JAL-2557 removal of Sequence.sequenceFeatures

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

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index bada3ca..4439bb9 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -40,6 +40,7 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
 import jalview.gui.JvOptionPane;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
@@ -1179,12 +1180,12 @@ public class AlignmentUtilsTests
     /*
      * check cds2 acquired a variant feature in position 5
      */
-    SequenceFeature[] sfs = cds2Dss.getSequenceFeatures();
+    List<SequenceFeature> sfs = cds2Dss.getSequenceFeatures();
     assertNotNull(sfs);
-    assertEquals(1, sfs.length);
-    assertEquals("variant", sfs[0].type);
-    assertEquals(5, sfs[0].begin);
-    assertEquals(5, sfs[0].end);
+    assertEquals(1, sfs.size());
+    assertEquals("variant", sfs.get(0).type);
+    assertEquals(5, sfs.get(0).begin);
+    assertEquals(5, sfs.get(0).end);
   }
 
   /**
@@ -1489,39 +1490,39 @@ public class AlignmentUtilsTests
      * that partially overlap 5' or 3' (start or end) of target sequence
      */
     AlignmentUtils.transferFeatures(dna, cds, map, null);
-    SequenceFeature[] sfs = cds.getSequenceFeatures();
-    assertEquals(6, sfs.length);
+    List<SequenceFeature> sfs = cds.getSequenceFeatures();
+    assertEquals(6, sfs.size());
 
-    SequenceFeature sf = sfs[0];
+    SequenceFeature sf = sfs.get(0);
     assertEquals("type2", sf.getType());
     assertEquals("desc2", sf.getDescription());
     assertEquals(2f, sf.getScore());
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
 
-    sf = sfs[1];
+    sf = sfs.get(1);
     assertEquals("type3", sf.getType());
     assertEquals("desc3", sf.getDescription());
     assertEquals(3f, sf.getScore());
     assertEquals(1, sf.getBegin());
     assertEquals(3, sf.getEnd());
 
-    sf = sfs[2];
+    sf = sfs.get(2);
     assertEquals("type4", sf.getType());
     assertEquals(2, sf.getBegin());
     assertEquals(5, sf.getEnd());
 
-    sf = sfs[3];
+    sf = sfs.get(3);
     assertEquals("type5", sf.getType());
     assertEquals(1, sf.getBegin());
     assertEquals(6, sf.getEnd());
 
-    sf = sfs[4];
+    sf = sfs.get(4);
     assertEquals("type8", sf.getType());
     assertEquals(6, sf.getBegin());
     assertEquals(6, sf.getEnd());
 
-    sf = sfs[5];
+    sf = sfs.get(5);
     assertEquals("type9", sf.getType());
     assertEquals(6, sf.getBegin());
     assertEquals(6, sf.getEnd());
@@ -1551,10 +1552,10 @@ public class AlignmentUtilsTests
 
     // desc4 and desc8 are the 'omit these' varargs
     AlignmentUtils.transferFeatures(dna, cds, map, null, "type4", "type8");
-    SequenceFeature[] sfs = cds.getSequenceFeatures();
-    assertEquals(1, sfs.length);
+    List<SequenceFeature> sfs = cds.getSequenceFeatures();
+    assertEquals(1, sfs.size());
 
-    SequenceFeature sf = sfs[0];
+    SequenceFeature sf = sfs.get(0);
     assertEquals("type5", sf.getType());
     assertEquals(1, sf.getBegin());
     assertEquals(6, sf.getEnd());
@@ -1584,10 +1585,10 @@ public class AlignmentUtilsTests
 
     // "type5" is the 'select this type' argument
     AlignmentUtils.transferFeatures(dna, cds, map, "type5");
-    SequenceFeature[] sfs = cds.getSequenceFeatures();
-    assertEquals(1, sfs.length);
+    List<SequenceFeature> sfs = cds.getSequenceFeatures();
+    assertEquals(1, sfs.size());
 
