X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=9e226dee5eaac735a624ce1831783f161faa308d;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=d0546dccc266acf4ffd169d0b0f89c6814afcc60;hpb=b78278b3ee2cb653c439fa207b78a469d53ce697;p=jalview.git

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index d0546dc..9e226de 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,64 +1,106 @@
-/* Jalview - a java multiple alignment editor
- * Copyright (C) 1998  Michele Clamp
- *
- * 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., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
- */
-
-package jalview.schemes;
-
-
-import java.util.*;
-import java.awt.*;
-import jalview.gui.*;
-import jalview.datamodel.*;
-
-public class Blosum62ColourScheme extends ResidueColourScheme
-{
-
-  // need to keep an eye on the changing visible consensus sequence
-  AlignViewport av;
-
-  public Blosum62ColourScheme(AlignViewport av)
-  {
-    super();
-    this.av = av;
-  }
-
-  public Color findColour(String s, int j, Vector aa)
-  {
-
-      if (!jalview.util.Comparison.isGap((s.charAt(0))))
-      {
-        String max = av.getVisibleConsensus().charAt(j) + "";
-
-        if (s.equals(max))
-          return new Color(154, 154, 255);
-        else if (ResidueProperties.getBLOSUM62(max, s) > 0)
-          return new Color(204, 204, 255);
-        else
-          return Color.white;
-
-      }
-      else
-        return Color.white;
-
-  }
-
-  public boolean canThreshold()
-  {
-    return false;
-  }
-
-}
+/*
+ * 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;
+  }
+}