Merge branch 'develop' into trial_merge/JAL-1950

[jalview.git] / test / jalview / ext / ensembl / EnsemblGeneTest.java

diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java
index 6cfd85b..a8c491c 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblGeneTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java
@@ -22,7 +22,6 @@ package jalview.ext.ensembl;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.api.FeatureSettingsModelI;
@@ -76,7 +75,9 @@ public class EnsemblGeneTest
     genomic.setEnd(50000);
     String geneId = "ABC123";
 
-    // gene at (start+10000) length 501
+    // gene at (start+20000) length 501
+    // should be ignored - the first 'gene' found defines the whole range
+    // (note features are found in position order, not addition order)
     SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
             null);
     sf.setValue("ID", "gene:" + geneId);
@@ -84,7 +85,6 @@ public class EnsemblGeneTest
     genomic.addSequenceFeature(sf);
 
     // gene at (start + 10500) length 101
-    // should be ignored - the first 'gene' found defines the whole range
     sf = new SequenceFeature("gene", "", 10500, 10600, 0f, null);
     sf.setValue("ID", "gene:" + geneId);
     sf.setStrand("+");
@@ -94,13 +94,13 @@ public class EnsemblGeneTest
             23);
     List<int[]> fromRanges = ranges.getFromRanges();
     assertEquals(1, fromRanges.size());
-    assertEquals(20000, fromRanges.get(0)[0]);
-    assertEquals(20500, fromRanges.get(0)[1]);
+    assertEquals(10500, fromRanges.get(0)[0]);
+    assertEquals(10600, fromRanges.get(0)[1]);
     // to range should start from given start numbering
     List<int[]> toRanges = ranges.getToRanges();
     assertEquals(1, toRanges.size());
     assertEquals(23, toRanges.get(0)[0]);
-    assertEquals(523, toRanges.get(0)[1]);
+    assertEquals(123, toRanges.get(0)[1]);
   }
 
   /**
@@ -115,7 +115,9 @@ public class EnsemblGeneTest
     genomic.setEnd(50000);
     String geneId = "ABC123";
 
-    // gene at (start+10000) length 501
+    // gene at (start+20000) length 501
+    // should be ignored - the first 'gene' found defines the whole range
+    // (real data would only have one such feature)
     SequenceFeature sf = new SequenceFeature("ncRNA_gene", "", 20000,
             20500, 0f, null);
     sf.setValue("ID", "gene:" + geneId);
@@ -123,8 +125,6 @@ public class EnsemblGeneTest
     genomic.addSequenceFeature(sf);
 
     // gene at (start + 10500) length 101
-    // should be ignored - the first 'gene' found defines the whole range
-    // (real data would only have one such feature)
     sf = new SequenceFeature("gene", "", 10500, 10600, 0f, null);
     sf.setValue("ID", "gene:" + geneId);
     sf.setStrand("+");
@@ -135,13 +135,13 @@ public class EnsemblGeneTest
     List<int[]> fromRanges = ranges.getFromRanges();
     assertEquals(1, fromRanges.size());
     // from range on reverse strand:
-    assertEquals(20500, fromRanges.get(0)[0]);
-    assertEquals(20000, fromRanges.get(0)[1]);
+    assertEquals(10500, fromRanges.get(0)[0]);
+    assertEquals(10600, fromRanges.get(0)[1]);
     // to range should start from given start numbering
     List<int[]> toRanges = ranges.getToRanges();
     assertEquals(1, toRanges.size());
     assertEquals(23, toRanges.get(0)[0]);
-    assertEquals(523, toRanges.get(0)[1]);
+    assertEquals(123, toRanges.get(0)[1]);
   }
 
   /**
@@ -164,7 +164,7 @@ public class EnsemblGeneTest
     genomic.addSequenceFeature(sf1);
 
     // transcript sub-type feature
-    SequenceFeature sf2 = new SequenceFeature("snRNA", "", 20000, 20500,
+    SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500,
             0f, null);
     sf2.setValue("Parent", "gene:" + geneId);
     sf2.setValue("transcript_id", "transcript2");
@@ -172,13 +172,13 @@ public class EnsemblGeneTest
 
     // NMD_transcript_variant treated like transcript in Ensembl
     SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
-            20000, 20500, 0f, null);
+            22000, 22500, 0f, null);
     sf3.setValue("Parent", "gene:" + geneId);
     sf3.setValue("transcript_id", "transcript3");
     genomic.addSequenceFeature(sf3);
 
     // transcript for a different gene - ignored
-    SequenceFeature sf4 = new SequenceFeature("snRNA", "", 20000, 20500,
+    SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500,
             0f, null);
     sf4.setValue("Parent", "gene:XYZ");
     sf4.setValue("transcript_id", "transcript4");
@@ -192,9 +192,9 @@ public class EnsemblGeneTest
     List<SequenceFeature> features = testee.getTranscriptFeatures(geneId,
             genomic);
     assertEquals(3, features.size());
-    assertSame(sf1, features.get(0));
-    assertSame(sf2, features.get(1));
-    assertSame(sf3, features.get(2));
+    assertTrue(features.contains(sf1));
+    assertTrue(features.contains(sf2));
+    assertTrue(features.contains(sf3));
   }
 
   /**
@@ -211,22 +211,24 @@ public class EnsemblGeneTest
     sf.setValue("ID", "gene:" + geneId);
     assertFalse(testee.retainFeature(sf, geneId));
 
-    sf.setType("transcript");
+    sf = new SequenceFeature("transcript", "", 20000, 20500, 0f, null);
     sf.setValue("Parent", "gene:" + geneId);
     assertTrue(testee.retainFeature(sf, geneId));
 
-    sf.setType("mature_transcript");
+    sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
+            null);
     sf.setValue("Parent", "gene:" + geneId);
     assertTrue(testee.retainFeature(sf, geneId));
 
-    sf.setType("NMD_transcript_variant");
+    sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
+            0f, null);
     sf.setValue("Parent", "gene:" + geneId);
     assertTrue(testee.retainFeature(sf, geneId));
 
     sf.setValue("Parent", "gene:XYZ");
     assertFalse(testee.retainFeature(sf, geneId));
 
-    sf.setType("anything");
+    sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
     assertTrue(testee.retainFeature(sf, geneId));
   }
 
@@ -253,15 +255,18 @@ public class EnsemblGeneTest
     assertTrue(testee.identifiesSequence(sf, accId));
 
     // gene sub-type with right ID is valid
-    sf.setType("snRNA_gene");
+    sf = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null);
+    sf.setValue("ID", "gene:" + accId);
     assertTrue(testee.identifiesSequence(sf, accId));
 
     // transcript not valid:
-    sf.setType("transcript");
+    sf = new SequenceFeature("transcript", "", 1, 2, 0f, null);
+    sf.setValue("ID", "gene:" + accId);
     assertFalse(testee.identifiesSequence(sf, accId));
 
     // exon not valid:
-    sf.setType("exon");
+    sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
+    sf.setValue("ID", "gene:" + accId);
     assertFalse(testee.identifiesSequence(sf, accId));
   }