X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueColourScheme.java;h=f6b7c5e16e31cd3da8f34f14597aa751cb071c90;hb=8b1e1c7cf7bcf6499dad546699c85d8d52e6d86c;hp=f16bccac39f58c3c8f22b7afa8594fd29f10c03c;hpb=341565559999a3c6a88f263e4ff0a6e8eacf09bd;p=jalview.git
diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index f16bcca..f6b7c5e 100755
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,90 +1,346 @@
-package jalview.schemes;
-
-import jalview.datamodel.*;
-import java.util.*;
-import java.awt.*;
-
-public class ResidueColourScheme implements ColourSchemeI{
- Color [] colors;
- int threshold = 90;
-
- public ResidueColourScheme(Color[] colors, int threshold) {
- this.colors = colors;
- this.threshold = threshold;
- }
-
- public ResidueColourScheme() {
- }
-
- public Color findColour(String aa)
- {
- return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];
- }
-
- public Color findColour(SequenceI seq,String s, int j, Vector aa) {
- try {
- return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];
- } catch (Exception e) {
- return Color.white;
- }
- }
-
- // aa should maybe be a class
- /* public Color getColour(SequenceI seq, int j,Vector aa) {
-
- Color c = Color.white;
- String s = seq.getSequence(j,j+1);
-
- if (threshold > 0 && aa != null)
- {
- if (aboveThreshold(aa,seq,j,threshold))
- c = findColour(seq,s,j,aa);
- }
- else
- c = findColour(seq,s,j,aa);
-
-
- return c;
- }*/
-
- public int getThreshold() {
- return threshold;
- }
-
- public void setThreshold(int ct) {
- threshold = ct;
- }
-
- public boolean aboveThreshold(Vector aa,SequenceI seq, int j, int threshold) {
- String s = seq.getSequence(j,j+1);
- Hashtable hash = (Hashtable)aa.elementAt(j);
-
- if (j < aa.size()) {
- String maxRes = (String)hash.get("maxResidue");
-
- double sc = 0;
-
- if (((Integer)hash.get("maxCount")).intValue() != -1 && hash.contains(s)) {
- int maxCount = ((Integer)hash.get("maxCount")).intValue();
- int resCount = ((Integer)hash.get(s)).intValue();
-
- sc = resCount * 100.0 / resCount;
-
- // This should be isGap somewhere
- if ( !s.equals("-") && !s.equals(".") && !s.equals(" ")) {
- if (sc >= (double)threshold) {
- return true;
- }
- }
- }
- }
- return false;
- }
-
- public boolean canThreshold() {
- return true;
- }
- public boolean isUserDefinable() {
- 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 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);
+
+ return ColorUtils.bleachColour(currentColour, bleachFactor);
+ }
+
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map