JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 2c0836d..9e226de 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,88 +1,106 @@
-/*\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
-\r
-import java.awt.*;\r
-\r
-public class Blosum62ColourScheme\r
-    extends ResidueColourScheme\r
-{\r
-  public Blosum62ColourScheme()\r
-  {\r
-    super();\r
-  }\r
-\r
-  public Color findColour(String s, int j)\r
-  {\r
-    char res = s.charAt(0);\r
-    if ('a' <= res && res <= 'z' )\r
-    {\r
-       // TO UPPERCASE !!!\r
-       s = String.valueOf( res -= ('a' - 'A') );\r
-    }\r
-\r
-\r
-    if ( j>=consensus.length || (threshold != 0 && !aboveThreshold(s, j) ))\r
-    {\r
-      return Color.white;\r
-    }\r
-\r
-    if (!jalview.util.Comparison.isGap( res ))\r
-    {\r
-      String max = (String) consensus[j].get("maxResidue");\r
-\r
-      if (max.indexOf(s) > -1)\r
-      {\r
-        currentColour = new Color(154, 154, 255);\r
-      }\r
-      else\r
-      {\r
-        int c = 0;\r
-        int max_aa = 0;\r
-        int n = max.length();\r
-\r
-        do\r
-        {\r
-          c += ResidueProperties.getBLOSUM62(max.substring(max_aa,\r
-              max_aa + 1), s);\r
-        }\r
-        while (++max_aa < n);\r
-\r
-        if (c > 0)\r
-        {\r
-          currentColour = new Color(204, 204, 255);\r
-        }\r
-        else\r
-        {\r
-          currentColour = Color.white;\r
-        }\r
-      }\r
-\r
-      if(conservationColouring)\r
-         applyConservation(j);\r
-    }\r
-    else\r
-    {\r
-      return Color.white;\r
-    }\r
-\r
-    return currentColour;\r
-  }\r
-}\r
+/*
+ * 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;
+  }
+}