X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=9e226dee5eaac735a624ce1831783f161faa308d;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=2c0836de99c6d7dec867547d7579e9c3cd4c30e2;hpb=b0c3862ae342f88419e5e685de2b56f060358c05;p=jalview.git

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 2c0836d..9e226de 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,88 +1,106 @@
-/*
- * 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 ( j>=consensus.length || (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 2.9)
+ * Copyright (C) 2015 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.AAFrequency;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.Map;
+
+public class Blosum62ColourScheme extends ResidueColourScheme
+{
+  public Blosum62ColourScheme()
+  {
+    super();
+  }
+
+  @Override
+  public Color findColour(char res, int j, SequenceI seq)
+  {
+    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)
+      {
+        // TODO use a constant here?
+        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)
+        {
+          // TODO use a constant here?
+          currentColour = new Color(204, 204, 255);
+        }
+        else
+        {
+          currentColour = Color.white;
+        }
+      }
+
+      if (conservationColouring)
+      {
+        currentColour = applyConservation(currentColour, j);
+      }
+    }
+    else
+    {
+      return Color.white;
+    }
+
+    return currentColour;
+  }
+
+  @Override
+  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    ColourSchemeI newcs = super.applyTo(sg, hiddenRepSequences);
+    return newcs;
+  }
+}