From: kiramt <k.mourao@dundee.ac.uk>
Date: Thu, 8 Jun 2017 09:55:52 +0000 (+0100)
Subject: JAL-2591 More HiddenColumns refactoring. Tests passing.
X-Git-Tag: Release_2_10_3b1~183^2~8
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=607a4aecda2f99866bb1acf7d364a6dde4e215bd;p=jalview.git

JAL-2591 More HiddenColumns refactoring. Tests passing.
---

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 94f1caa..d4bf49a 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -570,7 +570,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI
       if (av.hasHiddenColumns())
       {
         HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-        for (int[] region : hidden)
+        for (int[] region : hidden.getHiddenColumnsCopyAsList())
         {
           int hideStart = region[0];
           int hideEnd = region[1];
diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index 837a10b..31af5f8 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -90,7 +90,7 @@ public class CigarArray extends CigarBase
   {
     this(constructSeqCigarArray(alignment, selectionGroup));
     constructFromAlignment(alignment,
-            hidden != null ? hidden.getHiddenRegions()
+            hidden != null ? hidden.getHiddenColumnsCopyAsList()
                     : null, selectionGroup);
   }
 
diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index 5966312..b53fc8b 100644
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -45,7 +45,7 @@ public class HiddenColumns
    * 
    * @return empty list or List of hidden column intervals
    */
-  public List<int[]> getHiddenRegions()
+  private List<int[]> getHiddenRegions()
   {
     return hiddenColumns == null ? Collections.<int[]> emptyList()
             : hiddenColumns;
@@ -660,8 +660,14 @@ public class HiddenColumns
 
   private ArrayList<int[]> copyHiddenRegionsToArrayList()
   {
-    ArrayList<int[]> copy = new ArrayList<>(hiddenColumns.size());
-    for (int i = 0, j = hiddenColumns.size(); i < j; i++)
+    int size = 0;
+    if (hiddenColumns != null)
+    {
+      size = hiddenColumns.size();
+    }
+    ArrayList<int[]> copy = new ArrayList<>(size);
+
+    for (int i = 0, j = size; i < j; i++)
     {
       int[] rh;
       int[] cp;
@@ -673,6 +679,7 @@ public class HiddenColumns
         copy.add(cp);
       }
     }
+
     return copy;
   }
 
diff --git a/src/jalview/datamodel/VisibleColsIterator.java b/src/jalview/datamodel/VisibleColsIterator.java
index 70de1e3..5c78f96 100644
--- a/src/jalview/datamodel/VisibleColsIterator.java
+++ b/src/jalview/datamodel/VisibleColsIterator.java
@@ -48,7 +48,7 @@ public class VisibleColsIterator implements Iterator<Integer>
     last = lastcol;
     current = firstcol;
     next = firstcol;
-    hidden = hiddenCols.getHiddenRegions();
+    hidden = hiddenCols.getHiddenColumnsCopyAsList();
     lasthiddenregion = -1;
 
     if (hidden != null)
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 4114385..c46e752 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -667,7 +667,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       int blockStart = startRes;
       int blockEnd = endRes;
 
-      for (int[] region : av.getAlignment().getHiddenColumns())
+      for (int[] region : av.getAlignment().getHiddenColumns()
+              .getHiddenColumnsCopyAsList())
       {
         int hideStart = region[0];
         int hideEnd = region[1];
diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index f75286a..1fe55f3 100644
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -518,7 +518,6 @@ public final class MappingUtils
     AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo;
     List<AlignedCodonFrame> codonFrames = protein.getAlignment()
             .getCodonFrames();
-    // ColumnSelection mappedColumns = new ColumnSelection();
 
     if (colsel == null)
     {
@@ -540,7 +539,7 @@ public final class MappingUtils
               toSequences, fromGapChar);
     }
 
