X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSequenceFeatureTest.java;h=673ea290a7e74ca7c1de3e7d04fc56e528060624;hb=5a631296dd1dcc1df7b50487a647c27333696c74;hp=c95597928b4490fa0c72683f84054c7f93f4b57e;hpb=baa077bd19420018433d78927aad3ad139e47351;p=jalview.git diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java index c955979..673ea29 100644 --- a/test/jalview/datamodel/SequenceFeatureTest.java +++ b/test/jalview/datamodel/SequenceFeatureTest.java @@ -26,11 +26,11 @@ import static org.testng.AssertJUnit.assertNull; import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; -import jalview.gui.JvOptionPane; - import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; +import jalview.gui.JvOptionPane; + public class SequenceFeatureTest { @@ -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 = "
" - + "" + String expected = "
Typevariant
Start/end22
" + + "" + "
LocationTestSeq22
Typevariant
DescriptionG,C
"; - assertEquals(expected, sf.getDetailsReport()); + assertEquals(expected, sf.getDetailsReport(seqName, null)); // contact feature sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31, null); - expected = "
" - + "" + expected = "
TypeDisulphide Bond
Start/end28:31
" + + "" + "
LocationTestSeq28:31
TypeDisulphide Bond
Descriptiona description
"; - assertEquals(expected, sf.getDetailsReport()); + assertEquals(expected, sf.getDetailsReport(seqName, null)); sf = new SequenceFeature("variant", "G,C", 22, 33, 12.5f, "group"); sf.setValue("Parent", "ENSG001"); sf.setValue("Child", "ENSP002"); - expected = "
" - + "" + expected = "
Typevariant
Start/end22-33
" + + "" + "" + "" + "" + "" + "
LocationTestSeq22-33
Typevariant
DescriptionG,C
Score12.5
Groupgroup
ChildENSP002
ParentENSG001
"; - assertEquals(expected, sf.getDetailsReport()); + assertEquals(expected, sf.getDetailsReport(seqName, null)); /* * 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 = "
" - + "" + expected = "
TypePfam
Start/end8-83
" + + "" + "" + "
LocationTestSeq8-83
TypePfam
DescriptionFer2 Status: True Positive Pfam 8_8
GroupUniprot
"; - assertEquals(expected, sf.getDetailsReport()); + assertEquals(expected, sf.getDetailsReport(seqName, null)); } }