Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet

[jalview.git] / test / jalview / analysis / GeneticCodesTest.java

diff --git a/test/jalview/analysis/GeneticCodesTest.java b/test/jalview/analysis/GeneticCodesTest.java
index d5634db..f80b92d 100644 (file)
--- a/test/jalview/analysis/GeneticCodesTest.java
+++ b/test/jalview/analysis/GeneticCodesTest.java
@@ -14,26 +14,26 @@ public class GeneticCodesTest
   @Test(groups = "Functional")
   public void testGetCodeTable()
   {
-    GeneticCodes codes = GeneticCodes.getInstance();
-    assertEquals(codes.getStandardCodeTable().getName(), "Standard");
-    assertEquals(codes.getStandardCodeTable().getId(), "1");
-    assertSame(codes.getStandardCodeTable(), codes.getCodeTable("1"));
-    assertEquals(codes.getCodeTable("2").getName(),
+    assertEquals(GeneticCodes.getStandardCodeTable().getName(), "Standard");
+    assertEquals(GeneticCodes.getStandardCodeTable().getId(), "1");
+    assertSame(GeneticCodes.getStandardCodeTable(),
+            GeneticCodes.getCodeTable("1"));
+    assertEquals(GeneticCodes.getCodeTable("2").getName(),
             "Vertebrate Mitochondrial");
-    assertEquals(codes.getCodeTable("11").getName(),
+    assertEquals(GeneticCodes.getCodeTable("11").getName(),
             "Bacterial, Archaeal and Plant Plastid");
-    assertEquals(codes.getCodeTable("31").getName(),
+    assertEquals(GeneticCodes.getCodeTable("31").getName(),
             "Blastocrithidia Nuclear");
   }
 
   @Test(groups = "Functional")
   public void testGetCodeTables()
   {
-    GeneticCodes codes = GeneticCodes.getInstance();
-    Iterator<GeneticCodeI> tableIterator = codes.getCodeTables().iterator();
+    Iterator<GeneticCodeI> tableIterator = GeneticCodes.getCodeTables()
+            .iterator();
     String[] ids = new String[] { "1", "2", "3", "4", "5", "6", "9", "10",
-        "11", "12", "13", "14", "16", "21", "22", "23", "24", "25", "26",
-        "27", "28", "29", "30", "31" };
+        "11", "12", "13", "14", "15", "16", "21", "22", "23", "24", "25",
+        "26", "27", "28", "29", "30", "31" };
     for (int i = 0; i < ids.length; i++)
     {
       assertEquals(tableIterator.next().getId(), ids[i]);
@@ -44,21 +44,19 @@ public class GeneticCodesTest
   @Test(groups = "Functional")
   public void testTranslate()
   {
-    GeneticCodes codes = GeneticCodes.getInstance();
-
-    GeneticCodeI gc = codes.getCodeTable("1");
+    GeneticCodeI gc = GeneticCodes.getCodeTable("1");
     assertNull(gc.translate("XYZ"));
     assertEquals(gc.translate("AGA"), "R");
 
-    gc = codes.getCodeTable("2");
+    gc = GeneticCodes.getCodeTable("2");
     assertEquals(gc.translate("AGA"), "*"); // variant
     assertEquals(gc.translate("ttc"), "F"); // non-variant
 
     // table 11 has no variant translations - should serve the standard values
-    gc = codes.getCodeTable("11");
+    gc = GeneticCodes.getCodeTable("11");
     assertEquals(gc.translate("ttc"), "F");
 
-    gc = codes.getCodeTable("31");
+    gc = GeneticCodes.getCodeTable("31");
     assertEquals(gc.translate("TGA"), "W"); // variant
     assertEquals(gc.translate("tag"), "E"); // variant
     assertEquals(gc.translate("AGC"), "S"); // non-variant
@@ -70,7 +68,7 @@ public class GeneticCodesTest
   @Test(groups = { "Functional" })
   public void testTranslate_standardTable()
   {
-    GeneticCodeI st = GeneticCodes.getInstance().getStandardCodeTable();
+    GeneticCodeI st = GeneticCodes.getStandardCodeTable();
     assertEquals("F", st.translate("TTT"));
     assertEquals("F", st.translate("TTC"));
     assertEquals("L", st.translate("TTA"));
@@ -144,7 +142,7 @@ public class GeneticCodesTest
   @Test(groups = { "Functional" })
   public void testTranslate_standardTableAmbiguityCodes()
   {
-    GeneticCodeI st = GeneticCodes.getInstance().getStandardCodeTable();
+    GeneticCodeI st = GeneticCodes.getStandardCodeTable();
     // Y is C or T
     assertEquals("C", st.translate("TGY"));
     // Phenylalanine first base variation
@@ -236,13 +234,13 @@ public class GeneticCodesTest
   @Test(groups = { "Functional" })
   public void testTranslate_nonStandardTableAmbiguityCodes()
   {
-    GeneticCodeI standard = GeneticCodes.getInstance()
+    GeneticCodeI standard = GeneticCodes
             .getStandardCodeTable();
 
     /*
      * Vertebrate Mitochondrial (Table 2)
      */
-    GeneticCodeI gc = GeneticCodes.getInstance().getCodeTable("2");
+    GeneticCodeI gc = GeneticCodes.getCodeTable("2");
     // AGR is AGA or AGG - R in standard code, * in table 2
     assertEquals(gc.translate("AGR"), "*");
     assertEquals(standard.translate("AGR"), "R");
@@ -253,7 +251,7 @@ public class GeneticCodesTest
     /*
      * Yeast Mitochondrial (Table 3)
      */
-    gc = GeneticCodes.getInstance().getCodeTable("3");
+    gc = GeneticCodes.getCodeTable("3");
     // CTN is L in standard code, T in table 3
     assertEquals(gc.translate("ctn"), "T");
     assertEquals(standard.translate("CTN"), "L");
@@ -261,7 +259,7 @@ public class GeneticCodesTest
     /*
      * Alternative Yeast Nuclear (Table 12)
      */
-    gc = GeneticCodes.getInstance().getCodeTable("12");
+    gc = GeneticCodes.getCodeTable("12");
     // CTG is S; in the standard code CTN is L
     assertEquals(gc.translate("CTG"), "S");
     assertNull(gc.translate("CTK")); // K is G or T -> S or L
@@ -273,7 +271,7 @@ public class GeneticCodesTest
     /*
      * Trematode Mitochondrial (Table 21)
      */
-    gc = GeneticCodes.getInstance().getCodeTable("21");
+    gc = GeneticCodes.getCodeTable("21");
     // AAR is K in standard code, ambiguous in table 21 as AAA=N not K
     assertNull(gc.translate("AAR"));
     assertEquals(standard.translate("AAR"), "K");
@@ -282,15 +280,13 @@ public class GeneticCodesTest
   @Test(groups = "Functional")
   public void testTranslateCanonical()
   {
-    GeneticCodes codes = GeneticCodes.getInstance();
-
-    GeneticCodeI gc = codes.getCodeTable("1");
+    GeneticCodeI gc = GeneticCodes.getCodeTable("1");
     assertNull(gc.translateCanonical("XYZ"));
     assertEquals(gc.translateCanonical("AGA"), "R");
     // translateCanonical should not resolve ambiguity codes
     assertNull(gc.translateCanonical("TGY"));
 
-    gc = codes.getCodeTable("2");
+    gc = GeneticCodes.getCodeTable("2");
     assertNull(gc.translateCanonical("AGR"));
     assertEquals(gc.translateCanonical("AGA"), "*"); // variant
     assertEquals(gc.translateCanonical("ttc"), "F"); // non-variant