-    for (int[] hidden : hiddencols)
+    for (int[] hidden : hiddencols.getHiddenColumnsCopyAsList())
     {
       mapHiddenColumns(hidden, codonFrames, newHidden, fromSequences,
               toSequences, fromGapChar);
diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java
index 7237e63..b47285c 100644
--- a/test/jalview/datamodel/ColumnSelectionTest.java
+++ b/test/jalview/datamodel/ColumnSelectionTest.java
@@ -132,7 +132,7 @@ public class ColumnSelectionTest
     // hide column 5 (and adjacent):
     cs.hideSelectedColumns(5, al.getHiddenColumns());
     // 4,5,6 now hidden:
-    List<int[]> hidden = al.getHiddenColumns().getHiddenRegions();
+    List<int[]> hidden = al.getHiddenColumns().getHiddenColumnsCopyAsList();
     assertEquals(1, hidden.size());
     assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
     // none now selected:
@@ -145,7 +145,7 @@ public class ColumnSelectionTest
     cs.addElement(5);
     cs.addElement(6);
     cs.hideSelectedColumns(4, al.getHiddenColumns());
-    hidden = al.getHiddenColumns().getHiddenRegions();
+    hidden = al.getHiddenColumns().getHiddenColumnsCopyAsList();
     assertEquals(1, hidden.size());
     assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
     assertTrue(cs.getSelected().isEmpty());
@@ -157,7 +157,7 @@ public class ColumnSelectionTest
     cs.addElement(5);
     cs.addElement(6);
     cs.hideSelectedColumns(6, al.getHiddenColumns());
-    hidden = al.getHiddenColumns().getHiddenRegions();
+    hidden = al.getHiddenColumns().getHiddenColumnsCopyAsList();
     assertEquals(1, hidden.size());
     assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
     assertTrue(cs.getSelected().isEmpty());
@@ -168,7 +168,7 @@ public class ColumnSelectionTest
     cs.addElement(4);
     cs.addElement(6);
     cs.hideSelectedColumns(5, al.getHiddenColumns());
-    hidden = al.getHiddenColumns().getHiddenRegions();
+    hidden = al.getHiddenColumns().getHiddenColumnsCopyAsList();
     assertEquals(1, hidden.size());
     assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
     assertTrue(cs.getSelected().isEmpty());
@@ -196,7 +196,7 @@ public class ColumnSelectionTest
 
     cs.hideSelectedColumns(al);
     assertTrue(cs.getSelected().isEmpty());
-    List<int[]> hidden = cols.getHiddenRegions();
+    List<int[]> hidden = cols.getHiddenColumnsCopyAsList();
     assertEquals(4, hidden.size());
     assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));
     assertEquals("[7, 9]", Arrays.toString(hidden.get(1)));
diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java
index 62c2d22..13cb526 100644
--- a/test/jalview/datamodel/HiddenColumnsTest.java
+++ b/test/jalview/datamodel/HiddenColumnsTest.java
@@ -23,7 +23,6 @@ package jalview.datamodel;
 import static org.testng.Assert.assertNull;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.analysis.AlignmentGenerator;
@@ -233,14 +232,17 @@ public class HiddenColumnsTest
     HiddenColumns cs = new HiddenColumns();
     cs.hideColumns(10, 11);
     cs.hideColumns(5, 7);
-    assertEquals("[5, 7]", Arrays.toString(cs.getHiddenRegions().get(0)));
+    assertEquals("[5, 7]",
+            Arrays.toString(cs.getHiddenColumnsCopyAsList().get(0)));
 
     HiddenColumns cs2 = new HiddenColumns(cs);
     assertTrue(cs2.hasHiddenColumns());
-    assertEquals(2, cs2.getHiddenRegions().size());
+    assertEquals(2, cs2.getHiddenColumnsCopyAsList().size());
     // hidden columns are held in column order
-    assertEquals("[5, 7]", Arrays.toString(cs2.getHiddenRegions().get(0)));
-    assertEquals("[10, 11]", Arrays.toString(cs2.getHiddenRegions().get(1)));
+    assertEquals("[5, 7]",
+            Arrays.toString(cs2.getHiddenColumnsCopyAsList().get(0)));
+    assertEquals("[10, 11]",
+            Arrays.toString(cs2.getHiddenColumnsCopyAsList().get(1)));
   }
 
