X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=8188f4d91583c39aeddbbee3d22e4968c477b081;hb=a7169b1c72607f3c9357195b4999869650a2a891;hp=0a943bdfa9247782977b7be9cbb794917d988271;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 0a943bd..8188f4d 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,88 +1,118 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * 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.analysis.scoremodels.ScoreModels;
+import jalview.api.AlignViewportI;
+import jalview.api.analysis.PairwiseScoreModelI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
-import jalview.analysis.*;
+import java.awt.Color;
public class Blosum62ColourScheme extends ResidueColourScheme
{
+ private static final Color LIGHT_BLUE = new Color(204, 204, 255);
+
+ private static final Color DARK_BLUE = new Color(154, 154, 255);
+
public Blosum62ColourScheme()
{
super();
}
- public Color findColour(char res, int j)
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
+ return new Blosum62ColourScheme();
+ }
+
+ @Override
+ public Color findColour(char res, int j, SequenceI seq,
+ String consensusResidue, float pid)
+ {
+ PairwiseScoreModelI sm = ScoreModels.getInstance().getBlosum62();
+
+ /*
+ * compare as upper case; note consensusResidue is
+ * always computed as uppercase
+ */
if ('a' <= res && res <= 'z')
{
- // TO UPPERCASE !!!
res -= ('a' - 'A');
}
- if (consensus == null || j >= consensus.length || consensus[j] == null
- || (threshold != 0 && !aboveThreshold(res, j)))
+ if (Comparison.isGap(res) || consensusResidue == null)
{
return Color.white;
}
- Color currentColour;
+ Color colour;
- if (!jalview.util.Comparison.isGap(res))
+ if (consensusResidue.indexOf(res) > -1)
{
- String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
+ colour = DARK_BLUE;
+ }
+ else
+ {
+ float score = 0;
- if (max.indexOf(res) > -1)
+ for (char consensus : consensusResidue.toCharArray())
{
- currentColour = new Color(154, 154, 255);
+ score += sm.getPairwiseScore(consensus, res);
}
- else
+
+ if (score > 0)
{
- int c = 0;
- int max_aa = 0;
- int n = max.length();
-
- do
- {
- c += ResidueProperties.getBLOSUM62(max.charAt(max_aa), res);
- } while (++max_aa < n);
-
- if (c > 0)
- {
- currentColour = new Color(204, 204, 255);
- }
- else
- {
- currentColour = Color.white;
- }
+ colour = LIGHT_BLUE;
}
-
- if (conservationColouring)
+ else
{
- currentColour = applyConservation(currentColour, j);
+ colour = Color.white;
}
}
- else
- {
- return Color.white;
- }
+ return colour;
+ }
- return currentColour;
+ @Override
+ public boolean isPeptideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.Blosum62.toString();
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
}
}