/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
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!
/**
* DOCUMENT ME!
*
- * @param s
- * DOCUMENT ME!
- * @param j
+ * @param c
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- @Override
- public Color findColour(char c, int j, SequenceI seq)
+ 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);
}
}