From db438b70796b94abcc873a2dde1d3d46189346ed Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 1 Nov 2016 16:59:41 +0000
Subject: [PATCH] JAL-345 JAL-1738 new tests (failing) for
 SearchResultsI.markColumns

---
 test/jalview/datamodel/SearchResultsTest.java |   77 ++++++++++++++++++++++++-
 1 file changed, 76 insertions(+), 1 deletion(-)

diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java
index e3cbb00..3118d2a 100644
--- a/test/jalview/datamodel/SearchResultsTest.java
+++ b/test/jalview/datamodel/SearchResultsTest.java
@@ -25,7 +25,7 @@ import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.datamodel.SearchResults.Match;
+import java.util.BitSet;
 
 import org.testng.annotations.Test;
 
@@ -189,4 +189,79 @@ public class SearchResultsTest
     assertEquals(2, m.getStart());
     assertEquals(5, m.getEnd());
   }
+
+  /**
+   * test markColumns for creating column selections
+   */
+  @Test(groups = { "Functional" })
+  public void testMarkColumns()
+  {
+    int marked = 0;
+    SequenceI seq1 = new Sequence("", "abcdefghijklm");
+    SequenceI seq2 = new Sequence("", "abcdefghijklm");
+    SequenceGroup s1g=new SequenceGroup(), s2g=new SequenceGroup(), sallg=new SequenceGroup();
+    s1g.addSequence(seq1, false);
+    s2g.addSequence(seq2, false);
+    sallg.addSequence(seq1, false);
+    sallg.addSequence(seq2, false);
+    
+    SearchResultsI sr = new SearchResults();
+    BitSet bs = new BitSet();
+    
+    sr.addResult(seq1, 1,1);
+    sr.addResult(seq2, 1,2);
+    
+    // set start/end range for groups to cover matches
+
+    s1g.setStartRes(0);
+    s1g.setEndRes(5);
+    s2g.setStartRes(0);
+    s2g.setEndRes(5);
+    sallg.setStartRes(0);
+    sallg.setEndRes(5);
+
+    /*
+     * just seq1
+     */
+    marked = sr.markColumns(s1g, bs);
+    // check the bitset cardinality before checking the return value
+    assertEquals("Didn't mark expected number", 1, bs.cardinality());
+    assertEquals("Didn't return count of number of bits marked", 1, marked);
+    assertTrue("Didn't mark expected position", bs.get(0));
+    // now check return value for marking the same again
+    assertEquals(
+            "Didn't count number of bits marked for existing marked set",
+            0,
+            sr.markColumns(s1g, bs));
+    bs.clear();
+    
+    /*
+     * just seq2
+     */
+    marked = sr.markColumns(s2g, bs);
+    assertEquals("Didn't mark expected number", 2, bs.cardinality());
+    assertEquals("Didn't return count of number of bits marked", 2, marked);
+    assertTrue("Didn't mark expected position (1)", bs.get(0));
+    assertTrue("Didn't mark expected position (2)", bs.get(0));
+    
+    /*
+     * both seq1 and seq2 
+     * should be same as seq2
+     */
+    BitSet allbs = new BitSet();
+    assertEquals(2, sr.markColumns(sallg, allbs));
+    assertEquals(bs, allbs);
+
+    // now check range selecvtion
+
+    /*
+     * limit s2g to just the second column, sallg to the first column
+     */
+    s2g.setStartRes(1);
+    s2g.setEndRes(1);
+    sallg.setEndRes(0);
+    BitSet tbs;
+    assertEquals(1, sr.markColumns(s2g, tbs = new BitSet()));
+    assertEquals(1, sr.markColumns(sallg, tbs = new BitSet()));
+  }
 }
-- 
1.7.10.2