JAL-3675 release notes for JAL-3750 JAL-3751

[jalview.git] / src / jalview / schemes / Blosum62ColourScheme.java

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 9c720ee..8188f4d 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,63 +1,118 @@
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
-*/\r
-package jalview.schemes;\r
-\r
-import java.awt.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-public class Blosum62ColourScheme extends ResidueColourScheme {\r
-    public Blosum62ColourScheme() {\r
-        super();\r
-    }\r
-\r
-    public Color findColour(String s, int j) {\r
-        if ((threshold != 0) && !aboveThreshold(s, j)) {\r
-            return Color.white;\r
-        }\r
-\r
-        Hashtable hash = (Hashtable) consensus.elementAt(j);\r
-\r
-        if (!jalview.util.Comparison.isGap((s.charAt(0)))) {\r
-            String max = (String) hash.get("maxResidue");\r
-\r
-            if (max.indexOf(s) > -1) {\r
-                return new Color(154, 154, 255);\r
-            } else {\r
-                int c = 0;\r
-                int max_aa = 0;\r
-                int n = max.length();\r
-\r
-                do {\r
-                    c += ResidueProperties.getBLOSUM62(max.substring(max_aa,\r
-                            max_aa + 1), s);\r
-                } while (++max_aa < n);\r
-\r
-                if (c > 0) {\r
-                    return new Color(204, 204, 255);\r
-                } else {\r
-                    return Color.white;\r
-                }\r
-            }\r
-        } else {\r
-            return Color.white;\r
-        }\r
-    }\r
-}\r
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+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 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();
+  }
+
+  /**
+   * 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')
+    {
+      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;
+  }
+}