From b4be31307e3a1e6d3dbb43bd14dfd012be6a3dfd Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 17 Jan 2017 15:01:01 +0000
Subject: [PATCH] JAL-2370 fix bug when hiding a range including two or more
 hidden ranges

---
 src/jalview/datamodel/ColumnSelection.java      |   18 +++++++
 src/jalview/gui/ScalePanel.java                 |    7 ++-
 test/jalview/datamodel/ColumnSelectionTest.java |   62 +++++++++++++++++++++--
 3 files changed, 81 insertions(+), 6 deletions(-)

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index d651c0b..c467f4a 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -866,6 +866,24 @@ public class ColumnSelection
          */
         region[0] = Math.min(region[0], start);
         region[1] = Math.max(region[1], end);
+
+        /*
+         * also update or remove any subsequent ranges 
+         * that are overlapped
+         */
+        while (i < hiddenColumns.size() - 1)
+        {
+          int[] nextRegion = hiddenColumns.get(i + 1);
+          if (nextRegion[0] > end + 1)
+          {
+            /*
+             * gap to next hidden range - no more to update
+             */
+            break;
+          }
+          region[1] = Math.max(nextRegion[1], end);
+          hiddenColumns.remove(i + 1);
+        }
         return;
       }
     }
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 0aa2459..00d465a 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -424,6 +424,9 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
   {
   }
 
+  /**
+   * Creates a tooltip when the mouse is over a hidden columns marker
+   */
   @Override
   public void mouseMoved(MouseEvent evt)
   {
@@ -448,11 +451,11 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
           ToolTipManager.sharedInstance().registerComponent(this);
           this.setToolTipText(MessageManager
                   .getString("label.reveal_hidden_columns"));
-          break;
+          repaint();
+          return;
         }
       }
     }
-    repaint();
   }
 
   /**
diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java
index a9ad4c2..4faa482 100644
--- a/test/jalview/datamodel/ColumnSelectionTest.java
+++ b/test/jalview/datamodel/ColumnSelectionTest.java
@@ -205,12 +205,11 @@ public class ColumnSelectionTest
     assertEquals("[5, 5]", Arrays.toString(hidden.get(1)));
 
     // hiding column 4 expands [3, 3] to [3, 4]
-    // not fancy enough to coalesce this into [3, 5] though
+    // and merges to [5, 5] to make [3, 5]
     cs.hideColumns(4);
     hidden = cs.getHiddenColumns();
-    assertEquals(2, hidden.size());
-    assertEquals("[3, 4]", Arrays.toString(hidden.get(0)));
-    assertEquals("[5, 5]", Arrays.toString(hidden.get(1)));
+    assertEquals(1, hidden.size());
+    assertEquals("[3, 5]", Arrays.toString(hidden.get(0)));
 
     // clear hidden columns (note they are added to selected)
     cs.revealAllHiddenColumns();
@@ -761,4 +760,59 @@ public class ColumnSelectionTest
     assertEquals("[5, 7]", Arrays.toString(cs2.getHiddenColumns().get(0)));
     assertEquals("[10, 11]", Arrays.toString(cs2.getHiddenColumns().get(1)));
   }
+
+  /**
+   * Test for the case when a hidden range encloses more one already hidden
+   * range
+   */
+  @Test(groups = { "Functional" })
+  public void testHideColumns_subsumingHidden()
+  {
+    /*
+     * JAL-2370 bug scenario:
+     * two hidden ranges subsumed by a third
+     */
+    ColumnSelection cs = new ColumnSelection();
+    cs.hideColumns(49, 59);
+    cs.hideColumns(69, 79);
+    List<int[]> hidden = cs.getHiddenColumns();
+    assertEquals(2, hidden.size());
+    assertEquals("[49, 59]", Arrays.toString(hidden.get(0)));
+    assertEquals("[69, 79]", Arrays.toString(hidden.get(1)));
+  
+    cs.hideColumns(48, 80);
+    hidden = cs.getHiddenColumns();
+    assertEquals(1, hidden.size());
+    assertEquals("[48, 80]", Arrays.toString(hidden.get(0)));
+
+    /*
+     * another...joining hidden ranges
+     */
+    cs = new ColumnSelection();
+    cs.hideColumns(10, 20);
+    cs.hideColumns(30, 40);
+    cs.hideColumns(50, 60);
+    // hiding 21-49 should merge to one range
+    cs.hideColumns(21, 49);
+    hidden = cs.getHiddenColumns();
+    assertEquals(1, hidden.size());
+    assertEquals("[10, 60]", Arrays.toString(hidden.get(0)));
+
+    /*
+     * another...lef overlap, subsumption, right overlap,
+     * no overlap of existing hidden ranges
+     */
+    cs = new ColumnSelection();
+    cs.hideColumns(10, 20);
+    cs.hideColumns(10, 20);
+    cs.hideColumns(30, 35);
+    cs.hideColumns(40, 50);
+    cs.hideColumns(60, 70);
+
+    cs.hideColumns(15, 45);
+    hidden = cs.getHiddenColumns();
+    assertEquals(2, hidden.size());
+    assertEquals("[10, 50]", Arrays.toString(hidden.get(0)));
+    assertEquals("[60, 70]", Arrays.toString(hidden.get(1)));
+  }
 }
-- 
1.7.10.2