-    SequenceFeature sf = sfs[0];
+    SequenceFeature sf = sfs.get(0);
     assertEquals("type5", sf.getType());
     assertEquals(1, sf.getBegin());
     assertEquals(6, sf.getEnd());
@@ -2078,24 +2079,29 @@ public class AlignmentUtilsTests
      * var6 P -> H COSMIC
      * var6 P -> R COSMIC
      */
-    SequenceFeature[] sfs = peptide.getSequenceFeatures();
-    assertEquals(5, sfs.length);
+    List<SequenceFeature> sfs = peptide.getSequenceFeatures();
+    SequenceFeatures.sortFeatures(sfs, true);
+    assertEquals(5, sfs.size());
 
-    SequenceFeature sf = sfs[0];
+    /*
+     * features are sorted by start position ascending, but in no
+     * particular order where start positions match; asserts here
+     * simply match the data returned (the order is not important)
+     */
+    SequenceFeature sf = sfs.get(0);
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
-    assertEquals("p.Lys1Glu", sf.getDescription());
-    assertEquals("var1.125A>G", sf.getValue("ID"));
-    assertNull(sf.getValue("clinical_significance"));
-    assertEquals("ID=var1.125A>G", sf.getAttributes());
+    assertEquals("p.Lys1Asn", sf.getDescription());
+    assertEquals("var4", sf.getValue("ID"));
+    assertEquals("Benign", sf.getValue("clinical_significance"));
+    assertEquals("ID=var4;clinical_significance=Benign", sf.getAttributes());
     assertEquals(1, sf.links.size());
-    // link to variation is urlencoded
     assertEquals(
-            "p.Lys1Glu var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG",
+            "p.Lys1Asn var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
             sf.links.get(0));
     assertEquals(ensembl, sf.getFeatureGroup());
 
-    sf = sfs[1];
+    sf = sfs.get(1);
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
     assertEquals("p.Lys1Gln", sf.getDescription());
@@ -2108,43 +2114,44 @@ public class AlignmentUtilsTests
             sf.links.get(0));
     assertEquals(dbSnp, sf.getFeatureGroup());
 
-    sf = sfs[2];
+    sf = sfs.get(2);
     assertEquals(1, sf.getBegin());
     assertEquals(1, sf.getEnd());
-    assertEquals("p.Lys1Asn", sf.getDescription());
-    assertEquals("var4", sf.getValue("ID"));
-    assertEquals("Benign", sf.getValue("clinical_significance"));
-    assertEquals("ID=var4;clinical_significance=Benign", sf.getAttributes());
+    assertEquals("p.Lys1Glu", sf.getDescription());
+    assertEquals("var1.125A>G", sf.getValue("ID"));
+    assertNull(sf.getValue("clinical_significance"));
+    assertEquals("ID=var1.125A>G", sf.getAttributes());
     assertEquals(1, sf.links.size());
+    // link to variation is urlencoded
     assertEquals(
-            "p.Lys1Asn var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
+            "p.Lys1Glu var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG",
             sf.links.get(0));
     assertEquals(ensembl, sf.getFeatureGroup());
 
-    // var5 generates two distinct protein variant features
-    sf = sfs[3];
+    sf = sfs.get(3);
     assertEquals(3, sf.getBegin());
     assertEquals(3, sf.getEnd());
-    assertEquals("p.Pro3His", sf.getDescription());
+    assertEquals("p.Pro3Arg", sf.getDescription());
     assertEquals("var6", sf.getValue("ID"));
     assertEquals("Good", sf.getValue("clinical_significance"));
     assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
-            "p.Pro3His var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
+            "p.Pro3Arg var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
             sf.links.get(0));
     assertEquals(cosmic, sf.getFeatureGroup());
 
-    sf = sfs[4];
+    // var5 generates two distinct protein variant features
+    sf = sfs.get(4);
     assertEquals(3, sf.getBegin());
     assertEquals(3, sf.getEnd());
-    assertEquals("p.Pro3Arg", sf.getDescription());
+    assertEquals("p.Pro3His", sf.getDescription());
     assertEquals("var6", sf.getValue("ID"));
     assertEquals("Good", sf.getValue("clinical_significance"));
     assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
     assertEquals(1, sf.links.size());
     assertEquals(
-            "p.Pro3Arg var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
+            "p.Pro3His var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
             sf.links.get(0));
     assertEquals(cosmic, sf.getFeatureGroup());
   }