From 1e856963b6c483b5e73c44e9b7b6d4d44b30bae8 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 13 Mar 2018 15:58:43 +0000
Subject: [PATCH] JAL-2839 additional test case

---
 test/jalview/analysis/FinderTest.java |   47 +++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index e959e62..f05bfb3 100644
--- a/test/jalview/analysis/FinderTest.java
+++ b/test/jalview/analysis/FinderTest.java
@@ -670,4 +670,51 @@ public class FinderTest
     assertEquals(match.getStart(), 6);
     assertEquals(match.getEnd(), 6);
   }
+
+  @Test(groups = "Functional")
+  public void testFind_withHiddenColumnsAndSelection()
+  {
+    /*
+     * 0    5   9
+     * ABCD--EF-GHI
+     * A--BCDefHI
+     * --bcdEFH
+     * aa---aMMMMMaaa
+     */
+  
+    /*
+     * hide columns 2-4 and 6-7
+     */
+    HiddenColumns hc = new HiddenColumns();
+    hc.hideColumns(2, 4);
+    hc.hideColumns(6, 7);
+    al.setHiddenColumns(hc);
+  
+    /*
+     * select rows 2-3
+     */
+    SequenceGroup sg = new SequenceGroup();
+    sg.addSequence(al.getSequenceAt(1), false);
+    sg.addSequence(al.getSequenceAt(2), false);
+    sg.setStartRes(0);
+    sg.setEndRes(13);
+
+    /*
+     * find all search for A or H
+     * should match seq2/1, seq2/7, not seq3/6
+     */
+    Finder f = new Finder(al, sg);
+    f.setFindAll(true);
+    f.find("[AH]");
+    SearchResultsI searchResults = f.getSearchResults();
+    assertEquals(searchResults.getSize(), 2);
+    SearchResultMatchI match = searchResults.getResults().get(0);
+    assertSame(match.getSequence(), al.getSequenceAt(1));
+    assertEquals(match.getStart(), 1);
+    assertEquals(match.getEnd(), 1);
+    match = searchResults.getResults().get(1);
+    assertSame(match.getSequence(), al.getSequenceAt(1));
+    assertEquals(match.getStart(), 7);
+    assertEquals(match.getEnd(), 7);
+  }
 }
-- 
1.7.10.2