Merge branch 'releases/Release_2_11_4_Branch'

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

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index f8b7856..9d83069 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -42,6 +42,8 @@ public class ResidueProperties
 
   public static final int[] purinepyrimidineIndex;
 
+  public static final int[] secondaryStructureIndex;
+
   public static final Map<String, Integer> aa3Hash = new HashMap<>();
 
   public static final Map<String, String> aa2Triplet = new HashMap<>();
@@ -196,6 +198,19 @@ public class ResidueProperties
     purinepyrimidineIndex['n'] = 2;
   }
 
+  static
+  {
+    secondaryStructureIndex = new int[255];
+    for (int i = 0; i < 255; i++)
+    {
+      secondaryStructureIndex[i] = 3;
+    }
+
+    secondaryStructureIndex['H'] = 0;
+    secondaryStructureIndex['E'] = 1;
+    secondaryStructureIndex['C'] = 2;
+  }
+
   private static final Integer ONE = Integer.valueOf(1);
 
   private static final Integer ZERO = Integer.valueOf(0);
@@ -384,6 +399,12 @@ public class ResidueProperties
       Color.white // Gap
   };
 
+  // Secondary structure
+  public static final Color[] secondarystructure = { Color.red, // H
+      Color.green, // E
+      Color.gray // C
+  };
+
   // Zappo
   public static final Color[] zappo = { Color.pink, // A
       midBlue, // R
@@ -2449,7 +2470,8 @@ public class ResidueProperties
           jalview.bin.Console.outPrintln(", ");
         }
       }
-      jalview.bin.Console.outPrintln("]" + (res.hasMoreElements() ? "," : ""));
+      jalview.bin.Console
+              .outPrintln("]" + (res.hasMoreElements() ? "," : ""));
     }
     jalview.bin.Console.outPrintln("};");
   }