X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=fc922b936dc50605078944ddfe1cba2f407e0396;hb=f2a83f0360d406859b80cc798099a9d270461bb3;hp=312ae7d534ce8a8ce8bcc38419e4063788c9f262;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git
diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 312ae7d..fc922b9 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,61 +1,106 @@
-package jalview.schemes;
-
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-
-import java.util.*;
-import java.awt.*;
-
-public class PIDColourScheme extends ResidueColourScheme {
- public Color[] pidColours;
- public float[] thresholds;
-
- SequenceGroup group;
-
- public PIDColourScheme() {
- this.pidColours = ResidueProperties.pidColours;
- this.thresholds = ResidueProperties.pidThresholds;
- }
- public Color getColour(SequenceI seq, int j,Vector aa) {
- Color c = Color.white;
-
- String s = seq.getSequence(j,j+1);
-
- if (aa != null && j < aa.size()) {
- c = findColour(seq,s,j,aa);
- }
-
- return c;
- }
-
- public Color findColour(SequenceI seq,String s, int j,Vector aa) {
- Color c = Color.white;
- Hashtable hash = null;
-
- if (aa != null) {
- hash = (Hashtable)aa.elementAt(j);
- }
- else
- return c;
-
- String max = (String)hash.get("maxResidue");
-
- double sc = 0;
- if (((Integer)hash.get("maxCount")).intValue() != -1 && hash.contains(s)) {
- sc = ((Integer)hash.get(s)).intValue()*100.0/Integer.parseInt((String)hash.get("maxResidue"));
-
- // MC Should be isGap
- if ( !s.equals("-") && !s.equals(".") && !s.equals(" ")) {
- for (int i=0; i < thresholds.length; i++) {
- if (sc > thresholds[i]) {
- c = pidColours[i];
- break;
- }
- }
- } else {
- c = Color.white;
- }
- }
- return c;
- }
-}
+/*
+ * 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.schemes;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+
+import java.awt.Color;
+import java.util.Map;
+
+public class PIDColourScheme extends ResidueColourScheme
+{
+ private static final Color[] pidColours = { new Color(100, 100, 255),
+ new Color(153, 153, 255), new Color(204, 204, 255), };
+
+ private static final float[] thresholds = { 80, 60, 40, };
+
+ SequenceGroup group;
+
+ public PIDColourScheme()
+ {
+ }
+
+ @Override
+ public Color findColour(char c, int j, SequenceI seq,
+ String consensusResidue, float pid)
+ {
+ /*
+ * compare as upper case; note consensusResidue is
+ * always computed as uppercase
+ */
+ if ('a' <= c && c <= 'z')
+ {
+ c -= ('a' - 'A');
+ }
+
+ if (consensusResidue == null || Comparison.isGap(c))
+ {
+ return Color.white;
+ }
+
+ Color colour = Color.white;
+
+ /*
+ * test whether this is the consensus (or joint consensus) residue
+ */
+ boolean matchesConsensus = consensusResidue.contains(String.valueOf(c));
+ if (matchesConsensus)
+ {
+ for (int i = 0; i < thresholds.length; i++)
+ {
+ if (pid > thresholds[i])
+ {
+ colour = pidColours[i];
+ break;
+ }
+ }
+ }
+
+ return colour;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.PID.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map hrs)
+ {
+ return new PIDColourScheme();
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
+}