JAL-2557 removal of Sequence.sequenceFeatures

[jalview.git] / test / jalview / io / FeaturesFileTest.java

diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index b88c2ee..45340d9 100644 (file)
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -23,7 +23,6 @@ package jalview.io;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNotNull;
-import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.api.FeatureColourI;
@@ -33,6 +32,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
 import jalview.gui.AlignFrame;
 import jalview.gui.JvOptionPane;
 
@@ -86,10 +86,15 @@ public class FeaturesFileTest
     /*
      * verify (some) features on sequences
      */
-    SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
+    List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
             .getSequenceFeatures(); // FER_CAPAA
-    assertEquals(8, sfs.length);
-    SequenceFeature sf = sfs[0];
+    SequenceFeatures.sortFeatures(sfs, true);
+    assertEquals(8, sfs.size());
+
+    /*
+     * verify (in ascending start position order)
+     */
+    SequenceFeature sf = sfs.get(0);
     assertEquals("Pfam family%LINK%", sf.description);
     assertEquals(0, sf.begin);
     assertEquals(0, sf.end);
@@ -99,46 +104,52 @@ public class FeaturesFileTest
     assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111",
             sf.links.get(0));
 
-    sf = sfs[1];
+    sf = sfs.get(1);
+    assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
+    assertEquals(3, sf.begin);
+    assertEquals(93, sf.end);
+    assertEquals("uniprot", sf.featureGroup);
+    assertEquals("Cath", sf.type);
+
+    sf = sfs.get(2);
+    assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
+            sf.description);
+    assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
+            sf.links.get(0));
+    assertEquals(8, sf.begin);
+    assertEquals(83, sf.end);
+    assertEquals("uniprot", sf.featureGroup);
+    assertEquals("Pfam", sf.type);
+
+    sf = sfs.get(3);
     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
     assertEquals(39, sf.begin);
     assertEquals(39, sf.end);
     assertEquals("uniprot", sf.featureGroup);
     assertEquals("METAL", sf.type);
-    sf = sfs[2];
+
+    sf = sfs.get(4);
     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
     assertEquals(44, sf.begin);
     assertEquals(44, sf.end);
     assertEquals("uniprot", sf.featureGroup);
     assertEquals("METAL", sf.type);
-    sf = sfs[3];
+
+    sf = sfs.get(5);
     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
     assertEquals(47, sf.begin);
     assertEquals(47, sf.end);
     assertEquals("uniprot", sf.featureGroup);
     assertEquals("METAL", sf.type);
-    sf = sfs[4];
+
+    sf = sfs.get(6);
     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
     assertEquals(77, sf.begin);
     assertEquals(77, sf.end);
     assertEquals("uniprot", sf.featureGroup);
     assertEquals("METAL", sf.type);
-    sf = sfs[5];
-    assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
-            sf.description);
-    assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111",
-            sf.links.get(0));
-    assertEquals(8, sf.begin);
-    assertEquals(83, sf.end);
-    assertEquals("uniprot", sf.featureGroup);
-    assertEquals("Pfam", sf.type);
-    sf = sfs[6];
-    assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
-    assertEquals(3, sf.begin);
-    assertEquals(93, sf.end);
-    assertEquals("uniprot", sf.featureGroup);
-    assertEquals("Cath", sf.type);
-    sf = sfs[7];
+
+    sf = sfs.get(7);
     assertEquals(
             "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
             sf.description);
@@ -181,10 +192,10 @@ public class FeaturesFileTest
     assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
 
     // verify feature on FER_CAPAA
-    SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
+    List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
             .getSequenceFeatures();
-    assertEquals(1, sfs.length);
-    SequenceFeature sf = sfs[0];
+    assertEquals(1, sfs.size());
+    SequenceFeature sf = sfs.get(0);
     assertEquals("Iron-sulfur,2Fe-2S", sf.description);
     assertEquals(44, sf.begin);
     assertEquals(45, sf.end);
@@ -194,8 +205,8 @@ public class FeaturesFileTest
 
     // verify feature on FER1_SOLLC
     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
-    assertEquals(1, sfs.length);
-    sf = sfs[0];
+    assertEquals(1, sfs.size());
+    sf = sfs.get(0);
     assertEquals("uniprot", sf.description);
     assertEquals(55, sf.begin);
     assertEquals(130, sf.end);
@@ -242,10 +253,10 @@ public class FeaturesFileTest
             featuresFile.parse(al.getDataset(), colours, true));
 
     // verify feature on FER_CAPAA
-    SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
+    List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
             .getSequenceFeatures();
-    assertEquals(1, sfs.length);
-    SequenceFeature sf = sfs[0];
+    assertEquals(1, sfs.size());
+    SequenceFeature sf = sfs.get(0);
     // description parsed from Note attribute
     assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
     assertEquals(39, sf.begin);
@@ -258,8 +269,8 @@ public class FeaturesFileTest
 
     // verify feature on FER1_SOLLC1
     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
-    assertEquals(1, sfs.length);
-    sf = sfs[0];
+    assertEquals(1, sfs.size());
+    sf = sfs.get(0);
     // ID used for description if available
     assertEquals("$23", sf.description);
     assertEquals(55, sf.begin);
@@ -295,10 +306,10 @@ public class FeaturesFileTest
             featuresFile.parse(al.getDataset(), colours, true));
 
     // verify FER_CAPAA feature
-    SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
+    List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
             .getSequenceFeatures();
-    assertEquals(1, sfs.length);
-    SequenceFeature sf = sfs[0];
+    assertEquals(1, sfs.size());
+    SequenceFeature sf = sfs.get(0);
     assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
     assertEquals(39, sf.begin);
     assertEquals(39, sf.end);
@@ -306,8 +317,8 @@ public class FeaturesFileTest
 
     // verify FER1_SOLLC feature
     sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
-    assertEquals(1, sfs.length);
-    sf = sfs[0];
+    assertEquals(1, sfs.size());
+    sf = sfs.get(0);
     assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
     assertEquals(86, sf.begin);
     assertEquals(87, sf.end);
@@ -337,14 +348,14 @@ public class FeaturesFileTest
     assertFalse("dummy replacement buggy for seq2",
             placeholderseq.equals(seq2.getSequenceAsString()));
     assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
-    assertEquals("Wrong number of features", 3,
-            seq1.getSequenceFeatures().length);
-    assertNull(seq2.getSequenceFeatures());
+    assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
+            .size());
+    assertTrue(seq2.getSequenceFeatures().isEmpty());
     assertEquals(
             "Wrong number of features",
             0,
             seq2.getSequenceFeatures() == null ? 0 : seq2
-                    .getSequenceFeatures().length);
+                    .getSequenceFeatures().size());
     assertTrue(
             "Expected at least one CDNA/Protein mapping for seq1",
             dataset.getCodonFrame(seq1) != null