JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

[jalview.git] / src / jalview / analysis / GeneticCodes.java

diff --git a/src/jalview/analysis/GeneticCodes.java b/src/jalview/analysis/GeneticCodes.java
index 137b7f8..69a3846 100644 (file)
--- a/src/jalview/analysis/GeneticCodes.java
+++ b/src/jalview/analysis/GeneticCodes.java
@@ -12,13 +12,30 @@ import java.util.Map;
 import java.util.StringTokenizer;
 
 /**
- * A singleton that provides instances of genetic code translation tables
+ * A static class that provides instances of genetic code translation tables
  * 
  * @author gmcarstairs
  * @see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
  */
 public final class GeneticCodes
 {
+
+  /**
+   * As implemented, this has to be the first table defined in the data file.
+   */
+  private static GeneticCodeI standardTable;
+
+  /**
+   * 
+   * @return the standard code table (table 1)
+   */
+  public static GeneticCodeI getStandardCodeTable()
+  {
+    return (standardTable == null
+            ? standardTable = codeTables.values().iterator().next()
+            : standardTable);
+  }
+
   private static final int CODON_LENGTH = 3;
 
   private static final String QUOTE = "\"";
@@ -39,42 +56,31 @@ public final class GeneticCodes
 
   private static final String RESOURCE_FILE = "/GeneticCodes.dat";
 
-  private static GeneticCodes instance = new GeneticCodes();
-
-  private Map<String, String> ambiguityCodes;
+  private static final Map<String, String> ambiguityCodes;
 
   /*
    * loaded code tables, with keys in order of loading 
    */
-  private Map<String, GeneticCodeI> codeTables;
+  private static final Map<String, GeneticCodeI> codeTables;
 
-  /**
-   * Private constructor enforces singleton
-   */
-  private GeneticCodes()
+  static
   {
-    if (instance == null)
-    {
-      ambiguityCodes = new HashMap<>();
+    ambiguityCodes = new HashMap<>();
 
-      /*
-       * LinkedHashMap preserves order of addition of entries,
-       * so we can assume the Standard Code Table is the first
-       */
-      codeTables = new LinkedHashMap<>();
-      loadAmbiguityCodes(AMBIGUITY_CODES_FILE);
-      loadCodes(RESOURCE_FILE);
-    }
+    /*
+     * LinkedHashMap preserves order of addition of entries,
+     * so we can assume the Standard Code Table is the first
+     */
+    codeTables = new LinkedHashMap<>();
+    loadAmbiguityCodes(AMBIGUITY_CODES_FILE);
+    loadCodes(RESOURCE_FILE);
   }
 
   /**
-   * Returns the singleton instance of this class
-   * 
-   * @return
+   * Private constructor enforces no instantiation
    */
-  public static GeneticCodes getInstance()
+  private GeneticCodes()
   {
-    return instance;
   }
 
   /**
@@ -82,41 +88,30 @@ public final class GeneticCodes
    * 
    * @return
    */
-  public Iterable<GeneticCodeI> getCodeTables()
+  public static Iterable<GeneticCodeI> getCodeTables()
   {
     return codeTables.values();
   }
 
   /**
-   * Answers the code table with the given id
+   * Answers the code table with the given id -- test suite only
    * 
    * @param id
    * @return
    */
-  public GeneticCodeI getCodeTable(String id)
+  public static GeneticCodeI getCodeTable(String id)
   {
     return codeTables.get(id);
   }
 
   /**
-   * A convenience method that returns the standard code table (table 1). As
-   * implemented, this has to be the first table defined in the data file.
-   * 
-   * @return
-   */
-  public GeneticCodeI getStandardCodeTable()
-  {
-    return codeTables.values().iterator().next();
-  }
-
-  /**
    * Loads the code tables from a data file
    */
-  protected void loadCodes(String fileName)
+  private static void loadCodes(String fileName)
   {
     try
     {
-      InputStream is = getClass().getResourceAsStream(fileName);
+      InputStream is = GeneticCodes.class.getResourceAsStream(fileName);
       if (is == null)
       {
         System.err.println("Resource file not found: " + fileName);
@@ -163,11 +158,11 @@ public final class GeneticCodes
    * 
    * @param fileName
    */
-  protected void loadAmbiguityCodes(String fileName)
+  private static void loadAmbiguityCodes(String fileName)
   {
     try
     {
-      InputStream is = getClass().getResourceAsStream(fileName);
+      InputStream is = GeneticCodes.class.getResourceAsStream(fileName);
       if (is == null)
       {
         System.err.println("Resource file not found: " + fileName);
@@ -209,7 +204,7 @@ public final class GeneticCodes
    * @return
    * @throws IOException
    */
-  protected String readLine(BufferedReader dataIn) throws IOException
+  private static String readLine(BufferedReader dataIn) throws IOException
   {
     String line = dataIn.readLine();
     while (line != null && line.startsWith("#"))
@@ -247,7 +242,8 @@ public final class GeneticCodes
    * @return
    * @throws IOException
    */
-  protected String loadOneTable(BufferedReader dataIn) throws IOException
+  private static String loadOneTable(BufferedReader dataIn)
+          throws IOException
   {
     String name = null;
     String id = null;
@@ -307,7 +303,7 @@ public final class GeneticCodes
    * @param name
    * @param codons
    */
-  protected void registerCodeTable(final String id, final String name,
+  private static void registerCodeTable(final String id, final String name,
           final Map<String, String> codons)
   {
     codeTables.put(id, new GeneticCodeI()
@@ -365,7 +361,7 @@ public final class GeneticCodes
    * @param codeTable
    * @return
    */
-  protected String getAmbiguousTranslation(String codon,
+  protected static String getAmbiguousTranslation(String codon,
           Map<String, String> ambiguous, GeneticCodeI codeTable)
   {
     if (codon.length() != CODON_LENGTH)
@@ -423,4 +419,5 @@ public final class GeneticCodes
     ambiguous.put(codon, peptide);
     return peptide;
   }
+
 }