X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Frenderer%2FResidueShader.java;h=c0311700f1e61e5afc93c16984a6d8b98f14d5c5;hb=8ab24374eabe70d3d55bc92bcbbae401c743baa5;hp=c591031b1b5da96668cd777477fc6c6b64cabea4;hpb=b2b7e99113e1f0962140fc72d989cc826799a2d4;p=jalview.git
diff --git a/src/jalview/renderer/ResidueShader.java b/src/jalview/renderer/ResidueShader.java
index c591031..c031170 100644
--- a/src/jalview/renderer/ResidueShader.java
+++ b/src/jalview/renderer/ResidueShader.java
@@ -1,6 +1,27 @@
+/*
+ * 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;
+import jalview.api.ViewStyleI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.ProfileI;
import jalview.datamodel.ProfilesI;
@@ -18,7 +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
*
*
@@ -27,19 +49,47 @@ import java.util.Map;
*/
public class ResidueShader implements ResidueShaderI
{
+ private static final int INITIAL_CONSERVATION = 30;
+
+ /*
+ * the colour scheme that gives the colour of each residue
+ * before applying any conservation or PID shading
+ */
private ColourSchemeI colourScheme;
+ /*
+ * the consensus data for each column
+ */
private ProfilesI consensus;
+ /*
+ * if true, apply shading of colour by conservation
+ */
private boolean conservationColouring;
+ /*
+ * the physico-chemical property conservation scores for columns, with values
+ * 0-9, '+' (all properties conserved), '*' (residue fully conserved) or '-' (gap)
+ * (may be null if colour by conservation is not selected)
+ */
private char[] conservation;
- private int threshold;
+ /*
+ * minimum percentage identity for colour to be applied;
+ * if above zero, residue must match consensus (or joint consensus)
+ * and column have >= pidThreshold identity with the residue
+ */
+ private int pidThreshold;
+ /*
+ * if true, ignore gaps in percentage identity calculation
+ */
private boolean ignoreGaps;
- private int inc;
+ /*
+ * setting of the By Conservation slider
+ */
+ private int conservationIncrement = INITIAL_CONSERVATION;
public ResidueShader(ColourSchemeI cs)
{
@@ -54,6 +104,33 @@ public class ResidueShader implements ResidueShaderI
}
/**
+ * Constructor given view style settings
+ *
+ * @param viewStyle
+ */
+ public ResidueShader(ViewStyleI viewStyle)
+ {
+ // TODO remove duplicated storing of conservation / pid thresholds?
+ this();
+ setConservationApplied(viewStyle.isConservationColourSelected());
+ // setThreshold(viewStyle.getThreshold());
+ }
+
+ /**
+ * Copy constructor
+ */
+ public ResidueShader(ResidueShader rs)
+ {
+ this.colourScheme = rs.colourScheme;
+ this.consensus = rs.consensus;
+ this.conservation = rs.conservation;
+ this.conservationColouring = rs.conservationColouring;
+ this.conservationIncrement = rs.conservationIncrement;
+ this.ignoreGaps = rs.ignoreGaps;
+ this.pidThreshold = rs.pidThreshold;
+ }
+
+ /**
* @see jalview.renderer.ResidueShaderI#setConsensus(jalview.datamodel.ProfilesI)
*/
@Override
@@ -97,7 +174,7 @@ public class ResidueShader implements ResidueShaderI
conservation = cons.getConsSequence().getSequenceAsString()
.toCharArray();
}
-
+
}
/**
@@ -120,7 +197,7 @@ public class ResidueShader implements ResidueShaderI
@Override
public void setThreshold(int consensusThreshold, boolean ignoreGaps)
{
- threshold = consensusThreshold;
+ pidThreshold = consensusThreshold;
this.ignoreGaps = ignoreGaps;
}
@@ -130,7 +207,7 @@ public class ResidueShader implements ResidueShaderI
@Override
public void setConservationInc(int i)
{
- inc = i;
+ conservationIncrement = i;
}
/**
@@ -139,7 +216,7 @@ public class ResidueShader implements ResidueShaderI
@Override
public int getConservationInc()
{
- return inc;
+ return conservationIncrement;
}
/**
@@ -148,7 +225,7 @@ public class ResidueShader implements ResidueShaderI
@Override
public int getThreshold()
{
- return threshold;
+ return pidThreshold;
}
/**
@@ -158,21 +235,29 @@ 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;
}
@@ -200,7 +285,7 @@ public class ResidueShader implements ResidueShaderI
{
colour = Color.white;
}
-
+
if (conservationColouring)
{
colour = applyConservation(colour, column);
@@ -224,7 +309,7 @@ public class ResidueShader implements ResidueShaderI
*/
protected boolean aboveThreshold(char residue, int column)
{
- if (threshold == 0)
+ if (pidThreshold == 0)
{
return true;
}
@@ -234,26 +319,26 @@ 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
*/
if (profile != null
&& profile.getModalResidue().contains(String.valueOf(residue)))
{
- if (profile.getPercentageIdentity(ignoreGaps) >= threshold)
+ if (profile.getPercentageIdentity(ignoreGaps) >= pidThreshold)
{
return true;
}
}
-
+
return false;
}
@@ -281,7 +366,7 @@ 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
@@ -292,24 +377,24 @@ 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 *= (inc / 20f);
-
+ bleachFactor *= (conservationIncrement / 20f);
+
return ColorUtils.bleachColour(currentColour, bleachFactor);
}