JAL-3490 Finder match across entirely gapped hidden regions

[jalview.git] / test / jalview / analysis / FinderTest.java

diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index 5f64b28..f3ae69f 100644 (file)
--- a/test/jalview/analysis/FinderTest.java
+++ b/test/jalview/analysis/FinderTest.java
@@ -71,7 +71,7 @@ public class FinderTest
     Cache.applicationProperties.setProperty("PAD_GAPS",
             Boolean.FALSE.toString());
 
-    String seqData = "seq1seq1/8-18 ABCD--EF-GHIJI\n" + "seq2 A--BCDefHI\n"
+    String seqData = "seq1/8-18 ABCD--EF-GHIJI\n" + "seq2 A--BCDefHI\n"
             + "seq3 --bcdEFH\n" + "seq4 aa---aMMMMMaaa\n";
     af = new FileLoader().LoadFileWaitTillLoaded(seqData,
             DataSourceType.PASTE);
@@ -615,7 +615,8 @@ public class FinderTest
   }
 
   /**
-   * Test that find does not report hidden positions
+   * Test that find does not report hidden positions, but does report matches that
+   * span hidden gaps
    */
   @Test(groups = "Functional")
   public void testFind_withHiddenColumns()
@@ -629,28 +630,73 @@ public class FinderTest
      */
 
     /*
-     * hide 2-4 (CD- -BC bcd ---)
+     * hide column 3 only, search for aaa
+     * should find two matches: aa-[-]-aa and trailing aaa
      */
     HiddenColumns hc = new HiddenColumns();
-    hc.hideColumns(2, 4);
+    hc.hideColumns(3, 3);
     al.setHiddenColumns(hc);
+    Finder f = new Finder(av);
+    f.findAll("aaa", false, false);
+    SearchResultsI searchResults = f.getSearchResults();
+    assertEquals(searchResults.getSize(), 2);
+    SearchResultMatchI match = searchResults.getResults().get(0);
+    assertSame(match.getSequence(), al.getSequenceAt(3));
+    assertEquals(match.getStart(), 1);
+    assertEquals(match.getEnd(), 3);
+    match = searchResults.getResults().get(1);
+    assertSame(match.getSequence(), al.getSequenceAt(3));
+    assertEquals(match.getStart(), 9);
+    assertEquals(match.getEnd(), 11);
+
+    /*
+     * hide 2-4 (CD- -BC bcd ---)
+     */
+    hc.hideColumns(2, 4);
 
     /*
      * find all search for D should ignore hidden positions in seq1 and seq3,
      * find the visible D in seq2
      */
-    Finder f = new Finder(av);
+    f = new Finder(av);
     f.findAll("D", false, false);
-    SearchResultsI searchResults = f.getSearchResults();
+    searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
-    SearchResultMatchI match = searchResults.getResults().get(0);
+    match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 4);
     assertEquals(match.getEnd(), 4);
 
     /*
+     * search for AD should fail although these are now
+     * consecutive in the visible columns
+     */
+    f = new Finder(av);
+    f.findAll("AD", false, false);
+    searchResults = f.getSearchResults();
+    assertTrue(searchResults.isEmpty());
+
+    /*
+     * find all 'aaa' should find both start and end of seq4
+     * (first run includes hidden gaps)
+     */
+    f = new Finder(av);
+    f.findAll("aaa", false, false);
+    searchResults = f.getSearchResults();
+    assertEquals(searchResults.getSize(), 2);
+    match = searchResults.getResults().get(0);
+    assertSame(match.getSequence(), al.getSequenceAt(3));
+    assertEquals(match.getStart(), 1);
+    assertEquals(match.getEnd(), 3);
+    match = searchResults.getResults().get(1);
+    assertSame(match.getSequence(), al.getSequenceAt(3));
+    assertEquals(match.getStart(), 9);
+    assertEquals(match.getEnd(), 11);
+
+    /*
      * hide columns 2-5:
      * find all 'aaa' should find end of seq4 only
+     * (hidden columns not all gapped)
      */
     hc.hideColumns(2, 5);
     f = new Finder(av);