X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSequenceFeatureTest.java;h=2774a16c031e5fe0087c55c63223da3610f06e54;hb=84965b0d97f7db54b0855ac7122586d89cac7e46;hp=8c9cbc900050ef5a69df470cfdf5ec143cdd6993;hpb=14193747f3831242bc7dfac12394eb20eb0ba480;p=jalview.git
diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java
index 8c9cbc9..2774a16 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 +277,45 @@ public class SequenceFeatureTest
@Test(groups = { "Functional" })
public void testGetDetailsReport()
{
+ SequenceI seq = new Sequence("TestSeq", "PLRFQMD");
+
// single locus, no group, no score
SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22, null);
- String expected = "
Type | variant |
"
- + "Start/end | 22 |
"
- + "Description | G,C |
";
- assertEquals(expected, sf.getDetailsReport());
+ String expected = "
Location | TestSeq | 22 |
"
+ + "Type | variant | |
"
+ + "Description | G,C | |
";
+ assertEquals(expected, sf.getDetailsReport(seq));
// contact feature
sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31,
null);
- expected = "
Type | Disulphide Bond |
"
- + "Start/end | 28:31 |
"
- + "Description | a description |
";
- assertEquals(expected, sf.getDetailsReport());
+ expected = "
Location | TestSeq | 28:31 |
"
+ + "Type | Disulphide Bond | |
"
+ + "Description | a description | |
";
+ assertEquals(expected, sf.getDetailsReport(seq));
sf = new SequenceFeature("variant", "G,C", 22, 33,
12.5f, "group");
sf.setValue("Parent", "ENSG001");
sf.setValue("Child", "ENSP002");
- expected = "
Type | variant |
"
- + "Start/end | 22-33 |
"
- + "Description | G,C |
"
- + "Score | 12.5 |
"
- + "Group | group |
"
- + "Child | ENSP002 |
"
- + "Parent | ENSG001 |
";
- assertEquals(expected, sf.getDetailsReport());
+ expected = "
Location | TestSeq | 22-33 |
"
+ + "Type | variant | |
"
+ + "Description | G,C | |
"
+ + "Score | 12.5 | |
"
+ + "Group | group | |
"
+ + "Child | | ENSP002 |
"
+ + "Parent | | ENSG001 |
";
+ assertEquals(expected, sf.getDetailsReport(seq));
/*
* 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 = "
Type | Pfam |
"
- + "Start/end | 8-83 |
"
- + "Description | Fer2 Status: True Positive Pfam 8_8 |
"
- + "Group | Uniprot |
";
- assertEquals(expected, sf.getDetailsReport());
+ expected = "
Location | TestSeq | 8-83 |
"
+ + "Type | Pfam | |
"
+ + "Description | Fer2 Status: True Positive Pfam 8_8 | |
"
+ + "Group | Uniprot | |
";
+ assertEquals(expected, sf.getDetailsReport(seq));
}
}