From a5ad4f49249c216517d76303c731a8ca0d1f0c55 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 16 May 2017 10:25:28 +0100
Subject: [PATCH] JAL-2505 additional tests/asserts prior to refactoring

---
 test/jalview/io/gff/Gff3HelperTest.java         |   46 +++++++++++++++++++++++
 test/jalview/io/gff/InterProScanHelperTest.java |   12 ++++++
 2 files changed, 58 insertions(+)

diff --git a/test/jalview/io/gff/Gff3HelperTest.java b/test/jalview/io/gff/Gff3HelperTest.java
index bf038ac..cd5a0d8 100644
--- a/test/jalview/io/gff/Gff3HelperTest.java
+++ b/test/jalview/io/gff/Gff3HelperTest.java
@@ -37,7 +37,9 @@ import jalview.gui.JvOptionPane;
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -231,4 +233,48 @@ public class Gff3HelperTest
             .getToRanges().get(0));
   }
 
+  @Test(groups = "Functional")
+  public void testGetDescription()
+  {
+    Gff3Helper testee = new Gff3Helper();
+    SequenceFeature sf = new SequenceFeature("type", "desc", 10, 20, 3f,
+            "group");
+    Map<String, List<String>> attributes = new HashMap<String, List<String>>();
+    assertNull(testee.getDescription(sf, attributes));
+
+    // ID if any is a fall-back for description
+    sf.setValue("ID", "Patrick");
+    assertEquals("Patrick", testee.getDescription(sf, attributes));
+
+    // Target is set by Exonerate
+    sf.setValue("Target", "Destination Moon");
+    assertEquals("Destination", testee.getDescription(sf, attributes));
+
+    // Ensembl variant feature - extract "alleles" value
+    // may be sequence_variant or a sub-type in the sequence ontology
+    sf = new SequenceFeature("feature_variant", "desc", 10, 20, 3f, "group");
+    List<String> atts = new ArrayList<String>();
+    atts.add("A");
+    atts.add("C");
+    atts.add("T");
+    attributes.put("alleles", atts);
+    assertEquals("A,C,T", testee.getDescription(sf, attributes));
+
+    // Ensembl transcript or exon feature - extract Name
+    List<String> atts2 = new ArrayList<String>();
+    atts2.add("ENSE00001871077");
+    attributes.put("Name", atts2);
+    sf = new SequenceFeature("transcript", "desc", 10, 20, 3f, "group");
+    assertEquals("ENSE00001871077", testee.getDescription(sf, attributes));
+    // transcript sub-type in SO
+    sf = new SequenceFeature("mRNA", "desc", 10, 20, 3f, "group");
+    assertEquals("ENSE00001871077", testee.getDescription(sf, attributes));
+    // special usage of feature by Ensembl
+    sf = new SequenceFeature("NMD_transcript_variant", "desc", 10, 20, 3f,
+            "group");
+    assertEquals("ENSE00001871077", testee.getDescription(sf, attributes));
+    // exon feature
+    sf = new SequenceFeature("exon", "desc", 10, 20, 3f, "group");
+    assertEquals("ENSE00001871077", testee.getDescription(sf, attributes));
+  }
 }
diff --git a/test/jalview/io/gff/InterProScanHelperTest.java b/test/jalview/io/gff/InterProScanHelperTest.java
index bcccf35..59935dd 100644
--- a/test/jalview/io/gff/InterProScanHelperTest.java
+++ b/test/jalview/io/gff/InterProScanHelperTest.java
@@ -21,6 +21,7 @@
 package jalview.io.gff;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
@@ -30,6 +31,7 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceDummy;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.JvOptionPane;
 
@@ -76,6 +78,16 @@ public class InterProScanHelperTest
     assertEquals(1, newseqs.size());
     assertTrue(newseqs.get(0) instanceof SequenceDummy);
     assertEquals("match$17_5_30", newseqs.get(0).getName());
+
+    assertNotNull(newseqs.get(0).getSequenceFeatures());
+    assertEquals(1, newseqs.get(0).getSequenceFeatures().length);
+    SequenceFeature sf = newseqs.get(0).getSequenceFeatures()[0];
+    assertEquals(1, sf.getBegin());
+    assertEquals(26, sf.getEnd());
+    assertEquals("Pfam", sf.getType());
+    assertEquals("4Fe-4S dicluster domain", sf.getDescription());
+    assertEquals("InterProScan", sf.getFeatureGroup());
+
     assertEquals(1, align.getCodonFrames().size());
     AlignedCodonFrame mapping = align.getCodonFrames().iterator().next();
 
-- 
1.7.10.2