From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 13 Nov 2017 13:43:57 +0000 (+0000)
Subject: JAL-2830 failing test added for Replace
X-Git-Tag: Release_2_11_1_0~98^2~13
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c29cd7be43dcd8575d1b4b1e53920117af706ca4;p=jalview.git

JAL-2830 failing test added for Replace
---

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index f71fb79..06f59cb 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -806,9 +806,9 @@ public class EditCommand implements CommandI
         {
           // first edit the original dataset sequence string
           SequenceI oldds = command.seqs[i].getDatasetSequence();
-          String fullseq, osp = oldds.getSequenceAsString();
+          String osp = oldds.getSequenceAsString();
 
-          fullseq = osp.substring(0, ipos) + nogaprep
+          String fullseq = osp.substring(0, ipos) + nogaprep
                   + osp.substring(ipos + nogaprep.length());
 
           // and check if new sequence data is different..
diff --git a/test/jalview/commands/EditCommandTest.java b/test/jalview/commands/EditCommandTest.java
index a0c2ccf..61ca5a6 100644
--- a/test/jalview/commands/EditCommandTest.java
+++ b/test/jalview/commands/EditCommandTest.java
@@ -282,6 +282,27 @@ public class EditCommandTest
   }
 
   /**
+   * Test the replace command (used to manually edit a sequence)
+   */
+  @Test(groups = { "Functional" })
+  public void testReplace_withGaps()
+  {
+    SequenceI seq = new Sequence("seq", "ABC--DEF");
+    seq.createDatasetSequence();
+    assertEquals("ABCDEF", seq.getDatasetSequence().getSequenceAsString());
+
+    /*
+     * replace C- with XYZ
+     * NB arg4 = start column of selection for edit (base 0)
+     * arg5 = column after end of selection for edit
+     */
+    new EditCommand("", Action.REPLACE, "XYZ", new SequenceI[] { seq }, 2,
+            4, al);
+    assertEquals("ABXYZ-DEF", seq.getSequenceAsString());
+    assertEquals("ABXYZDEF", seq.getDatasetSequence().getSequenceAsString());
+  }
+
+  /**
    * Test replace command when it doesn't cause a sequence edit (see comment in
    */
   @Test(groups = { "Functional" })