   /**
@@ -337,66 +339,78 @@ public class HiddenColumnsTest
     ColumnSelection colsel = new ColumnSelection();
     HiddenColumns cs = al.getHiddenColumns();
     colsel.hideSelectedColumns(5, al.getHiddenColumns());
-    List<int[]> hidden = cs.getHiddenRegions();
+    List<int[]> hidden = cs.getHiddenColumnsCopyAsList();
     assertEquals(1, hidden.size());
     assertEquals("[5, 5]", Arrays.toString(hidden.get(0)));
 
     colsel.hideSelectedColumns(3, al.getHiddenColumns());
+    hidden = cs.getHiddenColumnsCopyAsList();
     assertEquals(2, hidden.size());
     // two hidden ranges, in order:
-    assertSame(hidden, cs.getHiddenRegions());
+    assertEquals(hidden.size(), cs.getHiddenColumnsCopyAsList().size());
     assertEquals("[3, 3]", Arrays.toString(hidden.get(0)));
     assertEquals("[5, 5]", Arrays.toString(hidden.get(1)));
 
     // hiding column 4 expands [3, 3] to [3, 4]
     // and merges to [5, 5] to make [3, 5]
     colsel.hideSelectedColumns(4, al.getHiddenColumns());
-    hidden = cs.getHiddenRegions();
+    hidden = cs.getHiddenColumnsCopyAsList();
     assertEquals(1, hidden.size());
     assertEquals("[3, 5]", Arrays.toString(hidden.get(0)));
 
     // clear hidden columns (note they are added to selected)
     cs.revealAllHiddenColumns(colsel);
     // it is now actually null but getter returns an empty list
-    assertTrue(cs.getHiddenRegions().isEmpty());
+    assertTrue(cs.getHiddenColumnsCopyAsList().isEmpty());
 
     cs.hideColumns(3, 6);
-    hidden = cs.getHiddenRegions();
+    hidden = cs.getHiddenColumnsCopyAsList();
     int[] firstHiddenRange = hidden.get(0);
     assertEquals("[3, 6]", Arrays.toString(firstHiddenRange));
 
     // adding a subrange of already hidden should do nothing
     cs.hideColumns(4, 5);
+    hidden = cs.getHiddenColumnsCopyAsList();
     assertEquals(1, hidden.size());
-    assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));
+    assertEquals("[3, 6]",
+            Arrays.toString(cs.getHiddenColumnsCopyAsList().get(0)));
     cs.hideColumns(3, 5);
+    hidden = cs.getHiddenColumnsCopyAsList();
     assertEquals(1, hidden.size());
-    assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));
+    assertEquals("[3, 6]",
+            Arrays.toString(cs.getHiddenColumnsCopyAsList().get(0)));
     cs.hideColumns(4, 6);
+    hidden = cs.getHiddenColumnsCopyAsList();
     assertEquals(1, hidden.size());
-    assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));
+    assertEquals("[3, 6]",
+            Arrays.toString(cs.getHiddenColumnsCopyAsList().get(0)));
     cs.hideColumns(3, 6);
+    hidden = cs.getHiddenColumnsCopyAsList();
     assertEquals(1, hidden.size());
-    assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));
+    assertEquals("[3, 6]",
+            Arrays.toString(cs.getHiddenColumnsCopyAsList().get(0)));
 
     cs.revealAllHiddenColumns(colsel);
     cs.hideColumns(2, 4);
-    hidden = cs.getHiddenRegions();
+    hidden = cs.getHiddenColumnsCopyAsList();
     assertEquals(1, hidden.size());
     assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));
 
     // extend contiguous with 2 positions overlap
     cs.hideColumns(3, 5);
+    hidden = cs.getHiddenColumnsCopyAsList();
     assertEquals(1, hidden.size());
     assertEquals("[2, 5]", Arrays.toString(hidden.get(0)));
 
     // extend contiguous with 1 position overlap
     cs.hideColumns(5, 6);
+    hidden = cs.getHiddenColumnsCopyAsList();
     assertEquals(1, hidden.size());
     assertEquals("[2, 6]", Arrays.toString(hidden.get(0)));
 
