X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=02f9b3e3d9f55bf5159699a8da8eb145931a3ce6;hb=7047b076a62df177047ceb16c3611efe020bdd76;hp=6e91e0b2256677455e368362efb51ae48ca60cb3;hpb=95a46891288f4fc63d690cab4f56879678f54fb6;p=jalview.git
diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 6e91e0b..02f9b3e 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,88 +1,119 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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 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.
- *
- * 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
- */
-package jalview.schemes;
-
-
-import java.awt.*;
-
-public class Blosum62ColourScheme
- extends ResidueColourScheme
-{
- public Blosum62ColourScheme()
- {
- super();
- }
-
- public Color findColour(String s, int j)
- {
- char res = s.charAt(0);
- if ('a' <= res && res <= 'z' )
- {
- // TO UPPERCASE !!!
- s = String.valueOf( res -= ('a' - 'A') );
- }
-
-
- if ( (threshold != 0) && !aboveThreshold(s, j))
- {
- return Color.white;
- }
-
- if (!jalview.util.Comparison.isGap( res ))
- {
- String max = (String) consensus[j].get("maxResidue");
-
- if (max.indexOf(s) > -1)
- {
- currentColour = new Color(154, 154, 255);
- }
- else
- {
- int c = 0;
- int max_aa = 0;
- int n = max.length();
-
- do
- {
- c += ResidueProperties.getBLOSUM62(max.substring(max_aa,
- max_aa + 1), s);
- }
- while (++max_aa < n);
-
- if (c > 0)
- {
- currentColour = new Color(204, 204, 255);
- }
- else
- {
- currentColour = Color.white;
- }
- }
-
- if(conservationColouring)
- applyConservation(j);
- }
- else
- {
- return Color.white;
- }
-
- return currentColour;
- }
-}
+/*
+ * 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.analysis.PairwiseScoreModelI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+
+import java.awt.Color;
+import java.util.Map;
+
+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();
+ }
+
+ /**
+ * 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 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')
+ {
+ res -= ('a' - 'A');
+ }
+
+ if (Comparison.isGap(res) || consensusResidue == null)
+ {
+ return Color.white;
+ }
+
+ Color colour;
+
+ if (consensusResidue.indexOf(res) > -1)
+ {
+ colour = DARK_BLUE;
+ }
+ else
+ {
+ float score = 0;
+
+ for (char consensus : consensusResidue.toCharArray())
+ {
+ score += sm.getPairwiseScore(consensus, res);
+ }
+
+ if (score > 0)
+ {
+ colour = LIGHT_BLUE;
+ }
+ else
+ {
+ colour = Color.white;
+ }
+ }
+ return colour;
+ }
+
+ @Override
+ public boolean isPeptideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.Blosum62.toString();
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
+}