/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
- *
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import java.awt.*;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.Map;
/**
* DOCUMENT ME!
* @param max
* DOCUMENT ME!
*/
- public ScoreColourScheme(double[] scores, double min, double max)
+ public ScoreColourScheme(int symbolIndex[], double[] scores, double min,
+ double max)
{
- super();
+ super(symbolIndex);
this.scores = scores;
this.min = min;
/**
* DOCUMENT ME!
*
- * @param s
- * DOCUMENT ME!
- * @param j
+ * @param c
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public Color findColour(char c, int j)
+ public Color makeColour(float c)
{
- 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 new Color(c, (float) 0.0, (float) 1.0 - c);
+ }
- return currentColour;
+ @Override
+ public String getSchemeName()
+ {
+ return "Score";
}
/**
- * DOCUMENT ME!
- *
- * @param c
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
*/
- public Color makeColour(float c)
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
{
- return new Color(c, (float) 0.0, (float) 1.0 - c);
+ return new ScoreColourScheme(symbolIndex, scores, min, max);
}
}