X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSequenceFeatureTest.java;h=cd8f9eb5bc415837a026e5514fcb02e7910d9a55;hb=e9a1285c3e0df3505d85121d84c2d33d899820f2;hp=fbeb36555301747795801ea9e3f9349b76b6aaa5;hpb=6ec47c00025dbeb48dba5f5db77754ec50b7a6b5;p=jalview.git
diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java
index fbeb365..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));
}
@@ -273,4 +273,50 @@ public class SequenceFeatureTest
"group");
assertTrue(sf.isContactFeature());
}
+
+ @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 = "
Location | TestSeq | 22 |
"
+ + "Type | variant | |
"
+ + "Description | G,C | |
";
+ assertEquals(expected, sf.getDetailsReport(seqName));
+
+ // contact feature
+ sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31,
+ null);
+ expected = "
Location | TestSeq | 28:31 |
"
+ + "Type | Disulphide Bond | |
"
+ + "Description | a 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 = "
Location | TestSeq | 22-33 |
"
+ + "Type | variant | |
"
+ + "Description | G,C | |
"
+ + "Score | 12.5 | |
"
+ + "Group | group | |
"
+ + "Child | | ENSP002 |
"
+ + "Parent | | ENSG001 |
";
+ 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 = "
Location | TestSeq | 8-83 |
"
+ + "Type | Pfam | |
"
+ + "Description | Fer2 Status: True Positive Pfam 8_8 | |
"
+ + "Group | Uniprot | |
";
+ assertEquals(expected, sf.getDetailsReport(seqName));
+ }
}