JAL-2189 format tests

[jalview.git] / test / jalview / ext / ensembl / EnsemblGenomeTest.java

diff --git a/test/jalview/ext/ensembl/EnsemblGenomeTest.java b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
index c711279..377c8c7 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblGenomeTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
@@ -43,15 +43,14 @@ public class EnsemblGenomeTest
     genomic.setStart(10000);
     genomic.setEnd(50000);
     String transcriptId = "ABC123";
-  
+
     // transcript at (start+10000) length 501
     SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
-            20500, 0f,
-            null);
+            20500, 0f, null);
     sf.setValue("ID", "transcript:" + transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
-  
+
     // transcript (sub-type) at (start + 10500) length 101
     sf = new SequenceFeature("ncRNA", "", 10500, 10600, 0f, null);
     sf.setValue("ID", "transcript:" + transcriptId);
@@ -65,12 +64,12 @@ public class EnsemblGenomeTest
     sf.setValue("ID", "transcript:" + transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
-  
+
     // transcript with a different ID doesn't count
     sf = new SequenceFeature("transcript", "", 11500, 12600, 0f, null);
     sf.setValue("ID", "transcript:anotherOne");
     genomic.addSequenceFeature(sf);
-  
+
     // parent of transcript feature doesn't count
     sf = new SequenceFeature("gene_member_region", "", 10000, 50000, 0f,
             null);
@@ -107,13 +106,13 @@ public class EnsemblGenomeTest
     SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
             20500, 0f, null);
     assertFalse(testee.retainFeature(sf, accId));
-  
+
     sf.setType("mature_transcript");
     assertFalse(testee.retainFeature(sf, accId));
-  
+
     sf.setType("NMD_transcript_variant");
     assertFalse(testee.retainFeature(sf, accId));
-  
+
     // other feature with no parent is kept
     sf.setType("anything");
     assertTrue(testee.retainFeature(sf, accId));
@@ -136,20 +135,20 @@ public class EnsemblGenomeTest
   {
     String accId = "ABC123";
     EnsemblGenome testee = new EnsemblGenome();
-  
+
     // transcript with no ID not valid
     SequenceFeature sf = new SequenceFeature("transcript", "", 1, 2, 0f,
             null);
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // transcript with wrong ID not valid
     sf.setValue("ID", "transcript");
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // transcript with right ID is valid
     sf.setValue("ID", "transcript:" + accId);
     assertTrue(testee.identifiesSequence(sf, accId));
-  
+
     // transcript sub-type with right ID is valid
     sf.setType("ncRNA");
     assertTrue(testee.identifiesSequence(sf, accId));
@@ -157,11 +156,11 @@ public class EnsemblGenomeTest
     // Ensembl treats NMD_transcript_variant as if a transcript
     sf.setType("NMD_transcript_variant");
     assertTrue(testee.identifiesSequence(sf, accId));
-  
+
     // gene not valid:
     sf.setType("gene");
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // exon not valid:
     sf.setType("exon");
     assertFalse(testee.identifiesSequence(sf, accId));