X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2Fgff%2FExonerateHelperTest.java;fp=test%2Fjalview%2Fio%2Fgff%2FExonerateHelperTest.java;h=49f574bf18d39e77d2958ddcbee00083404682d4;hb=c0501eaa85c0594f9275766f64de8ea44a59c368;hp=825af240aee3dc8d241447e0a86ee06e8945a6c2;hpb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;p=jalview.git

diff --git a/test/jalview/io/gff/ExonerateHelperTest.java b/test/jalview/io/gff/ExonerateHelperTest.java
index 825af24..49f574b 100644
--- a/test/jalview/io/gff/ExonerateHelperTest.java
+++ b/test/jalview/io/gff/ExonerateHelperTest.java
@@ -62,9 +62,8 @@ public class ExonerateHelperTest
   public void testGetMappingType()
   {
     // protein-to-dna:
-    assertSame(MappingType.PeptideToNucleotide,
-            ExonerateHelper
-                    .getMappingType("exonerate:protein2genome:local"));
+    assertSame(MappingType.PeptideToNucleotide, ExonerateHelper
+            .getMappingType("exonerate:protein2genome:local"));
     assertSame(MappingType.PeptideToNucleotide,
             ExonerateHelper.getMappingType("exonerate:protein2dna:local"));
 
@@ -117,11 +116,11 @@ public class ExonerateHelperTest
     assertSame(newseqs.get(0), mapping.getdnaSeqs()[0]);
     assertEquals(1, mapping.getdnaToProt().length);
     assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
-    assertArrayEquals(new int[] { 400, 423 }, mapping.getdnaToProt()[0]
-            .getFromRanges().get(0));
+    assertArrayEquals(new int[] { 400, 423 },
+            mapping.getdnaToProt()[0].getFromRanges().get(0));
     assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
-    assertArrayEquals(new int[] { 3, 10 }, mapping.getdnaToProt()[0]
-            .getToRanges().get(0));
+    assertArrayEquals(new int[] { 3, 10 },
+            mapping.getdnaToProt()[0].getToRanges().get(0));
   }
 
   /**
@@ -160,11 +159,11 @@ public class ExonerateHelperTest
     assertSame(newseqs.get(0), mapping.getdnaSeqs()[0]);
     assertEquals(1, mapping.getdnaToProt().length);
     assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
-    assertArrayEquals(new int[] { 400, 377 }, mapping.getdnaToProt()[0]
-            .getFromRanges().get(0));
+    assertArrayEquals(new int[] { 400, 377 },
+            mapping.getdnaToProt()[0].getFromRanges().get(0));
     assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
-    assertArrayEquals(new int[] { 3, 10 }, mapping.getdnaToProt()[0]
-            .getToRanges().get(0));
+    assertArrayEquals(new int[] { 3, 10 },
+            mapping.getdnaToProt()[0].getToRanges().get(0));
   }
 
   /**
@@ -206,11 +205,11 @@ public class ExonerateHelperTest
     assertEquals(1, mapping.getdnaSeqs().length);
     assertEquals(1, mapping.getdnaToProt().length);
     assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
-    assertArrayEquals(new int[] { 400, 423 }, mapping.getdnaToProt()[0]
-            .getFromRanges().get(0));
+    assertArrayEquals(new int[] { 400, 423 },
+            mapping.getdnaToProt()[0].getFromRanges().get(0));
     assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
-    assertArrayEquals(new int[] { 3, 10 }, mapping.getdnaToProt()[0]
-            .getToRanges().get(0));
+    assertArrayEquals(new int[] { 3, 10 },
+            mapping.getdnaToProt()[0].getToRanges().get(0));
   }
 
   /**
@@ -252,11 +251,11 @@ public class ExonerateHelperTest
     assertEquals(1, mapping.getdnaSeqs().length);
     assertEquals(1, mapping.getdnaToProt().length);
     assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
-    assertArrayEquals(new int[] { 400, 377 }, mapping.getdnaToProt()[0]
-            .getFromRanges().get(0));
+    assertArrayEquals(new int[] { 400, 377 },
+            mapping.getdnaToProt()[0].getFromRanges().get(0));
     assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
-    assertArrayEquals(new int[] { 3, 10 }, mapping.getdnaToProt()[0]
-            .getToRanges().get(0));
+    assertArrayEquals(new int[] { 3, 10 },
+            mapping.getdnaToProt()[0].getToRanges().get(0));
   }
 
   /**
@@ -268,20 +267,19 @@ public class ExonerateHelperTest
   {
     FileLoader loader = new FileLoader(false);
     AlignFrame af = loader.LoadFileWaitTillLoaded(
-            "examples/testdata/exonerateseqs.fa",
-            DataSourceType.FILE);
-  
+            "examples/testdata/exonerateseqs.fa", DataSourceType.FILE);
+
     af.loadJalviewDataFile("examples/testdata/exonerateoutput.gff",
             DataSourceType.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();
@@ -292,7 +290,7 @@ 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();
@@ -301,23 +299,23 @@ 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);