X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=e1b60cafac5e8d50419c31bc6503c5b127f4e383;hb=refs%2Fheads%2Fbug%2FJAL-2842;hp=134ed4cb64cc2695c54647b6346832f48562eb1c;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 134ed4c..e1b60ca 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,121 +1,127 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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.*;
-
-/**
- * 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(double[] scores, double min, double max)
- {
- super();
-
- 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 s DOCUMENT ME!
- * @param j DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Color findColour(char c, int j)
- {
- if (threshold > 0)
- {
- if (!aboveThreshold(c, j))
- {
- return Color.white;
- }
- }
-
- if (jalview.util.Comparison.isGap(c))
- {
- return Color.white;
- }
-
- Color currentColour = colors[ResidueProperties.aaIndex[c]];
-
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
-
- return currentColour;
- }
-
- /**
- * 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);
- }
-}
+/*
+ * 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 jalview.util.Comparison;
+
+import java.awt.Color;
+import java.util.Map;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class ScoreColourScheme extends ResidueColourScheme
+{
+ public double min;
+
+ public double max;
+
+ 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 iSize = scores.length;
+ colors = new Color[scores.length];
+ for (int i = 0; i < iSize; i++)
+ {
+ /*
+ * scale score between min and max to the range 0.0 - 1.0
+ */
+ float score = (float) (scores[i] - (float) min) / (float) (max - min);
+
+ if (score > 1.0f)
+ {
+ score = 1.0f;
+ }
+
+ if (score < 0.0f)
+ {
+ score = 0.0f;
+ }
+ colors[i] = makeColour(score);
+ }
+ }
+
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ if (Comparison.isGap(c))
+ {
+ return Color.white;
+ }
+ return super.findColour(c);
+ }
+
+ /**
+ * 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);
+ }
+}