From 57924096fd7009330b3d879874f7d42874b4f416 Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Mon, 15 May 2023 14:46:34 +0100
Subject: [PATCH] JAL-4182 failing test

---
 test/jalview/analysis/AlignmentUtilsTests.java |   80 ++++++++++++++++++++++++
 1 file changed, 80 insertions(+)

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 54093ee..0f3ea96 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -20,6 +20,7 @@
  */
 package jalview.analysis;
 
+import static org.testng.Assert.assertNotEquals;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNotNull;
@@ -54,6 +55,7 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SeqDistanceContactMatrix;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.JvOptionPane;
 import jalview.io.AppletFormatAdapter;
@@ -62,6 +64,7 @@ import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
 import jalview.io.gff.SequenceOntologyI;
+import jalview.util.Comparison;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 
@@ -2602,6 +2605,83 @@ public class AlignmentUtilsTests
     assertSame(seq, cds1.getDatasetSequence());
   }
 
+
+  @Test(groups = "Functional")
+  public void testAddReferenceAnnotations()
+  {
+    SequenceI longseq= new Sequence("longA","ASDASDASDASDAASDASDASDASDA");
+    Annotation[] aa = new Annotation[longseq.getLength()];
+    
+    for (int p=0;p<aa.length; p++)
+    {
+      aa[p] = new Annotation("P", "pos "+(p+1), (char)0, (float)p+1);
+    }
+    AlignmentAnnotation refAnnot=new AlignmentAnnotation("LongSeqAnnot","Annotations",aa);
+    refAnnot.setCalcId("Test");
+    longseq.addAlignmentAnnotation(refAnnot);
+    verifyExpectedSequenceAnnotation(refAnnot);
+
+    Alignment ourAl = new Alignment(new SequenceI[] { longseq.getSubSequence(5, 10),longseq.getSubSequence(7, 12)});
+    ourAl.createDatasetAlignment();
+    
+    // transfer annotation
+    SortedMap<String, String> tipEntries = new TreeMap<>();
+    Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
+
+    AlignmentUtils.findAddableReferenceAnnotations(ourAl.getSequences(),
+            tipEntries, candidates, ourAl);
+    AlignmentUtils.addReferenceAnnotations(candidates, ourAl, null);
+
+    assertNotNull(ourAl.getAlignmentAnnotation());
+    assertEquals(ourAl.getAlignmentAnnotation().length,2);
+    
+    for (AlignmentAnnotation alan:ourAl.getAlignmentAnnotation())
+    {
+      verifyExpectedSequenceAnnotation(alan);
+    }
+    // Everything above works for 2.11.3 and 2.11.2.x.
+    // now simulate copy/paste to new alignment
+    SequenceI[] newSeqAl = new SequenceI[2];
+    // copy sequences but no annotation
+    newSeqAl[0]=new Sequence(ourAl.getSequenceAt(0),ourAl.getSequenceAt(0).getAnnotation());
+    newSeqAl[1]=new Sequence(ourAl.getSequenceAt(1),ourAl.getSequenceAt(1).getAnnotation());
+    
+    Alignment newAl = new Alignment(newSeqAl);
+    // delete annotation
+    for (SequenceI sq:newAl.getSequences())
+    {
+      sq.setAlignmentAnnotation(new AlignmentAnnotation[0]);
+    }
+    // JAL-4182 scenario test
+    SequenceGroup sg = new SequenceGroup(Arrays.asList(newSeqAl));
+    sg.setStartRes(0);
+    sg.setEndRes(newAl.getWidth());
+    AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[0], newSeqAl[0].getDatasetSequence().getAnnotation()[0], sg);
+    AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[1], newSeqAl[1].getDatasetSequence().getAnnotation()[0], sg);
+    for (AlignmentAnnotation alan:newAl.getAlignmentAnnotation())
+    {
+      verifyExpectedSequenceAnnotation(alan);
+    }
+  }
+  
+  /**
+   * helper - tests annotation is mapped to position it was originally created for
+   * @param alan
+   */
+  private void verifyExpectedSequenceAnnotation(AlignmentAnnotation alan)
+  {
+    for (int c=0;c<alan.annotations.length;c++)
+    {
+      Annotation a = alan.annotations[c];
+      if (a!=null)
+      {
+        assertEquals("Misaligned annotation at "+c,(float)alan.sequenceRef.findPosition(c),a.value);
+      } else {
+        assertTrue("Unexpected Null at position "+c,c>=alan.sequenceRef.getLength() || Comparison.isGap(alan.sequenceRef.getCharAt(c)));
+      }
+    }
+  }
+
   @Test(groups = "Functional")
   public void testAddReferenceContactMap()
   {
-- 
1.7.10.2