JAL-3490 unit test for ignore hidden regions with selection group

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

diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index 43c48d0..725be33 100644 (file)
--- a/test/jalview/analysis/FinderTest.java
+++ b/test/jalview/analysis/FinderTest.java
@@ -144,8 +144,11 @@ public class FinderTest
 
     /*
      * find all matches should return seq1 and seq4 (others are too short)
+     * (and not matches in sequence ids)
      */
     f = new Finder(av);
+    String name = al.getSequenceAt(0).getName();
+    al.getSequenceAt(0).setName("Q9XA0");
     f.findAll("9", false, false, false);
     sr = f.getSearchResults();
     assertEquals(sr.getSize(), 2);
@@ -156,6 +159,7 @@ public class FinderTest
     assertEquals(matches.get(0).getEnd(), 9);
     assertEquals(matches.get(1).getStart(), 9);
     assertEquals(matches.get(1).getEnd(), 9);
+    al.getSequenceAt(0).setName(name);
 
     /*
      * parsing of search string as integer is strict
@@ -397,7 +401,7 @@ public class FinderTest
    * result
    */
   @Test(groups = "Functional")
-  public void testFind_maximalResultOnly()
+  public void testFindAll_maximalResultOnly()
   {
     Finder f = new Finder(av);
     f.findAll("M+", false, false, false);
@@ -452,7 +456,7 @@ public class FinderTest
    * Test finding all matches, case-sensitive
    */
   @Test(groups = "Functional")
-  public void testFind_findAllCaseSensitive()
+  public void testFindAll_caseSensitive()
   {
     Finder f = new Finder(av);
 
@@ -491,7 +495,7 @@ public class FinderTest
    * Test finding next match of a sequence pattern in a selection group
    */
   @Test(groups = "Functional")
-  public void testFind_inSelection()
+  public void testFindNext_inSelection()
   {
     /*
      * select sequences 2 and 3, columns 4-6 which contains
@@ -545,7 +549,7 @@ public class FinderTest
    * Test finding all matches of a search pattern in a selection group
    */
   @Test(groups = "Functional")
-  public void testFind_findAllInSelection()
+  public void testFindAll_inSelection()
   {
     /*
      * select sequences 2 and 3, columns 4-6 which contains
@@ -789,4 +793,117 @@ public class FinderTest
     assertEquals(match.getStart(), 7);
     assertEquals(match.getEnd(), 7);
   }
+
+  @Test(groups = "Functional")
+  public void testFind_ignoreHiddenColumns()
+  {
+    /*
+     * 0    5   9
+     * ABCD--EF-GHI
+     * A--BCDefHI
+     * --bcdEFH
+     * aa---aMMMMMaaa
+     */
+    HiddenColumns hc = new HiddenColumns();
+    hc.hideColumns(2, 4);
+    hc.hideColumns(7, 7);
+    al.setHiddenColumns(hc);
+
+    /*
+     * now have
+     * 015689
+     * AB-E-GHI
+     * A-DeHI
+     * --EF
+     * aaaMMMMaaa
+     */
+    Finder f = new Finder(av);
+    f.findAll("abe", false, false, true); // true = ignore hidden
+    SearchResultsI searchResults = f.getSearchResults();
+
+    /*
+     * match of seq1 ABE made up of AB and E
+     */
+    assertEquals(searchResults.getSize(), 2);
+    SearchResultMatchI match = searchResults.getResults().get(0);
+    assertSame(match.getSequence(), al.getSequenceAt(0));
+    assertEquals(match.getStart(), 8); // A
+    assertEquals(match.getEnd(), 9); // B
+    match = searchResults.getResults().get(1);
+    assertSame(match.getSequence(), al.getSequenceAt(0));
+    assertEquals(match.getStart(), 12); // E
+    assertEquals(match.getEnd(), 12);
+
+    f = new Finder(av);
+    f.findNext("a.E", false, false, true);
+    searchResults = f.getSearchResults();
+    assertEquals(searchResults.getSize(), 2);
+    match = searchResults.getResults().get(0);
+    assertSame(match.getSequence(), al.getSequenceAt(0));
+    assertEquals(match.getStart(), 8); // A
+    assertEquals(match.getEnd(), 9); // B
+    match = searchResults.getResults().get(1);
+    assertSame(match.getSequence(), al.getSequenceAt(0));
+    assertEquals(match.getStart(), 12); // E
+    assertEquals(match.getEnd(), 12);
+
+    f.findNext("a.E", false, false, true);
+    searchResults = f.getSearchResults();
+    assertEquals(searchResults.getSize(), 2);
+    match = searchResults.getResults().get(0);
+    assertSame(match.getSequence(), al.getSequenceAt(1));
+    assertEquals(match.getStart(), 1); // a
+    assertEquals(match.getEnd(), 1);
+    match = searchResults.getResults().get(1);
+    assertSame(match.getSequence(), al.getSequenceAt(1));
+    assertEquals(match.getStart(), 4); // D
+    assertEquals(match.getEnd(), 5); // e
+
+    /*
+     * find all matching across two hidden column regions
+     * note one 'match' is reported as three contiguous matches
+     */
+    f.findAll("BEG", false, false, true);
+    searchResults = f.getSearchResults();
+    assertEquals(searchResults.getSize(), 3);
+    match = searchResults.getResults().get(0);
+    assertSame(match.getSequence(), al.getSequenceAt(0));
+    assertEquals(match.getStart(), 9); // B
+    assertEquals(match.getEnd(), 9);
+    match = searchResults.getResults().get(1);
+    assertSame(match.getSequence(), al.getSequenceAt(0));
+    assertEquals(match.getStart(), 12); // E
+    assertEquals(match.getEnd(), 12);
+    match = searchResults.getResults().get(2);
+    assertSame(match.getSequence(), al.getSequenceAt(0));
+    assertEquals(match.getStart(), 14); // G
+    assertEquals(match.getEnd(), 14);
+
+    /*
+     * now select columns 0-9 and search for A.*H
+     * this should match in the second sequence (split as 3 matches)
+     * but not the first (as H is outside the selection)
+     */
+    SequenceGroup selection = new SequenceGroup();
+    selection.setStartRes(0);
+    selection.setEndRes(9);
+    al.getSequences().forEach(seq -> selection.addSequence(seq, false));
+    av.setSelectionGroup(selection);
+    f.findAll("A.*H", false, false, true);
+    searchResults = f.getSearchResults();
+    assertEquals(searchResults.getSize(), 3);
+    // match made of contiguous matches A, DE, H
+    match = searchResults.getResults().get(0);
+    assertSame(match.getSequence(), al.getSequenceAt(1));
+    assertEquals(match.getStart(), 1); // A
+    assertEquals(match.getEnd(), 1);
+    match = searchResults.getResults().get(1);
+    assertSame(match.getSequence(), al.getSequenceAt(1));
+    assertEquals(match.getStart(), 4); // D
+    assertEquals(match.getEnd(), 5); // E
+    match = searchResults.getResults().get(2);
+    assertSame(match.getSequence(), al.getSequenceAt(1));
+    assertEquals(match.getStart(), 7); // H (there is no G)
+    assertEquals(match.getEnd(), 7);
+  }
 }