     // extend contiguous with overlap both ends:
     cs.hideColumns(1, 7);
+    hidden = cs.getHiddenColumnsCopyAsList();
     assertEquals(1, hidden.size());
     assertEquals("[1, 7]", Arrays.toString(hidden.get(0)));
   }
@@ -414,7 +428,7 @@ public class HiddenColumnsTest
     colsel.addElement(10);
     cs.revealHiddenColumns(5, colsel);
     // hidden columns list now null but getter returns empty list:
-    assertTrue(cs.getHiddenRegions().isEmpty());
+    assertTrue(cs.getHiddenColumnsCopyAsList().isEmpty());
     // revealed columns are marked as selected (added to selection):
     assertEquals("[10, 5, 6, 7, 8]", colsel.getSelected().toString());
 
@@ -422,9 +436,9 @@ public class HiddenColumnsTest
     colsel = new ColumnSelection();
     cs = new HiddenColumns();
     cs.hideColumns(5, 8);
-    List<int[]> hidden = cs.getHiddenRegions();
+    List<int[]> hidden = cs.getHiddenColumnsCopyAsList();
     cs.revealHiddenColumns(6, colsel);
-    assertSame(hidden, cs.getHiddenRegions());
+    assertEquals(hidden.size(), cs.getHiddenColumnsCopyAsList().size());
     assertTrue(colsel.getSelected().isEmpty());
   }
 
@@ -443,7 +457,7 @@ public class HiddenColumnsTest
      * revealing hidden columns adds them (in order) to the (unordered)
      * selection list
      */
-    assertTrue(cs.getHiddenRegions().isEmpty());
+    assertTrue(cs.getHiddenColumnsCopyAsList().isEmpty());
     assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]", colsel.getSelected()
             .toString());
   }
@@ -479,13 +493,13 @@ public class HiddenColumnsTest
     HiddenColumns cs = new HiddenColumns();
     cs.hideColumns(49, 59);
     cs.hideColumns(69, 79);
-    List<int[]> hidden = cs.getHiddenRegions();
+    List<int[]> hidden = cs.getHiddenColumnsCopyAsList();
     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.getHiddenRegions();
+    hidden = cs.getHiddenColumnsCopyAsList();
     assertEquals(1, hidden.size());
     assertEquals("[48, 80]", Arrays.toString(hidden.get(0)));
 
@@ -498,7 +512,7 @@ public class HiddenColumnsTest
     cs.hideColumns(50, 60);
     // hiding 21-49 should merge to one range
     cs.hideColumns(21, 49);
-    hidden = cs.getHiddenRegions();
+    hidden = cs.getHiddenColumnsCopyAsList();
     assertEquals(1, hidden.size());
     assertEquals("[10, 60]", Arrays.toString(hidden.get(0)));
 
@@ -514,7 +528,7 @@ public class HiddenColumnsTest
     cs.hideColumns(60, 70);
 
     cs.hideColumns(15, 45);
-    hidden = cs.getHiddenRegions();
+    hidden = cs.getHiddenColumnsCopyAsList();
     assertEquals(2, hidden.size());
     assertEquals("[10, 50]", Arrays.toString(hidden.get(0)));
     assertEquals("[60, 70]", Arrays.toString(hidden.get(1)));
@@ -531,23 +545,23 @@ public class HiddenColumnsTest
     one.set(1);
     cs = new HiddenColumns();
     cs.hideMarkedBits(one);
-    assertEquals(1, cs.getHiddenRegions().size());
+    assertEquals(1, cs.getHiddenColumnsCopyAsList().size());
 
     one.set(2);
     cs = new HiddenColumns();
     cs.hideMarkedBits(one);
-    assertEquals(1, cs.getHiddenRegions().size());
+    assertEquals(1, cs.getHiddenColumnsCopyAsList().size());
 
     one.set(3);
     cs = new HiddenColumns();
     cs.hideMarkedBits(one);
-    assertEquals(1, cs.getHiddenRegions().size());
+    assertEquals(1, cs.getHiddenColumnsCopyAsList().size());
 
     // split
     one.clear(2);
     cs = new HiddenColumns();
     cs.hideMarkedBits(one);
-    assertEquals(2, cs.getHiddenRegions().size());
+    assertEquals(2, cs.getHiddenColumnsCopyAsList().size());
 
     assertEquals(0, cs.adjustForHiddenColumns(0));
     assertEquals(2, cs.adjustForHiddenColumns(1));
@@ -558,7 +572,7 @@ public class HiddenColumnsTest
     cs = new HiddenColumns();
     cs.hideMarkedBits(one);
 
