X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblCdsTest.java;h=02ce2b202d425e5b5d50097758ab0c2f23185550;hb=528c0f1815bc67b54618ad5b16c2162946974caf;hp=5344575f0bd62e7e869dd49435199c7e9a848a9b;hpb=2cef2c13e720e889304333e70f893a23d1a98f42;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblCdsTest.java b/test/jalview/ext/ensembl/EnsemblCdsTest.java
index 5344575..02ce2b2 100644
--- a/test/jalview/ext/ensembl/EnsemblCdsTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdsTest.java
@@ -44,25 +44,25 @@ public class EnsemblCdsTest
     genomic.setStart(10000);
     genomic.setEnd(50000);
     String transcriptId = "ABC123";
-  
+
     // CDS at (start+10000) length 501
     SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
             null);
     sf.setValue("Parent", "transcript:" + transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
-  
+
     // CDS (sub-type) at (start + 10500) length 101
     sf = new SequenceFeature("CDS_predicted", "", 10500, 10600, 0f, null);
     sf.setValue("Parent", "transcript:" + transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
-  
+
     // CDS belonging to a different transcript doesn't count
     sf = new SequenceFeature("CDS", "", 11500, 12600, 0f, null);
     sf.setValue("Parent", "transcript:anotherOne");
     genomic.addSequenceFeature(sf);
-  
+
     // exon feature doesn't count
     sf = new SequenceFeature("exon", "", 10000, 50000, 0f, null);
     genomic.addSequenceFeature(sf);
@@ -70,7 +70,7 @@ public class EnsemblCdsTest
     // mRNA_region feature doesn't count (parent of CDS)
     sf = new SequenceFeature("mRNA_region", "", 10000, 50000, 0f, null);
     genomic.addSequenceFeature(sf);
-  
+
     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
             transcriptId, 23);
     List<int[]> fromRanges = ranges.getFromRanges();
@@ -96,22 +96,22 @@ public class EnsemblCdsTest
   {
     String accId = "ABC123";
     EnsemblCds testee = new EnsemblCds();
-  
-    SequenceFeature sf = new SequenceFeature("CDS", "", 20000,
-            20500, 0f, null);
+
+    SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
+            null);
     assertFalse(testee.retainFeature(sf, accId));
-  
+
     sf.setType("CDS_predicted");
     assertFalse(testee.retainFeature(sf, accId));
-  
+
     // other feature with no parent is retained
     sf.setType("sequence_variant");
     assertTrue(testee.retainFeature(sf, accId));
-  
+
     // other feature with desired parent is retained
     sf.setValue("Parent", "transcript:" + accId);
     assertTrue(testee.retainFeature(sf, accId));
-  
+
     // feature with wrong parent is not retained
     sf.setValue("Parent", "transcript:XYZ");
     assertFalse(testee.retainFeature(sf, accId));
@@ -126,27 +126,27 @@ public class EnsemblCdsTest
   {
     String accId = "ABC123";
     EnsemblCds testee = new EnsemblCds();
-  
+
     // cds with no parent not valid
     SequenceFeature sf = new SequenceFeature("CDS", "", 1, 2, 0f, null);
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // cds with wrong parent not valid
     sf.setValue("Parent", "transcript:XYZ");
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // cds with right parent is valid
     sf.setValue("Parent", "transcript:" + accId);
     assertTrue(testee.identifiesSequence(sf, accId));
-  
+
     // cds sub-type with right parent is valid
     sf.setType("CDS_predicted");
     assertTrue(testee.identifiesSequence(sf, accId));
-  
+
     // transcript not valid:
     sf.setType("transcript");
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // exon not valid:
     sf.setType("exon");
     assertFalse(testee.identifiesSequence(sf, accId));