From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 11 Dec 2019 14:38:39 +0000 (+0000)
Subject: JAL-3490 tests for skip hidden regions (and a bug fix)
X-Git-Tag: Release_2_11_1_1~13^2~10^2~1^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4016a0a5baf92cea3f1303fdaae3804244857427;p=jalview.git

JAL-3490 tests for skip hidden regions (and a bug fix)
---

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index fc65379..5d42905 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -223,6 +223,7 @@ public class Finder implements FinderI
     if (ignoreHidden)
     {
       seqString = getVisibleSequence(seq);
+      this.searchedSequenceStartPosition = 1;
     }
     else
     {
@@ -262,8 +263,12 @@ public class Finder implements FinderI
    */
   private String getVisibleSequence(SequenceI seq)
   {
-    int seqStartCol = seq.findIndex(seq.getStart());
-    int seqEndCol = seq.findIndex(seq.getStart() + seq.getLength() - 1);
+    /*
+     * get start / end columns of sequence and convert to base 0
+     * (so as to match the visible column ranges)
+     */
+    int seqStartCol = seq.findIndex(seq.getStart()) - 1;
+    int seqEndCol = seq.findIndex(seq.getStart() + seq.getLength() - 1) - 1;
     Iterator<int[]> visibleColumns = viewport.getViewAsVisibleContigs(true);
     StringBuilder visibleSeq = new StringBuilder(seqEndCol - seqStartCol);
     List<int[]> fromRanges = new ArrayList<>();
@@ -291,7 +296,7 @@ public class Finder implements FinderI
          * so add the range to the mapping being constructed
          */
         int seqResFrom = seq.findPosition(range[0]);
-        int seqResTo = seq.findPosition(range[1]);
+        int seqResTo = seqResFrom + ungapped.length() - 1;
         fromRanges.add(new int[] { seqResFrom, seqResTo });
       }
     }
diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index 43c48d0..78a27ac 100644
--- 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
@@ -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);
 
@@ -789,4 +793,90 @@ public class FinderTest
     assertEquals(match.getStart(), 7);
     assertEquals(match.getEnd(), 7);
   }
+
+  @Test(groups = "Functional")
+  public void testFind_skipHiddenColumns()
+  {
+    /*
+     * 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);
+  }
 }