResidueShader implements ResidueShaderI
return true;
}
}
-
+
return false;
}
@@ -337,7 +410,7 @@ public class ResidueShader implements ResidueShaderI
return currentColour;
}
char conservationScore = conservation[column];
-
+
/*
* if residues are fully conserved (* or 11), or all properties
* are conserved (+ or 10), leave colour unchanged
@@ -348,27 +421,66 @@ public class ResidueShader implements ResidueShaderI
{
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);
}
+ 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()
*/