X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSequenceFeatureTest.java;h=cd8f9eb5bc415837a026e5514fcb02e7910d9a55;hb=0b573ed90b14079f7326281f50c0c9cffdace586;hp=8c9cbc900050ef5a69df470cfdf5ec143cdd6993;hpb=14193747f3831242bc7dfac12394eb20eb0ba480;p=jalview.git diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java index 8c9cbc9..cd8f9eb 100644 --- a/test/jalview/datamodel/SequenceFeatureTest.java +++ b/test/jalview/datamodel/SequenceFeatureTest.java @@ -48,7 +48,7 @@ public class SequenceFeatureTest 12.5f, "group"); sf1.setValue("STRAND", "+"); sf1.setValue("Note", "Testing"); - Integer count = new Integer(7); + Integer count = Integer.valueOf(7); sf1.setValue("Count", count); SequenceFeature sf2 = new SequenceFeature(sf1); @@ -106,7 +106,7 @@ public class SequenceFeatureTest assertEquals("+", sf1.getValue("STRAND")); assertNull(sf1.getValue("strand")); // case-sensitive assertEquals(".", sf1.getValue("unknown", ".")); - Integer i = new Integer(27); + Integer i = Integer.valueOf(27); assertSame(i, sf1.getValue("Unknown", i)); } @@ -277,43 +277,46 @@ public class SequenceFeatureTest @Test(groups = { "Functional" }) public void testGetDetailsReport() { + SequenceI seq = new Sequence("TestSeq", "PLRFQMD"); + String seqName = seq.getName(); + // single locus, no group, no score SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22, null); - String expected = "
" - + "" - + "
Typevariant
Start/end22
DescriptionG,C
"; - assertEquals(expected, sf.getDetailsReport()); + String expected = "
" + + "" + + "
LocationTestSeq22
Typevariant
DescriptionG,C
"; + assertEquals(expected, sf.getDetailsReport(seqName)); // contact feature sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31, null); - expected = "
" - + "" - + "
TypeDisulphide Bond
Start/end28:31
Descriptiona description
"; - assertEquals(expected, sf.getDetailsReport()); + expected = "
" + + "" + + "
LocationTestSeq28:31
TypeDisulphide Bond
Descriptiona description
"; + assertEquals(expected, sf.getDetailsReport(seqName)); sf = new SequenceFeature("variant", "G,C", 22, 33, 12.5f, "group"); sf.setValue("Parent", "ENSG001"); sf.setValue("Child", "ENSP002"); - expected = "
" - + "" - + "" - + "" - + "" - + "" - + "
Typevariant
Start/end22-33
DescriptionG,C
Score12.5
Groupgroup
ChildENSP002
ParentENSG001
"; - assertEquals(expected, sf.getDetailsReport()); + expected = "
" + + "" + + "" + + "" + + "" + + "" + + "
LocationTestSeq22-33
Typevariant
DescriptionG,C
Score12.5
Groupgroup
ChildENSP002
ParentENSG001
"; + assertEquals(expected, sf.getDetailsReport(seqName)); /* * feature with embedded html link in description */ String desc = "Fer2 Status: True Positive Pfam 8_8"; sf = new SequenceFeature("Pfam", desc, 8, 83, "Uniprot"); - expected = "
" - + "" - + "" - + "
TypePfam
Start/end8-83
DescriptionFer2 Status: True Positive Pfam 8_8
GroupUniprot
"; - assertEquals(expected, sf.getDetailsReport()); + expected = "
" + + "" + + "" + + "
LocationTestSeq8-83
TypePfam
DescriptionFer2 Status: True Positive Pfam 8_8
GroupUniprot
"; + assertEquals(expected, sf.getDetailsReport(seqName)); } }