From 964c6de914dd7b2ef51feeb0d374cca23742f3ef Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 8 Apr 2016 16:18:15 +0100
Subject: [PATCH] JAL-2050 JAL-1722 new getSelectedRange() method to quickly
 hide selected columns

---
 src/jalview/datamodel/ColumnSelection.java      |   39 ++++++++++++++++++++---
 test/jalview/datamodel/ColumnSelectionTest.java |   26 +++++++++++++++
 2 files changed, 61 insertions(+), 4 deletions(-)

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 0d2d3bf..c23b772 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -184,6 +184,26 @@ public class ColumnSelection
     {
       return selected.get(0) ? 0 : selected.nextSetBit(0);
     }
+
+    /**
+     * @return a series of selection intervals along the range
+     */
+    public List<int[]> getRanges()
+    {
+      List<int[]> rlist = new ArrayList<int[]>();
+      if (selected.isEmpty())
+      {
+        return rlist;
+      }
+      int next = selected.nextSetBit(0), clear = -1;
+      while (next != -1)
+      {
+        clear = selected.nextClearBit(next);
+        rlist.add(new int[] { next, clear - 1 });
+        next = selected.nextSetBit(clear);
+      }
+      return rlist;
+    }
   }
 
   IntList selected = new IntList();
@@ -255,6 +275,15 @@ public class ColumnSelection
   }
 
   /**
+   * @return list of int arrays containing start and end column position for
+   *         runs of selected columns ordered from right to left.
+   */
+  public List<int[]> getSelectedRanges()
+  {
+    return selected.getRanges();
+  }
+
+  /**
    * 
    * @param col
    *          index to search for in column selection
@@ -712,10 +741,12 @@ public class ColumnSelection
 
   public void hideSelectedColumns()
   {
-    while (!selected.isEmpty())
-    {
-      int column = selected.elementAt(0);
-      hideColumns(column);
+    synchronized (selected) {
+      for (int[] selregions:selected.getRanges())
+      {
+        hideColumns(selregions[0], selregions[1]);
+      }
+      selected.clear();
     }
 
   }
diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java
index 0f08ceb..0245b15 100644
--- a/test/jalview/datamodel/ColumnSelectionTest.java
+++ b/test/jalview/datamodel/ColumnSelectionTest.java
@@ -244,6 +244,32 @@ public class ColumnSelectionTest
   }
 
   /**
+   * Test the method that gets runs of selected columns ordered by column. If
+   * this fails, HideSelectedColumns may also fail
+   */
+  @Test(groups = { "Functional" })
+  public void testgetSelectedRanges()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    int[] sel = { 2, 3, 4, 7, 8, 9, 20, 21, 22 };
+    for (int col : sel)
+    {
+      cs.addElement(col);
+    }
+    List<int[]> range;
+    range = cs.getSelectedRanges();
+    assertEquals(3, range.size());
+    assertEquals("[2, 4]", Arrays.toString(range.get(0)));
+    assertEquals("[7, 9]", Arrays.toString(range.get(1)));
+    assertEquals("[20, 22]", Arrays.toString(range.get(2)));
+    cs.addElement(0);
+    cs.addElement(1);
+    range = cs.getSelectedRanges();
+    assertEquals(3, range.size());
+    assertEquals("[0, 4]", Arrays.toString(range.get(0)));
+  }
+
+  /**
    * Test the method that reveals a range of hidden columns given the start
    * column of the range
    */
-- 
1.7.10.2