X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=aa20121dc616bf9489ff9d5937ad8ca7050f62d7;hb=ff8c06845590fd9fd423aa59809dcce9610ab295;hp=9514ac52e54751805ee456b4e2f3bc22cc8dfe10;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git
diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 9514ac5..aa20121 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,24 +1,31 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * 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!
@@ -41,15 +48,16 @@ public class ScoreColourScheme extends ResidueColourScheme
* Creates a new ScoreColourScheme object.
*
* @param scores
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param min
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param max
- * DOCUMENT ME!
+ * 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;
@@ -79,48 +87,30 @@ public class ScoreColourScheme extends ResidueColourScheme
/**
* DOCUMENT ME!
*
- * @param s
- * DOCUMENT ME!
- * @param j
- * DOCUMENT ME!
+ * @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 hrs)
{
- return new Color(c, (float) 0.0, (float) 1.0 - c);
+ return new ScoreColourScheme(symbolIndex, scores, min, max);
}
}