JAL-3210 Barebones gradle/buildship/eclipse. See README

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

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index df6610a..5f84ca0 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -498,35 +498,34 @@ public class ResidueProperties
    * Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap
    */
 
-  public static final String STOP = "STOP";
+  public static String STOP = "STOP";
 
-  public static final List<String> STOP_CODONS = Arrays.asList("TGA", "TAA",
-          "TAG");
+  public static List<String> STOP_CODONS = Arrays.asList("TGA", "TAA", "TAG");
 
-  public static final String START = "ATG";
+  public static String START = "ATG";
 
   // Stores residue codes/names and colours and other things
-  public static final Map<String, Map<String, Integer>> propHash = new Hashtable<>();
+  public static Map<String, Map<String, Integer>> propHash = new Hashtable<>();
 
-  public static final Map<String, Integer> hydrophobic = new Hashtable<>();
+  public static Map<String, Integer> hydrophobic = new Hashtable<>();
 
-  public static final Map<String, Integer> polar = new Hashtable<>();
+  public static Map<String, Integer> polar = new Hashtable<>();
 
-  public static final Map<String, Integer> small = new Hashtable<>();
+  public static Map<String, Integer> small = new Hashtable<>();
 
-  public static final Map<String, Integer> positive = new Hashtable<>();
+  public static Map<String, Integer> positive = new Hashtable<>();
 
-  public static final Map<String, Integer> negative = new Hashtable<>();
+  public static Map<String, Integer> negative = new Hashtable<>();
 
-  public static final Map<String, Integer> charged = new Hashtable<>();
+  public static Map<String, Integer> charged = new Hashtable<>();
 
-  public static final Map<String, Integer> aromatic = new Hashtable<>();
+  public static Map<String, Integer> aromatic = new Hashtable<>();
 
-  public static final Map<String, Integer> aliphatic = new Hashtable<>();
+  public static Map<String, Integer> aliphatic = new Hashtable<>();
 
-  public static final Map<String, Integer> tiny = new Hashtable<>();
+  public static Map<String, Integer> tiny = new Hashtable<>();
 
-  public static final Map<String, Integer> proline = new Hashtable<>();
+  public static Map<String, Integer> proline = new Hashtable<>();
 
   static
   {
@@ -897,7 +896,8 @@ public class ResidueProperties
 
   public static String codonTranslate(String lccodon)
   {
-    String peptide = GeneticCodes.getStandardCodeTable().translate(lccodon);
+    String peptide = GeneticCodes.getInstance().getStandardCodeTable()
+            .translate(lccodon);
     if ("*".equals(peptide))
     {
       return "STOP";
@@ -909,7 +909,7 @@ public class ResidueProperties
    * lookup of (A-Z) alternative secondary structure symbols'
    * equivalents in DSSP3 notation
    */
-  private final static char[] toDssp3State;
+  private static char[] toDssp3State;
   static
   {
     toDssp3State = new char[9]; // for 'A'-'I'; extend if needed