From ce3d87d456ac70e1677909dc527eb548275e6daa Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Sun, 4 Jun 2017 12:05:49 +0100
Subject: [PATCH] JAL-2291 method taking a BitSet for hiding columns

---
 src/jalview/datamodel/HiddenColumns.java      |   17 +++++++++
 test/jalview/datamodel/HiddenColumnsTest.java |   46 +++++++++++++++++++++++++
 2 files changed, 63 insertions(+)

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index 3685ab0..96fff97 100644
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -4,6 +4,7 @@ import jalview.util.Comparison;
 import jalview.util.ShiftList;
 
 import java.util.ArrayList;
+import java.util.BitSet;
 import java.util.Collections;
 import java.util.List;
 import java.util.Vector;
@@ -1262,4 +1263,20 @@ public class HiddenColumns
     return hashCode;
   }
 
+  /**
+   * Hide columns corresponding to the marked bits
+   * 
+   * @param inserts
+   *          - columns map to bits starting from zero
+   */
+  public void hideMarkedBits(BitSet inserts)
+  {
+    for (int firstSet = inserts.nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts
+            .nextSetBit(lastSet))
+    {
+      lastSet = inserts.nextClearBit(firstSet);
+      hideColumns(firstSet, lastSet - 1);
+    }
+  }
+
 }
diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java
index b767cf7..a671263 100644
--- a/test/jalview/datamodel/HiddenColumnsTest.java
+++ b/test/jalview/datamodel/HiddenColumnsTest.java
@@ -29,6 +29,7 @@ import jalview.analysis.AlignmentGenerator;
 import jalview.gui.JvOptionPane;
 
 import java.util.Arrays;
+import java.util.BitSet;
 import java.util.List;
 
 import org.testng.annotations.BeforeClass;
@@ -517,4 +518,49 @@ public class HiddenColumnsTest
     assertEquals("[60, 70]", Arrays.toString(hidden.get(1)));
   }
 
+  @Test(groups = { "Functional" })
+  public void testHideBitset()
+  {
+    HiddenColumns cs;
+
+    BitSet one = new BitSet();
+
+    // one hidden range
+    one.set(1);
+    cs = new HiddenColumns();
+    cs.hideMarkedBits(one);
+    assertEquals(1, cs.getHiddenRegions().size());
+
+    one.set(2);
+    cs = new HiddenColumns();
+    cs.hideMarkedBits(one);
+    assertEquals(1, cs.getHiddenRegions().size());
+
+    one.set(3);
+    cs = new HiddenColumns();
+    cs.hideMarkedBits(one);
+    assertEquals(1, cs.getHiddenRegions().size());
+
+    // split
+    one.clear(2);
+    cs = new HiddenColumns();
+    cs.hideMarkedBits(one);
+    assertEquals(2, cs.getHiddenRegions().size());
+
+    assertEquals(0, cs.adjustForHiddenColumns(0));
+    assertEquals(2, cs.adjustForHiddenColumns(1));
+    assertEquals(4, cs.adjustForHiddenColumns(2));
+
+    // one again
+    one.clear(1);
+    cs = new HiddenColumns();
+    cs.hideMarkedBits(one);
+
+    assertEquals(1, cs.getHiddenRegions().size());
+
+    assertEquals(0, cs.adjustForHiddenColumns(0));
+    assertEquals(1, cs.adjustForHiddenColumns(1));
+    assertEquals(2, cs.adjustForHiddenColumns(2));
+    assertEquals(4, cs.adjustForHiddenColumns(3));
+  }
 }
-- 
1.7.10.2