Merge branch 'develop' into bug/JAL-1841rnaSecStr

[jalview.git] / test / jalview / analysis / AlignmentUtilsTests.java

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 7661c5d..a856231 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -1937,13 +1937,15 @@ public class AlignmentUtilsTests
   public void testComputePeptideVariants()
   {
     /*
-     * scenario: AAATTTCCC codes for KFP, with variants
-     *           GAA -> E
-     *           CAA -> Q
-     *           AAG synonymous
-     *           AAT -> N
-     *              TTC synonymous
-     *                 CAC,CGC -> H,R (as one variant)
+     * scenario: AAATTTCCC codes for KFP
+     * variants:
+     *           GAA -> E             source: Ensembl
+     *           CAA -> Q             source: dbSNP
+     *           AAG synonymous       source: COSMIC
+     *           AAT -> N             source: Ensembl
+     *           ...TTC synonymous    source: dbSNP
+     *           ......CAC,CGC -> H,R source: COSMIC
+     *                 (one variant with two alleles)
      */
     SequenceI peptide = new Sequence("pep/10-12", "KFP");
 
@@ -1951,32 +1953,35 @@ public class AlignmentUtilsTests
      * two distinct variants for codon 1 position 1
      * second one has clinical significance
      */
+    String ensembl = "Ensembl";
+    String dbSnp = "dbSNP";
+    String cosmic = "COSMIC";
     SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1,
-            0f, null);
+            0f, ensembl);
     sf1.setValue("alleles", "A,G"); // GAA -> E
     sf1.setValue("ID", "var1.125A>G");
     SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 1, 1,
-            0f, null);
+            0f, dbSnp);
     sf2.setValue("alleles", "A,C"); // CAA -> Q
     sf2.setValue("ID", "var2");
     sf2.setValue("clinical_significance", "Dodgy");
     SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 3, 3,
-            0f, null);
+            0f, cosmic);
     sf3.setValue("alleles", "A,G"); // synonymous
     sf3.setValue("ID", "var3");
     sf3.setValue("clinical_significance", "None");
     SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 3, 3,
-            0f, null);
+            0f, ensembl);
     sf4.setValue("alleles", "A,T"); // AAT -> N
     sf4.setValue("ID", "sequence_variant:var4"); // prefix gets stripped off
     sf4.setValue("clinical_significance", "Benign");
     SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 6, 6,
-            0f, null);
+            0f, dbSnp);
     sf5.setValue("alleles", "T,C"); // synonymous
     sf5.setValue("ID", "var5");
     sf5.setValue("clinical_significance", "Bad");
     SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 8, 8,
-            0f, null);
+            0f, cosmic);
     sf6.setValue("alleles", "C,A,G"); // CAC,CGC -> H,R
     sf6.setValue("ID", "var6");
     sf6.setValue("clinical_significance", "Good");
@@ -2024,14 +2029,15 @@ public class AlignmentUtilsTests
 
     /*
      * verify added sequence features for
-     * var1 K -> E
-     * var2 K -> Q
-     * var4 K -> N
-     * var6 P -> H
-     * var6 P -> R
+     * var1 K -> E Ensembl
+     * var2 K -> Q dbSNP
+     * var4 K -> N Ensembl
+     * var6 P -> H COSMIC
+     * var6 P -> R COSMIC
      */
     SequenceFeature[] sfs = peptide.getSequenceFeatures();
     assertEquals(5, sfs.length);
+
     SequenceFeature sf = sfs[0];
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
@@ -2044,7 +2050,8 @@ public class AlignmentUtilsTests
     assertEquals(
             "p.Lys1Glu var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG",
             sf.links.get(0));
-    assertEquals("Jalview", sf.getFeatureGroup());
+    assertEquals(ensembl, sf.getFeatureGroup());
+
     sf = sfs[1];
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
@@ -2056,7 +2063,8 @@ public class AlignmentUtilsTests
     assertEquals(
             "p.Lys1Gln var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2",
             sf.links.get(0));
-    assertEquals("Jalview", sf.getFeatureGroup());
+    assertEquals(dbSnp, sf.getFeatureGroup());
+
     sf = sfs[2];
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
@@ -2068,7 +2076,9 @@ public class AlignmentUtilsTests
     assertEquals(
             "p.Lys1Asn var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
             sf.links.get(0));
-    assertEquals("Jalview", sf.getFeatureGroup());
+    assertEquals(ensembl, sf.getFeatureGroup());
+
+    // var5 generates two distinct protein variant features
     sf = sfs[3];
     assertEquals(3, sf.getBegin());
     assertEquals(3, sf.getEnd());
@@ -2080,8 +2090,8 @@ public class AlignmentUtilsTests
     assertEquals(
             "p.Pro3His var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
             sf.links.get(0));
-    // var5 generates two distinct protein variant features
-    assertEquals("Jalview", sf.getFeatureGroup());
+    assertEquals(cosmic, sf.getFeatureGroup());
+
     sf = sfs[4];
     assertEquals(3, sf.getBegin());
     assertEquals(3, sf.getEnd());
@@ -2093,7 +2103,7 @@ public class AlignmentUtilsTests
     assertEquals(
             "p.Pro3Arg var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
             sf.links.get(0));
-    assertEquals("Jalview", sf.getFeatureGroup());
+    assertEquals(cosmic, sf.getFeatureGroup());
   }
 
   /**
@@ -2449,8 +2459,9 @@ public class AlignmentUtilsTests
   {
     SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
     SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
-    SequenceI as1 = dna1.deriveSequence(), as2 = dna1.deriveSequence()
-            .getSubSequence(3, 7), as3 = dna2.deriveSequence();
+    SequenceI as1 = dna1.deriveSequence();
+    SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7);
+    SequenceI as3 = dna2.deriveSequence();
     as1.insertCharAt(6, 5, '-');
     String s_as1 = as1.getSequenceAsString();
     as2.insertCharAt(6, 5, '-');
@@ -2461,8 +2472,9 @@ public class AlignmentUtilsTests
 
     // why do we need to cast this still ?
     ((Alignment) aligned).createDatasetAlignment();
-    SequenceI uas1 = dna1.deriveSequence(), uas2 = dna1.deriveSequence()
-            .getSubSequence(3, 7), uas3 = dna2.deriveSequence();
+    SequenceI uas1 = dna1.deriveSequence();
+    SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7);
+    SequenceI uas3 = dna2.deriveSequence();
     AlignmentI tobealigned = new Alignment(new SequenceI[] { uas1, uas2,
         uas3 });
     ((Alignment) tobealigned).createDatasetAlignment();