X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2Fgff%2FExonerateHelperTest.java;h=ce52ee51a4dfb4be002cfed972b8a5351d944444;hb=528c0f1815bc67b54618ad5b16c2162946974caf;hp=54d6eb24765f3f1ebf43eaa7851054d8b96b92e2;hpb=2cef2c13e720e889304333e70f893a23d1a98f42;p=jalview.git

diff --git a/test/jalview/io/gff/ExonerateHelperTest.java b/test/jalview/io/gff/ExonerateHelperTest.java
index 54d6eb2..ce52ee5 100644
--- a/test/jalview/io/gff/ExonerateHelperTest.java
+++ b/test/jalview/io/gff/ExonerateHelperTest.java
@@ -238,20 +238,19 @@ public class ExonerateHelperTest
   {
     FileLoader loader = new FileLoader(false);
     AlignFrame af = loader.LoadFileWaitTillLoaded(
-            "examples/testdata/exonerateseqs.fa",
-            FormatAdapter.FILE);
-  
+            "examples/testdata/exonerateseqs.fa", FormatAdapter.FILE);
+
     af.loadJalviewDataFile("examples/testdata/exonerateoutput.gff",
             FormatAdapter.FILE, null, null);
-  
+
     /*
      * verify one mapping to a dummy sequence, one to a real one
      */
-    List<AlignedCodonFrame> mappings = af
-            .getViewport().getAlignment().getDataset().getCodonFrames();
+    List<AlignedCodonFrame> mappings = af.getViewport().getAlignment()
+            .getDataset().getCodonFrames();
     assertEquals(2, mappings.size());
     Iterator<AlignedCodonFrame> iter = mappings.iterator();
-  
+
     // first mapping is to dummy sequence
     AlignedCodonFrame mapping = iter.next();
     Mapping[] mapList = mapping.getProtMappings();
@@ -262,7 +261,7 @@ public class ExonerateHelperTest
     // 143 in protein should map to codon [11270, 11269, 11268] in dna
     int[] mappedRegion = mapList[0].getMap().locateInFrom(143, 143);
     assertArrayEquals(new int[] { 11270, 11268 }, mappedRegion);
-  
+
     // second mapping is to a sequence in the alignment
     mapping = iter.next();
     mapList = mapping.getProtMappings();
@@ -271,23 +270,23 @@ public class ExonerateHelperTest
             .findName("DDB_G0280897");
     assertSame(proteinSeq.getDatasetSequence(), mapList[0].getTo());
     assertEquals(1, mapping.getdnaToProt().length);
-  
+
     // 143 in protein should map to codon [11270, 11269, 11268] in dna
     mappedRegion = mapList[0].getMap().locateInFrom(143, 143);
     assertArrayEquals(new int[] { 11270, 11268 }, mappedRegion);
-  
+
     // 182 in protein should map to codon [11153, 11152, 11151] in dna
     mappedRegion = mapList[0].getMap().locateInFrom(182, 182);
     assertArrayEquals(new int[] { 11153, 11151 }, mappedRegion);
-  
+
     // and the reverse mapping:
     mappedRegion = mapList[0].getMap().locateInTo(11151, 11153);
     assertArrayEquals(new int[] { 182, 182 }, mappedRegion);
-  
+
     // 11150 in dna should _not_ map to protein
     mappedRegion = mapList[0].getMap().locateInTo(11150, 11150);
     assertNull(mappedRegion);
-  
+
     // similarly 183 in protein should _not_ map to dna
     mappedRegion = mapList[0].getMap().locateInFrom(183, 183);
     assertNull(mappedRegion);