X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=56c573c8f792ba1ff397d32b8718a87ae7777fd0;hb=fc9aecdad8fb4d6ac38e504b094b29cf2223b32b;hp=3bd9bca184b107beb4e8191320f0f7eec23daa4e;hpb=66b1bf1a6480b320ddaa00d4f5e70b2051041c11;p=jalview.git
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 3bd9bca..56c573c 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,62 +1,363 @@
-package jalview.schemes;
-
-import java.util.*;
-import java.awt.*;
-
-public class ResidueColourScheme implements ColourSchemeI{
- Color [] colors;
- int threshold = 0;
- public Vector consensus;
-
- public ResidueColourScheme(Color[] colors, int threshold) {
- this.colors = colors;
- this.threshold = threshold;
- }
-
- public ResidueColourScheme()
- { }
-
- public void setConsensus(Vector consensus)
- {
- this.consensus = consensus;
- }
-
- public Color findColour(String aa)
- {
- return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];
- }
-
- public Color findColour(String s, int j) {
-
- if( threshold==0 || aboveThreshold(s,j))
- return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];
- else
- return Color.white;
-
- }
-
- public int getThreshold() {
- return threshold;
- }
-
- public void setThreshold(int ct) {
- threshold = ct;
- }
-
- public boolean aboveThreshold(String s, int j)
- {
- Hashtable hash = (Hashtable)consensus.elementAt(j);
-
- if ( ( (Integer) hash.get("maxCount")).intValue() != -1 && hash.contains(s))
- {
- //// resCount//////////////////// ///////////////seq count////////////
- double sc = ( (Integer) hash.get(s)).intValue() * 100.0 / ( (Integer) hash.get("size")).intValue();
-
- if (sc >= threshold)
- return true;
-
- }
-
- return false;
- }
-}
+/*
+ * 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
+ * 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
+ */
+ 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 by the percentage slider / 20
+ */
+ bleachFactor *= (inc / 20f);
+
+ int red = currentColour.getRed();
+ int green = currentColour.getGreen();
+ int blue = currentColour.getBlue();
+
+ /*
+ * bleach colours towards white (255, 255, 255),
+ * depending on the consensus score and the conservation slider value
+ * 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%
+ */
+ red += (255 - red) * bleachFactor;
+ green += (255 - green) * bleachFactor;
+ blue += (255 - blue) * bleachFactor;
+
+ if (red > 255 || green > 255 || blue > 255)
+ {
+ currentColour = Color.white;
+ }
+ else
+ {
+ currentColour = new Color(red, green, blue);
+ }
+ return currentColour;
+ }
+
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map