X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemes%2FScoreColourScheme.java;h=e1b60cafac5e8d50419c31bc6503c5b127f4e383;hb=f2a83f0360d406859b80cc798099a9d270461bb3;hp=b942d10e869308d8a4646bc8848a7511fdd25f2e;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index b942d10..e1b60ca 100755
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -1,23 +1,32 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 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 .
+ * 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 java.awt.*;
+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!
@@ -27,13 +36,10 @@ import java.awt.*;
*/
public class ScoreColourScheme extends ResidueColourScheme
{
- /** DOCUMENT ME!! */
public double min;
- /** DOCUMENT ME!! */
public double max;
- /** DOCUMENT ME!! */
public double[] scores;
/**
@@ -46,9 +52,10 @@ public class ScoreColourScheme extends ResidueColourScheme
* @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;
@@ -56,58 +63,36 @@ public class ScoreColourScheme extends ResidueColourScheme
// Make colours in constructor
// Why wasn't this done earlier?
- int i, iSize = scores.length;
+ int iSize = scores.length;
colors = new Color[scores.length];
- for (i = 0; i < iSize; i++)
+ for (int i = 0; i < iSize; i++)
{
- float red = (float) (scores[i] - (float) min) / (float) (max - min);
+ /*
+ * scale score between min and max to the range 0.0 - 1.0
+ */
+ float score = (float) (scores[i] - (float) min) / (float) (max - min);
- if (red > 1.0f)
+ if (score > 1.0f)
{
- red = 1.0f;
+ score = 1.0f;
}
- if (red < 0.0f)
+ if (score < 0.0f)
{
- red = 0.0f;
+ score = 0.0f;
}
- colors[i] = makeColour(red);
+ colors[i] = makeColour(score);
}
}
- /**
- * DOCUMENT ME!
- *
- * @param s
- * DOCUMENT ME!
- * @param j
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Color findColour(char c, int j)
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
{
- if (threshold > 0)
- {
- if (!aboveThreshold(c, j))
- {
- return Color.white;
- }
- }
-
- if (jalview.util.Comparison.isGap(c))
+ if (Comparison.isGap(c))
{
return Color.white;
}
-
- Color currentColour = colors[ResidueProperties.aaIndex[c]];
-
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
-
- return currentColour;
+ return super.findColour(c);
}
/**
@@ -122,4 +107,21 @@ public class ScoreColourScheme extends ResidueColourScheme
{
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);
+ }
}