-    assertEquals(1, cs.getHiddenRegions().size());
+    assertEquals(1, cs.getHiddenColumnsCopyAsList().size());
 
     assertEquals(0, cs.adjustForHiddenColumns(0));
     assertEquals(1, cs.adjustForHiddenColumns(1));
diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
index fed5992..721ffc8 100644
--- a/test/jalview/gui/AlignFrameTest.java
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -86,12 +86,12 @@ public class AlignFrameTest
     assertFalse(alignFrame.hideFeatureColumns("exon", true));
     assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
     assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
-            .getHiddenRegions()
+            .getHiddenColumnsCopyAsList()
             .isEmpty());
     assertFalse(alignFrame.hideFeatureColumns("exon", false));
     assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
     assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
-            .getHiddenRegions()
+            .getHiddenColumnsCopyAsList()
             .isEmpty());
 
     /*
@@ -101,7 +101,7 @@ public class AlignFrameTest
     assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
     List<int[]> hidden = alignFrame.getViewport().getAlignment()
             .getHiddenColumns()
-            .getHiddenRegions();
+            .getHiddenColumnsCopyAsList();
     assertTrue(hidden.isEmpty());
 
     /*
@@ -111,7 +111,7 @@ public class AlignFrameTest
      */
     assertTrue(alignFrame.hideFeatureColumns("Turn", true));
     hidden = alignFrame.getViewport().getAlignment().getHiddenColumns()
-            .getHiddenRegions();
+            .getHiddenColumnsCopyAsList();
     assertEquals(hidden.size(), 2);
     assertEquals(hidden.get(0)[0], 1);
     assertEquals(hidden.get(0)[1], 3);
diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java
index 2aff5cc..6da6f5f 100644
--- a/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@ -73,11 +73,11 @@ public class JSONFileTest
 
   private Alignment alignment;
 
-  private HashMap<String, SequenceI> expectedSeqs = new HashMap<String, SequenceI>();
+  private HashMap<String, SequenceI> expectedSeqs = new HashMap<>();
 
-  private HashMap<String, AlignmentAnnotation> expectedAnnots = new HashMap<String, AlignmentAnnotation>();
+  private HashMap<String, AlignmentAnnotation> expectedAnnots = new HashMap<>();
 
-  private HashMap<String, SequenceGroup> expectedGrps = new HashMap<String, SequenceGroup>();
+  private HashMap<String, SequenceGroup> expectedGrps = new HashMap<>();
 
   private HiddenColumns expectedColSel = new HiddenColumns();
 
@@ -131,7 +131,7 @@ public class JSONFileTest
     }
 
     // create and add a sequence group
-    List<SequenceI> grpSeqs = new ArrayList<SequenceI>();
+    List<SequenceI> grpSeqs = new ArrayList<>();
     grpSeqs.add(seqs[1]);
     grpSeqs.add(seqs[2]);
     grpSeqs.add(seqs[3]);
@@ -195,7 +195,7 @@ public class JSONFileTest
     TEST_SEQ_HEIGHT = expectedSeqs.size();
     TEST_GRP_HEIGHT = expectedGrps.size();
     TEST_ANOT_HEIGHT = expectedAnnots.size();
-    TEST_CS_HEIGHT = expectedColSel.getHiddenRegions().size();
+    TEST_CS_HEIGHT = expectedColSel.getHiddenColumnsCopyAsList().size();
 
     exportSettings = new AlignExportSettingI()
     {
@@ -315,11 +315,11 @@ public class JSONFileTest
   {
     HiddenColumns cs = testJsonFile.getHiddenColumns();
     Assert.assertNotNull(cs);
-    Assert.assertNotNull(cs.getHiddenRegions());
-    List<int[]> hiddenCols = cs.getHiddenRegions();
+    Assert.assertNotNull(cs.getHiddenColumnsCopyAsList());
+    List<int[]> hiddenCols = cs.getHiddenColumnsCopyAsList();
     Assert.assertEquals(hiddenCols.size(), TEST_CS_HEIGHT);
     Assert.assertEquals(hiddenCols.get(0), expectedColSel
-            .getHiddenRegions().get(0),
+            .getHiddenColumnsCopyAsList().get(0),
             "Mismatched hidden columns!");
   }
 
diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 19c8438..c8b6034 100644
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -689,7 +689,7 @@ public class MappingUtilsTest
     AlignedCodonFrame acf3 = new AlignedCodonFrame();
     acf3.addMap(seq3.getDatasetSequence(), seq1.getDatasetSequence(), map);
 
