JAL-1551 spotlessApply

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

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index c1eb9fd..c526fa1 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -27,21 +27,34 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.analysis.AlignmentUtils.DnaVariant;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GeneLociI;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SeqDistanceContactMatrix;
 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;
@@ -51,18 +64,6 @@ import jalview.io.FormatAdapter;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
-import jalview.ws.params.InvalidArgumentException;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
 
 public class AlignmentUtilsTests
 {
@@ -2457,7 +2458,7 @@ public class AlignmentUtilsTests
    * the given protein. That is, given a transcript-to-peptide mapping, find the
    * cds-to-peptide mapping that relates to both, and return the CDS sequence.
    */
-  @Test
+  @Test(groups = "Functional")
   public void testFindCdsForProtein()
   {
     List<AlignedCodonFrame> mappings = new ArrayList<>();
@@ -2527,7 +2528,7 @@ public class AlignmentUtilsTests
    * cds-to-peptide mapping that relates to both, and return the CDS sequence.
    * This test is for the case where transcript and CDS are the same length.
    */
-  @Test
+  @Test(groups = "Functional")
   public void testFindCdsForProtein_noUTR()
   {
     List<AlignedCodonFrame> mappings = new ArrayList<>();
@@ -2607,15 +2608,15 @@ public class AlignmentUtilsTests
     SequenceI sq = new Sequence("a", "SSSQ");
     ContactMatrixI cm = new SeqDistanceContactMatrix(4);
     AlignmentAnnotation cm_aan = sq.addContactList(cm);
+    cm_aan.description = cm_aan.description + " cm1";
     SequenceI dssq = sq.createDatasetSequence();
-    Alignment ds = new Alignment(new SequenceI[] { dssq });
 
     // remove annotation on our non-dataset sequence
     sq.removeAlignmentAnnotation(sq.getAnnotation()[0]);
     // test transfer
     Alignment al = new Alignment(new SequenceI[] { sq });
     SortedMap<String, String> tipEntries = new TreeMap<>();
-    final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
+    Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
 
     AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(),
             tipEntries, candidates, al);
@@ -2629,6 +2630,24 @@ public class AlignmentUtilsTests
     assertNotNull(
             "No contact matrix recovered after reference annotation transfer",
             cl);
+    // semantics of sequence associated contact list is slightly tricky - column
+    // 3 in alignment should have data
+    cl = al.getContactListFor(alan, 3);
+    assertNotNull(
+            "Contact matrix should have data for last position in sequence",
+            cl);
+
+    ContactMatrixI cm2 = new SeqDistanceContactMatrix(4);
+    dssq.addContactList(cm2);
+    tipEntries = new TreeMap<>();
+    candidates = new LinkedHashMap<>();
+
+    AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(),
+            tipEntries, candidates, al);
+    AlignmentUtils.addReferenceAnnotations(candidates, al, null);
+    assertTrue("Expected two contact map annotation transferred",
+            al.getAlignmentAnnotation() != null
+                    && al.getAlignmentAnnotation().length == 2);
 
   }
 }