From 1b548e8307dd533f127252a05c845313a2bf9dd0 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Thu, 18 Jan 2018 09:07:41 +0000
Subject: [PATCH] JAL-2759 unit tests (incomplete)

---
 src/jalview/datamodel/HiddenColumns.java      |   28 ++++++-----
 test/jalview/datamodel/HiddenColumnsTest.java |   64 ++++++++++++++-----------
 2 files changed, 52 insertions(+), 40 deletions(-)

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index 037afc4..d7628b7 100644
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -444,15 +444,10 @@ public class HiddenColumns
       // take the set of hidden columns, and the set of gaps in origseq,
       // and remove all the hidden gaps from hiddenColumns
 
-      // first get the gaps as a Bitset
+      // first get the non-gaps as a Bitset
+      // then calculate hidden ^ not(gap)
       BitSet gaps = origseq.gapBitset();
-
-      // now calculate hidden ^ not(gap)
-      BitSet hidden = new BitSet();
-      markHiddenRegions(hidden);
-      hidden.andNot(gaps);
-      hiddenColumns.clear();
-      this.hideColumns(hidden);
+      this.andNot(gaps);
 
       // for each sequence in the alignment, except the profile sequence,
       // insert gaps corresponding to each hidden region but where each hidden
@@ -1159,9 +1154,12 @@ public class HiddenColumns
     clearHiddenColumnsInRange(start, end);
 
     // make sure only bits between start and end are set
-    tohide.clear(0, start - 1);
-    tohide.clear(Math.min(end + 1, tohide.length() - 1),
-            tohide.length() - 1);
+    if (!tohide.isEmpty())
+    {
+      tohide.clear(0, start - 1);
+      tohide.clear(Math.min(end + 1, tohide.length() - 1),
+              tohide.length() - 1);
+    }
 
     hideColumns(tohide);
   }
@@ -1227,16 +1225,20 @@ public class HiddenColumns
    * @param inserts
    *          BitSet where hidden columns will be marked
    */
-  public void markHiddenRegions(BitSet inserts)
+  private void andNot(BitSet updates)
   {
     try
     {
       LOCK.readLock().lock();
 
+      BitSet hiddenBitSet = new BitSet();
       for (int[] range : hiddenColumns)
       {
-        inserts.set(range[0], range[1] + 1);
+        hiddenBitSet.set(range[0], range[1] + 1);
       }
+      hiddenBitSet.andNot(updates);
+      hiddenColumns.clear();
+      hideColumns(hiddenBitSet);
     } finally
     {
       LOCK.readLock().unlock();
diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java
index dbde943..462957b 100644
--- a/test/jalview/datamodel/HiddenColumnsTest.java
+++ b/test/jalview/datamodel/HiddenColumnsTest.java
@@ -31,7 +31,6 @@ import jalview.util.Comparison;
 import java.util.Arrays;
 import java.util.BitSet;
 import java.util.Iterator;
-import java.util.Random;
 
 import org.testng.annotations.Test;
 
@@ -726,32 +725,43 @@ public class HiddenColumnsTest
   }
 
   @Test(groups = { "Functional" })
-  public void testMarkHiddenRegions()
+  public void hideColumns_BitSetAndRange()
   {
-    BitSet toMark, fromMark;
-    long seed = -3241532;
-    Random number = new Random(seed);
-    for (int n = 0; n < 1000; n++)
-    {
-      // create a random bitfield
-      toMark = BitSet
-              .valueOf(new long[]
-      { number.nextLong(), number.nextLong(), number.nextLong() });
-      toMark.set(n * number.nextInt(10), n * (25 + number.nextInt(25)));
-      HiddenColumns hc = new HiddenColumns();
-
-      if (n == 0)
-      {
-        hc.markHiddenRegions(fromMark = new BitSet());
-        assertTrue(fromMark.isEmpty());
-      }
-
-      hc.hideColumns(toMark);
-
-      // see if we can recover bitfield
-      hc.markHiddenRegions(fromMark = new BitSet());
-      assertEquals(toMark, fromMark);
-    }
+    HiddenColumns hc = new HiddenColumns();
+    hc.hideColumns(3, 5);
+    hc.hideColumns(15, 20);
+    hc.hideColumns(45, 60);
+
+    BitSet tohide = new BitSet();
+
+    // all unhidden if tohide is empty and range covers hidden
+    hc.hideColumns(tohide, 1, 70);
+    assertTrue(!hc.hasHiddenColumns());
+
+    hc.hideColumns(3, 5);
+    hc.hideColumns(15, 20);
+    hc.hideColumns(45, 60);
+
+    // but not if range does not cover hidden
+    hc.hideColumns(tohide, 23, 40);
+    assertTrue(hc.hasHiddenColumns());
+
+    // and partial unhide if range partially covers
+    hc.hideColumns(tohide, 1, 17);
+    Iterator<int[]> it = hc.iterator();
+    assertTrue(it.hasNext());
+    int[] region = it.next();
+
+    assertEquals(18, region[0]);
+    assertEquals(20, region[1]);
+
+    assertTrue(it.hasNext());
+    region = it.next();
+
+    assertEquals(45, region[0]);
+    assertEquals(60, region[1]);
+
+    assertFalse(it.hasNext());
   }
 
   @Test(groups = { "Functional" })
@@ -1150,7 +1160,7 @@ public class HiddenColumnsTest
   }
 
   @Test(groups = "Functional")
-  public void testHideMarkedBits()
+  public void testHideColumns_BitSet()
   {
     HiddenColumns h = new HiddenColumns();
     HiddenColumns h2 = new HiddenColumns();
-- 
1.7.10.2