-    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings = new ArrayList<>();
     mappings.add(acf1);
     mappings.add(acf2);
     mappings.add(acf3);
@@ -764,7 +764,7 @@ public class MappingUtilsTest
     AlignedCodonFrame acf4 = new AlignedCodonFrame();
     acf4.addMap(seq3.getDatasetSequence(), seq4.getDatasetSequence(), map);
 
-    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings = new ArrayList<>();
     mappings.add(acf1);
     mappings.add(acf2);
     mappings.add(acf3);
@@ -821,7 +821,7 @@ public class MappingUtilsTest
     AlignedCodonFrame acf = new AlignedCodonFrame();
     MapList map = new MapList(new int[] { 8, 16 }, new int[] { 5, 7 }, 3, 1);
     acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
-    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings = new ArrayList<>();
     mappings.add(acf);
 
     AlignmentI prot = new Alignment(new SequenceI[] { protein });
@@ -913,7 +913,7 @@ public class MappingUtilsTest
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
     assertEquals("[]", dnaSelection.getSelected().toString());
-    List<int[]> hidden = dnaHidden.getHiddenRegions();
+    List<int[]> hidden = dnaHidden.getHiddenColumnsCopyAsList();
     assertEquals(1, hidden.size());
     assertEquals("[0, 4]", Arrays.toString(hidden.get(0)));
 
@@ -930,7 +930,7 @@ public class MappingUtilsTest
     proteinSelection.hideSelectedColumns(1, hiddenCols);
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
-    hidden = dnaHidden.getHiddenRegions();
+    hidden = dnaHidden.getHiddenColumnsCopyAsList();
     assertEquals(1, hidden.size());
     assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
 
@@ -944,7 +944,7 @@ public class MappingUtilsTest
     proteinSelection.hideSelectedColumns(2, hiddenCols);
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
-    assertTrue(dnaHidden.getHiddenRegions().isEmpty());
+    assertTrue(dnaHidden.getHiddenColumnsCopyAsList().isEmpty());
 
     /*
      * Column 3 in protein picks up Seq1/P, Seq2/Q, Seq3/S which map to columns
@@ -959,7 +959,7 @@ public class MappingUtilsTest
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
     assertEquals("[0, 1, 2, 3]", dnaSelection.getSelected().toString());
-    hidden = dnaHidden.getHiddenRegions();
+    hidden = dnaHidden.getHiddenColumnsCopyAsList();
     assertEquals(1, hidden.size());
     assertEquals("[5, 10]", Arrays.toString(hidden.get(0)));
 
@@ -974,7 +974,7 @@ public class MappingUtilsTest
     proteinSelection.hideSelectedColumns(3, hiddenCols);
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
-    hidden = dnaHidden.getHiddenRegions();
+    hidden = dnaHidden.getHiddenColumnsCopyAsList();
     assertEquals(2, hidden.size());
     assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
     assertEquals("[5, 10]", Arrays.toString(hidden.get(1)));
@@ -988,7 +988,7 @@ public class MappingUtilsTest
     /*
      * [start, end] ranges
      */
-    List<int[]> ranges = new ArrayList<int[]>();
+    List<int[]> ranges = new ArrayList<>();
     assertEquals(0, MappingUtils.getLength(ranges));
     ranges.add(new int[] { 1, 1 });
     assertEquals(1, MappingUtils.getLength(ranges));
@@ -1011,7 +1011,7 @@ public class MappingUtilsTest
   public void testContains()
   {
     assertFalse(MappingUtils.contains(null, 1));
-    List<int[]> ranges = new ArrayList<int[]>();
+    List<int[]> ranges = new ArrayList<>();
     assertFalse(MappingUtils.contains(ranges, 1));
 
     ranges.add(new int[] { 1, 4 });