X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=aa20121dc616bf9489ff9d5937ad8ca7050f62d7;hb=aa2c6fc3fbfa5a5a60ffd3bfeb6321f1d5e4a2f2;hp=12f252d69106e6cc70d73092b0adc162f90f2007;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git
diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 12f252d..aa20121 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,68 +1,116 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program 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 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-package jalview.schemes;
-
-import java.awt.*;
-
-
-public class ScoreColourScheme extends ResidueColourScheme {
- public double min;
- public double max;
- public double[] scores;
-
- public ScoreColourScheme(double[] scores, double min, double max) {
- super();
-
- this.scores = scores;
- this.min = min;
- this.max = max;
- }
-
- public Color findColour(String s, int j) {
- if (threshold > 0) {
- if (!aboveThreshold(s, j)) {
- return Color.white;
- }
- }
-
- float red = (float) (scores[((Integer) ResidueProperties.aaHash.get(s)).intValue()] -
- (float) min) / (float) (max - min);
-
- if (red > 1.0f) {
- red = 1.0f;
- }
-
- if (red < 0.0f) {
- red = 0.0f;
- }
-
- char c = s.charAt(0);
-
- if (jalview.util.Comparison.isGap((c))) {
- return Color.white;
- }
-
- // This isn';t great - pool of colours in here?
- return makeColour(red);
- }
-
- public Color makeColour(float c) {
- return new Color(c, (float) 0.0, (float) 1.0 - 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.SequenceI;
+
+import java.awt.Color;
+import java.util.Map;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ScoreColourScheme extends ResidueColourScheme
+{
+ /** DOCUMENT ME!! */
+ public double min;
+
+ /** DOCUMENT ME!! */
+ public double max;
+
+ /** DOCUMENT ME!! */
+ public double[] scores;
+
+ /**
+ * Creates a new ScoreColourScheme object.
+ *
+ * @param scores
+ * DOCUMENT ME!
+ * @param min
+ * DOCUMENT ME!
+ * @param max
+ * DOCUMENT ME!
+ */
+ public ScoreColourScheme(int symbolIndex[], double[] scores, double min,
+ double max)
+ {
+ super(symbolIndex);
+
+ this.scores = scores;
+ this.min = min;
+ this.max = max;
+
+ // Make colours in constructor
+ // Why wasn't this done earlier?
+ int i, iSize = scores.length;
+ colors = new Color[scores.length];
+ for (i = 0; i < iSize; i++)
+ {
+ float red = (float) (scores[i] - (float) min) / (float) (max - min);
+
+ if (red > 1.0f)
+ {
+ red = 1.0f;
+ }
+
+ if (red < 0.0f)
+ {
+ red = 0.0f;
+ }
+ colors[i] = makeColour(red);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color makeColour(float c)
+ {
+ return new Color(c, (float) 0.0, (float) 1.0 - c);
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return "Score";
+ }
+
+ /**
+ * 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 ScoreColourScheme(symbolIndex, scores, min, max);
+ }
+}