From 5504c1347eb582d05ae9086608223209ecb8c13d Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 11 Jan 2024 17:16:57 +0000
Subject: [PATCH] JAL-4366 test reconstruction of peptide alignment given 3di
 alignment and peptide seqs

---
 test/jalview/datamodel/AlignmentTest.java |   49 +++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 28a1ed2..67965c2 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -97,6 +97,28 @@ public class AlignmentTest
           "GCTCGUCGTACT\n" +
           ">Seq2Name/60-71\n" +
           "GGGTCAGGCAGT\n";
+  
+  private static final String AA_SEQS_2 = 
+          ">Seq1Name/5-8\n" +
+          "K-QY--L\n" +
+          ">Seq2Name/12-15\n" +
+          "-R-FP-W-\n";
+  private static final String AA_SEQS_2_DS = 
+          ">Seq1Name/5-8\n" +
+          "KQYL\n" +
+          ">Seq2Name/12-15\n" +
+          "RFPW\n";
+  private static final String TD_SEQS_2_DS = 
+          ">Seq1Name/5-8\n" +
+          "NMPR\n" +
+          ">Seq2Name/12-15\n" +
+          "VXYA\n";
+  private static final String TD_SEQS_2 = 
+          ">Seq1Name/5-8\n" +
+          "-NMP-R\n" +
+          ">Seq2Name/12-15\n" +
+          "VX--YA\n";
+
   // @formatter:on
 
   private AlignmentI al;
@@ -778,6 +800,33 @@ public class AlignmentTest
     assertEquals("-R-F-P-W", al2.getSequenceAt(1).getSequenceAsString());
   }
 
+  
+  /**
+   * Recover protein MSA from tdi msa
+   * 
+   * @throws IOException
+   */
+  @Test(groups = { "Functional" })
+  public void testAlignAs_prot_tdi() throws Exception
+  {
+    // see also AlignmentUtilsTests
+    AlignmentI al1 = loadAlignment(TD_SEQS_2, FileFormat.Fasta);
+    AlignmentI al2 = loadAlignment(AA_SEQS_2_DS, FileFormat.Fasta);
+    al1.setDataset(null);
+    al2.setDataset(null);
+    AlignmentI al1copy = new Alignment(al1);
+    AlignmentI al2copy = new Alignment(al2);
+    AlignmentUtils.map3diPeptideToProteinAligment(al2, al1);
+    if (al2.getCodonFrames().isEmpty()) {al2.getCodonFrames().addAll(al1.getCodonFrames()); }
+    else {al1.getCodonFrames().addAll(al2.getCodonFrames()); };
+    
+    ((Alignment) al2).alignAs(al1);
+    assertEquals("-NMP-R", al1.getSequenceAt(0).getSequenceAsString());
+    assertEquals("VX--YA", al1.getSequenceAt(1).getSequenceAsString());
+    assertEquals("-KQY-L", al2.getSequenceAt(0).getSequenceAsString());
+    assertEquals("RF--PW", al2.getSequenceAt(1).getSequenceAsString());
+    
+  }
   /**
    * Test aligning cdna as per protein alignment.
    * 
-- 
1.7.10.2