X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fdatamodel%2FSequenceFeatureTest.java;h=f8479a35123f4c4c6b9cb1b6d18f57a652d9a076;hb=6e0b6fc5ebc8ebb36cada5f6df8c9e7e4a995088;hp=9111e5ac2720320bbf39e594216e665a3c6d0957;hpb=3027bfb4b1b13af8686abcd419888e03141bd672;p=jalview.git
diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java
index 9111e5a..f8479a3 100644
--- a/test/jalview/datamodel/SequenceFeatureTest.java
+++ b/test/jalview/datamodel/SequenceFeatureTest.java
@@ -26,11 +26,15 @@ import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.gui.JvOptionPane;
+import java.util.ArrayList;
+import java.util.List;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.gui.JvOptionPane;
+import jalview.util.MapList;
+
public class SequenceFeatureTest
{
@@ -277,43 +281,79 @@ 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 = "
Type | variant | |
"
- + "Start/end | 22 | |
"
+ String expected = "
Location | TestSeq | 22 |
"
+ + "Type | variant | |
"
+ "Description | G,C | |
";
- assertEquals(expected, sf.getDetailsReport());
+ assertEquals(expected, sf.getDetailsReport(seqName, null));
// contact feature
sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31,
null);
- expected = "
Type | Disulphide Bond | |
"
- + "Start/end | 28:31 | |
"
+ expected = "
Location | TestSeq | 28:31 |
"
+ + "Type | Disulphide Bond | |
"
+ "Description | a 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 = "
Type | variant | |
"
- + "Start/end | 22-33 | |
"
+ expected = "
Location | TestSeq | 22-33 |
"
+ + "Type | variant | |
"
+ "Description | G,C | |
"
+ "Score | 12.5 | |
"
+ "Group | group | |
"
+ "Child | | ENSP002 |
"
+ "Parent | | ENSG001 |
";
- 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 = "
Type | Pfam | |
"
- + "Start/end | 8-83 | |
"
+ expected = "
Location | TestSeq | 8-83 |
"
+ + "Type | Pfam | |
"
+ "Description | Fer2 Status: True Positive Pfam 8_8 | |
"
+ "Group | Uniprot | |
";
- assertEquals(expected, sf.getDetailsReport());
+ assertEquals(expected, sf.getDetailsReport(seqName, null));
+ }
+
+ /**
+ * Feature details report for a virtual feature should include original and
+ * mapped locations, and also derived peptide consequence if it can be
+ * determined
+ */
+ @Test(groups = { "Functional" })
+ public void testGetDetailsReport_virtualFeature()
+ {
+ SequenceI cds = new Sequence("Cds/101-121", "CCTttgAGAtttCAAatgGAT");
+ SequenceI seq = new Sequence("TestSeq/8-14", "PLRFQMD");
+ MapList map = new MapList(new int[] { 101, 118 }, new int[] { 8, 13 },
+ 3, 1);
+ Mapping mapping = new Mapping(seq, map);
+ List features = new ArrayList<>();
+ // vary ttg (Leu) to ttc (Phe)
+ SequenceFeature sf = new SequenceFeature("variant", "G,C", 106, 106,
+ null);
+ sf.setValue("alleles", "G,C"); // needed to compute peptide consequence!
+ features.add(sf);
+
+ MappedFeatures mf = new MappedFeatures(mapping, cds, 9, 'L', features);
+
+ String expected = "
Location | Cds | 106 |
"
+ + "Peptide Location | TestSeq | 9 |
"
+ + "Type | variant | |
"
+ + "Description | G,C | |
"
+ + "Consequence | Translated by Jalview | p.Leu9Phe |
"
+ + "alleles | | G,C |
"
+ + "
";
+
+ assertEquals(expected, sf.getDetailsReport(seq.getName(), mf));
}
}