X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FDnaTest.java;fp=test%2Fjalview%2Fanalysis%2FDnaTest.java;h=262de12cdf8401eb55c94cad1ea7af51e2573449;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=27ae8cd61e9969e05e1720e799d2d1723b8cd482;hpb=49db0dff1da16c3355b43a41498c1fc93ef47e91;p=jalview.git

diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java
index 27ae8cd..262de12 100644
--- a/test/jalview/analysis/DnaTest.java
+++ b/test/jalview/analysis/DnaTest.java
@@ -139,8 +139,8 @@ public class DnaTest
     Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
             false);
     Dna dna = new Dna(av, contigs);
-    AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
-            .getStandardCodeTable());
+    AlignmentI translated = dna.translateCdna(
+            GeneticCodes.getInstance().getStandardCodeTable());
     assertNotNull("Couldn't do a full width translation of test data.",
             translated);
   }
@@ -167,20 +167,23 @@ public class DnaTest
         cs.hideColumns(0, ipos - 1);
       }
       cs.hideColumns(ipos + vwidth, alf.getWidth());
-      Iterator<int[]> vcontigs = cs.getVisContigsIterator(0,
-              alf.getWidth(), false);
+      Iterator<int[]> vcontigs = cs.getVisContigsIterator(0, alf.getWidth(),
+              false);
       AlignViewportI av = new AlignViewport(alf, cs);
       Dna dna = new Dna(av, vcontigs);
-      AlignmentI transAlf = dna.translateCdna(GeneticCodes.getInstance()
-              .getStandardCodeTable());
+      AlignmentI transAlf = dna.translateCdna(
+              GeneticCodes.getInstance().getStandardCodeTable());
 
-      assertTrue("Translation failed (ipos=" + ipos
-              + ") No alignment data.", transAlf != null);
+      assertTrue(
+              "Translation failed (ipos=" + ipos + ") No alignment data.",
+              transAlf != null);
       assertTrue("Translation failed (ipos=" + ipos + ") Empty alignment.",
               transAlf.getHeight() > 0);
-      assertTrue("Translation failed (ipos=" + ipos + ") Translated "
-              + transAlf.getHeight() + " sequences from " + alf.getHeight()
-              + " sequences", alf.getHeight() == transAlf.getHeight());
+      assertTrue(
+              "Translation failed (ipos=" + ipos + ") Translated "
+                      + transAlf.getHeight() + " sequences from "
+                      + alf.getHeight() + " sequences",
+              alf.getHeight() == transAlf.getHeight());
     }
   }
 
@@ -199,8 +202,8 @@ public class DnaTest
     Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
             false);
     Dna dna = new Dna(av, contigs);
-    AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
-            .getStandardCodeTable());
+    AlignmentI translated = dna.translateCdna(
+            GeneticCodes.getInstance().getStandardCodeTable());
     String aa = translated.getSequenceAt(0).getSequenceAsString();
     assertEquals(
             "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
@@ -225,10 +228,11 @@ public class DnaTest
     Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
             false);
     Dna dna = new Dna(av, contigs);
-    AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
-            .getStandardCodeTable());
+    AlignmentI translated = dna.translateCdna(
+            GeneticCodes.getInstance().getStandardCodeTable());
     String aa = translated.getSequenceAt(0).getSequenceAsString();
-    assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
+    assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW",
+            aa);
   }
 
   /**
@@ -306,15 +310,15 @@ public class DnaTest
     /*
      * Generate cDNA - 8 sequences of 12 bases each.
      */
-    AlignmentI cdna = new AlignmentGenerator(true)
-            .generate(12, 8, 97, 5, 5);
+    AlignmentI cdna = new AlignmentGenerator(true).generate(12, 8, 97, 5,
+            5);
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(cdna, cs);
     Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
             false);
     Dna dna = new Dna(av, contigs);
-    AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
-            .getStandardCodeTable());
+    AlignmentI translated = dna.translateCdna(
+            GeneticCodes.getInstance().getStandardCodeTable());
 
     /*
      * Jumble the cDNA sequences and translate.
@@ -330,8 +334,8 @@ public class DnaTest
     av = new AlignViewport(cdnaReordered, cs);
     contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
     dna = new Dna(av, contigs);
-    AlignmentI translated2 = dna.translateCdna(GeneticCodes.getInstance()
-            .getStandardCodeTable());
+    AlignmentI translated2 = dna.translateCdna(
+            GeneticCodes.getInstance().getStandardCodeTable());
 
     /*
      * Check translated sequences are the same in both alignments.
@@ -344,10 +348,10 @@ public class DnaTest
     int sortedSequenceIndex = 0;
     for (int originalSequenceIndex : jumbler)
     {
-      final String translation1 = translated.getSequenceAt(
-              originalSequenceIndex).getSequenceAsString();
-      final String translation2 = translated2.getSequenceAt(
-              sortedSequenceIndex).getSequenceAsString();
+      final String translation1 = translated
+              .getSequenceAt(originalSequenceIndex).getSequenceAsString();
+      final String translation2 = translated2
+              .getSequenceAt(sortedSequenceIndex).getSequenceAsString();
       assertEquals(translation2, translation1);
       sortedSequenceIndex++;
     }
@@ -391,8 +395,10 @@ public class DnaTest
 
   private void assertSymmetric(String codon1, String codon2)
   {
-    assertEquals("Comparison of '" + codon1 + "' and '" + codon2
-            + " not symmetric", Integer.signum(compare(codon1, codon2)),
+    assertEquals(
+            "Comparison of '" + codon1 + "' and '" + codon2
+                    + " not symmetric",
+            Integer.signum(compare(codon1, codon2)),
             -Integer.signum(compare(codon2, codon1)));
   }
 
@@ -421,8 +427,8 @@ public class DnaTest
    */
   private void assertPrecedes(String codon1, String codon2)
   {
-    assertEquals("Expected '" + codon1 + "'  precedes '" + codon2 + "'",
-            -1, compare(codon1, codon2));
+    assertEquals("Expected '" + codon1 + "'  precedes '" + codon2 + "'", -1,
+            compare(codon1, codon2));
   }
 
   /**
@@ -556,8 +562,8 @@ public class DnaTest
     SequenceI dna = new Sequence("Seq1", seq);
     Alignment al = new Alignment(new SequenceI[] { dna });
     al.createDatasetAlignment();
-    assertEquals(seqDs, al.getSequenceAt(0).getDatasetSequence()
-            .getSequenceAsString());
+    assertEquals(seqDs,
+            al.getSequenceAt(0).getDatasetSequence().getSequenceAsString());
 
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(al, cs);