From dbf82445cab4c7459debd30a94bc3edf6d411cb9 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Mon, 13 May 2024 16:01:36 +0100
Subject: [PATCH] JAL-518 failing test for case preservation on justify

---
 test/jalview/commands/EditCommandTest.java |   44 ++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/test/jalview/commands/EditCommandTest.java b/test/jalview/commands/EditCommandTest.java
index 8e04cdd..fa52c79 100644
--- a/test/jalview/commands/EditCommandTest.java
+++ b/test/jalview/commands/EditCommandTest.java
@@ -36,10 +36,13 @@ import jalview.datamodel.SequenceI;
 import jalview.datamodel.features.SequenceFeatures;
 import jalview.gui.JvOptionPane;
 
+import java.nio.charset.Charset;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.List;
 import java.util.Map;
+import java.util.spi.LocaleServiceProvider;
 
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
@@ -1179,4 +1182,45 @@ public class EditCommandTest
     assertEquals(10, sf.getBegin());
     assertEquals(11, sf.getEnd());
   }
+  private SequenceI mkDs(SequenceI as)
+  {
+    SequenceI ds = as.createDatasetSequence();
+    ds.setSequence(ds.getSequenceAsString().toUpperCase(Locale.ROOT));
+    return ds;
+  }
+  /**
+   * Test that mimics 'remove all gapped columns' action. This generates a
+   * series Delete Gap edits that each act on all sequences that share a gapped
+   * column region.
+   */
+  @Test(groups = { "Functional" })
+  public void testLeftRight_Justify_and_preserves_gaps()
+  {
+    EditCommand command = new EditCommand();
+    String original1 = "--ABc--DEF";
+    String original2 = "-G-Hi--J";
+    String original3 = "-M-No--PQ";
+
+    /*
+     * Set up the sequence array for operations
+     */
+    SequenceI seq1 = new Sequence("sq1", original1);
+    SequenceI ds1 = mkDs(seq1);
+    /*
+     * and check we are preserving data - if the calls below fail, something has broken the Jalview dataset derivation process
+     */
+    assertEquals("ABCDEF", seq1.getDatasetSequence().getSequenceAsString());
+    assertEquals(original1,seq1.getSequenceAsString());
+    SequenceI seq2 = new Sequence("sq2",original2);
+    SequenceI ds2 = mkDs(seq2);
+    SequenceI seq3 = new Sequence("sq3", original3);
+    SequenceI ds3 = mkDs(seq3);
+    List<SequenceI> sqs = Arrays.asList( seq1, seq2, seq3 );
+    Alignment al = new Alignment(sqs.toArray(new SequenceI[0]));
+    EditCommand lefj = new JustifyLeftOrRightCommand("Left J", true, sqs, 1, 7, al);
+    String exp = "-ABcD---EF";
+    assertEquals(exp.toUpperCase(Locale.ROOT),seq1.getSequenceAsString());
+    // check case
+    assertEquals(exp,seq1.getSequenceAsString());
+  }
 }
-- 
1.7.10.2