X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=8188f4d91583c39aeddbbee3d22e4968c477b081;hb=HEAD;hp=02545a3272fad1dfeb5973aa7f3f5fe1dfeff24f;hpb=4d2e0d36506302cc00677527725bcccbdf27d766;p=jalview.git

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 02545a3..8188f4d 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,92 +1,118 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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.*;
-import jalview.analysis.AAFrequency;
-
-public class Blosum62ColourScheme
-    extends ResidueColourScheme
-{
-  public Blosum62ColourScheme()
-  {
-    super();
-  }
-
-  public Color findColour(char res, int j)
-  {
-    if ('a' <= res && res <= 'z' )
-    {
-       // TO UPPERCASE !!!
-       res -= ('a' - 'A');
-    }
-
-    if (consensus == null ||
-        j >= consensus.length ||
-        consensus[j] == null ||
-        (threshold != 0 && !aboveThreshold(res, j)))
-    {
-      return Color.white;
-    }
-
-    Color currentColour;
-
-    if (!jalview.util.Comparison.isGap( res ))
-    {
-      String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
-
-      if (max.indexOf(res) > -1)
-      {
-        currentColour = new Color(154, 154, 255);
-      }
-      else
-      {
-        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;
-        }
-      }
-
-      if(conservationColouring)
-       currentColour =  applyConservation(currentColour, 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 <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;
+  }
+}