JAL-3438 spotless for 2.11.2.0

[jalview.git] / test / jalview / io / EmblFlatFileTest.java

diff --git a/test/jalview/io/EmblFlatFileTest.java b/test/jalview/io/EmblFlatFileTest.java
index f36e935..e05b03b 100644 (file)
--- a/test/jalview/io/EmblFlatFileTest.java
+++ b/test/jalview/io/EmblFlatFileTest.java
@@ -172,7 +172,7 @@ public class EmblFlatFileTest
         {
           assertEquals((ranges = map.getFromRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 1579);
-          assertEquals(ranges.get(0)[1], 2931);  // excludes stop 2934 
+          assertEquals(ranges.get(0)[1], 2931); // excludes stop 2934
           assertEquals((ranges = map.getToRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 1);
           assertEquals(ranges.get(0)[1], 451);
@@ -184,7 +184,7 @@ public class EmblFlatFileTest
         {
           assertEquals((ranges = map.getFromRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 2928);
-          assertEquals(ranges.get(0)[1], 3989);  // excludes stop 3992
+          assertEquals(ranges.get(0)[1], 3989); // excludes stop 3992
           assertEquals((ranges = map.getToRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 1);
           assertEquals(ranges.get(0)[1], 354);
@@ -230,6 +230,7 @@ public class EmblFlatFileTest
     }
     assertEquals(uniprotCount, 8);
   }
+
   /**
    * A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
    * one of them reverse strand
@@ -244,7 +245,7 @@ public class EmblFlatFileTest
     FileParse fp = new FileParse(dataFile, DataSourceType.FILE);
     EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
     List<SequenceI> seqs = parser.getSeqs();
-    assertTrue(seqs.get(0).getSequenceAsString().indexOf("u")>-1);
+    assertTrue(seqs.get(0).getSequenceAsString().indexOf("u") > -1);
   }
 
   @Test(groups = "Functional")
@@ -287,7 +288,7 @@ public class EmblFlatFileTest
      * dna should have dbref to itself, and to inferred EMBLCDSPROTEIN:QHD43415.1
      */
     assertEquals(dbrefs.size(), 2);
-    
+
     // dbref to self
     DBRefEntry dbref = dbrefs.get(0);
     assertEquals(dbref.getSource(), "EMBLTEST");
@@ -301,7 +302,7 @@ public class EmblFlatFileTest
     assertEquals(map.getToHighest(), 40);
     assertEquals(map.getFromRatio(), 1);
     assertEquals(map.getToRatio(), 1);
-    
+
     // dbref to inferred EMBLCDSPROTEIN:
     dbref = dbrefs.get(1);
     assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
@@ -330,17 +331,17 @@ public class EmblFlatFileTest
     assertSame(exons, EmblFlatFile.adjustForProteinLength(6, exons));
 
     // patch from JAL-3725 in EmblXmlSource propagated to Flatfile
-    // match if we assume exons include stop codon not in protein: 
+    // match if we assume exons include stop codon not in protein:
     int[] truncated = EmblFlatFile.adjustForProteinLength(5, exons);
     assertEquals(Arrays.toString(truncated), "[11, 15, 21, 25, 31, 35]");
-    
+
     // truncate last exon by 6bp
     truncated = EmblFlatFile.adjustForProteinLength(4, exons);
-    assertEquals(Arrays.toString(truncated),"[11, 15, 21, 25, 31, 32]");
+    assertEquals(Arrays.toString(truncated), "[11, 15, 21, 25, 31, 32]");
 
     // remove last exon and truncate preceding by 1bp (so 3bp in total)
     truncated = EmblFlatFile.adjustForProteinLength(3, exons);
-    assertEquals(Arrays.toString(truncated),"[11, 15, 21, 24]");
+    assertEquals(Arrays.toString(truncated), "[11, 15, 21, 24]");
 
     // exact removal of exon case:
     exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
@@ -356,8 +357,12 @@ public class EmblFlatFileTest
   public void testRemoveQuotes()
   {
     assertNull(EmblFlatFile.removeQuotes(null));
-    assertEquals(EmblFlatFile.removeQuotes("No quotes here"), "No quotes here");
-    assertEquals(EmblFlatFile.removeQuotes("\"Enclosing quotes\""), "Enclosing quotes");
-    assertEquals(EmblFlatFile.removeQuotes("\"Escaped \"\"quotes\"\" example\""), "Escaped \"quotes\" example");
+    assertEquals(EmblFlatFile.removeQuotes("No quotes here"),
+            "No quotes here");
+    assertEquals(EmblFlatFile.removeQuotes("\"Enclosing quotes\""),
+            "Enclosing quotes");
+    assertEquals(
+            EmblFlatFile.removeQuotes("\"Escaped \"\"quotes\"\" example\""),
+            "Escaped \"quotes\" example");
   }
 }