X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblGeneTest.java;h=4a6036fe1ce2c183e1ff315cb6a8cb828666feb2;hb=5504c1347eb582d05ae9086608223209ecb8c13d;hp=2de08f582a98bd2a5d0cb44f8c56420116c08642;hpb=ca74027f55fb1f8af9fef0d77348449a07a1b5d5;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java
index 2de08f5..4a6036f 100644
--- a/test/jalview/ext/ensembl/EnsemblGeneTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java
@@ -153,8 +153,8 @@ public class EnsemblGeneTest
     genomic.addSequenceFeature(sf1);
 
     // transcript sub-type feature
-    SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500,
-            0f, null);
+    SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500, 0f,
+            null);
     sf2.setValue("Parent", geneId);
     sf2.setValue("id", "transcript2");
     genomic.addSequenceFeature(sf2);
@@ -168,8 +168,8 @@ public class EnsemblGeneTest
     genomic.addSequenceFeature(sf3);
 
     // transcript for a different gene - ignored
-    SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500,
-            0f, null);
+    SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500, 0f,
+            null);
     sf4.setValue("Parent", "XYZ");
     sf4.setValue("id", "transcript4");
     genomic.addSequenceFeature(sf4);
@@ -210,8 +210,8 @@ public class EnsemblGeneTest
     sf.setValue("Parent", geneId);
     assertTrue(testee.retainFeature(sf, geneId));
 
-    sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
-            0f, null);
+    sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500, 0f,
+            null);
     sf.setValue("Parent", geneId);
     assertTrue(testee.retainFeature(sf, geneId));
 
@@ -247,12 +247,14 @@ public class EnsemblGeneTest
     seq.addSequenceFeature(sf3);
 
     // gene sub-type with right ID is valid
-    SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null);
+    SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f,
+            null);
     sf4.setValue("id", accId);
     seq.addSequenceFeature(sf4);
 
     // transcript not valid:
-    SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f, null);
+    SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
+            null);
     sf5.setValue("id", accId);
     seq.addSequenceFeature(sf5);
 
@@ -260,7 +262,7 @@ public class EnsemblGeneTest
     SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
     sf6.setValue("id", accId);
     seq.addSequenceFeature(sf6);
-    
+
     List<SequenceFeature> sfs = new EnsemblGene()
             .getIdentifyingFeatures(seq, accId);
     assertFalse(sfs.contains(sf1));
@@ -291,10 +293,10 @@ public class EnsemblGeneTest
     assertTrue(fc.isFeatureHidden("transcript"));
     assertTrue(fc.isFeatureHidden("CDS"));
 
-    assertEquals(Color.RED, fc.getFeatureColour("sequence_variant")
-            .getColour());
-    assertEquals(Color.RED, fc.getFeatureColour("feature_variant")
-            .getColour());
+    assertEquals(Color.RED,
+            fc.getFeatureColour("sequence_variant").getColour());
+    assertEquals(Color.RED,
+            fc.getFeatureColour("feature_variant").getColour());
     assertTrue(fc.getFeatureColour("exon").isColourByLabel());
     assertTrue(fc.getFeatureColour("coding_exon").isColourByLabel());
     assertEquals(1, fc.compare("sequence_variant", "exon"));
@@ -326,6 +328,6 @@ public class EnsemblGeneTest
     assertTrue(geneIds.contains("ENSDARG00000017661")); // zebrafish
     assertTrue(geneIds.contains("ENSGALG00000012865")); // chicken
     assertEquals(8, geneIds.size());
-    
+
   }
 }