JAL-2597 Fix and unit test

[jalview.git] / test / jalview / datamodel / HiddenColumnsTest.java

diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java
index 62c2d22..7c88d71 100644 (file)
--- 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.getHiddenColumnsCopy().get(0)));
 
     HiddenColumns cs2 = new HiddenColumns(cs);
     assertTrue(cs2.hasHiddenColumns());
-    assertEquals(2, cs2.getHiddenRegions().size());
+    assertEquals(2, cs2.getHiddenColumnsCopy().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.getHiddenColumnsCopy().get(0)));
+    assertEquals("[10, 11]",
+            Arrays.toString(cs2.getHiddenColumnsCopy().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.getHiddenColumnsCopy();
     assertEquals(1, hidden.size());
     assertEquals("[5, 5]", Arrays.toString(hidden.get(0)));
 
     colsel.hideSelectedColumns(3, al.getHiddenColumns());
+    hidden = cs.getHiddenColumnsCopy();
     assertEquals(2, hidden.size());
     // two hidden ranges, in order:
-    assertSame(hidden, cs.getHiddenRegions());
+    assertEquals(hidden.size(), cs.getHiddenColumnsCopy().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.getHiddenColumnsCopy();
     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.getHiddenColumnsCopy().isEmpty());
 
     cs.hideColumns(3, 6);
-    hidden = cs.getHiddenRegions();
+    hidden = cs.getHiddenColumnsCopy();
     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.getHiddenColumnsCopy();
     assertEquals(1, hidden.size());
-    assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));
+    assertEquals("[3, 6]",
+            Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
     cs.hideColumns(3, 5);
+    hidden = cs.getHiddenColumnsCopy();
     assertEquals(1, hidden.size());
-    assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));
+    assertEquals("[3, 6]",
+            Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
     cs.hideColumns(4, 6);
+    hidden = cs.getHiddenColumnsCopy();
     assertEquals(1, hidden.size());
-    assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));
+    assertEquals("[3, 6]",
+            Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
     cs.hideColumns(3, 6);
+    hidden = cs.getHiddenColumnsCopy();
     assertEquals(1, hidden.size());
-    assertSame(firstHiddenRange, cs.getHiddenRegions().get(0));
+    assertEquals("[3, 6]",
+            Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
 
     cs.revealAllHiddenColumns(colsel);
     cs.hideColumns(2, 4);
-    hidden = cs.getHiddenRegions();
+    hidden = cs.getHiddenColumnsCopy();
     assertEquals(1, hidden.size());
     assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));
 
     // extend contiguous with 2 positions overlap
     cs.hideColumns(3, 5);
+    hidden = cs.getHiddenColumnsCopy();
     assertEquals(1, hidden.size());
     assertEquals("[2, 5]", Arrays.toString(hidden.get(0)));
 
     // extend contiguous with 1 position overlap
     cs.hideColumns(5, 6);
+    hidden = cs.getHiddenColumnsCopy();
     assertEquals(1, hidden.size());
     assertEquals("[2, 6]", Arrays.toString(hidden.get(0)));
 
     // extend contiguous with overlap both ends:
     cs.hideColumns(1, 7);
+    hidden = cs.getHiddenColumnsCopy();
     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.getHiddenColumnsCopy().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.getHiddenColumnsCopy();
     cs.revealHiddenColumns(6, colsel);
-    assertSame(hidden, cs.getHiddenRegions());
+    assertEquals(hidden.size(), cs.getHiddenColumnsCopy().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.getHiddenColumnsCopy().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.getHiddenColumnsCopy();
     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.getHiddenColumnsCopy();
     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.getHiddenColumnsCopy();
     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.getHiddenColumnsCopy();
     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.getHiddenColumnsCopy().size());
 
     one.set(2);
     cs = new HiddenColumns();
     cs.hideMarkedBits(one);
-    assertEquals(1, cs.getHiddenRegions().size());
+    assertEquals(1, cs.getHiddenColumnsCopy().size());
 
     one.set(3);
     cs = new HiddenColumns();
     cs.hideMarkedBits(one);
-    assertEquals(1, cs.getHiddenRegions().size());
+    assertEquals(1, cs.getHiddenColumnsCopy().size());
 
     // split
     one.clear(2);
     cs = new HiddenColumns();
     cs.hideMarkedBits(one);
-    assertEquals(2, cs.getHiddenRegions().size());
+    assertEquals(2, cs.getHiddenColumnsCopy().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.getHiddenColumnsCopy().size());
 
     assertEquals(0, cs.adjustForHiddenColumns(0));
     assertEquals(1, cs.adjustForHiddenColumns(1));
@@ -675,4 +689,46 @@ public class HiddenColumnsTest
     assertNull(result);
   }
 
+  @Test(groups = "Functional")
+  public void testPropagateInsertions()
+  {
+    // create an alignment with no gaps - this will be the profile seq and other
+    // JPRED seqs
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI al = gen.generate(20, 10, 1234, 0, 0);
+
+    // get the profileseq
+    SequenceI profileseq = al.getSequenceAt(0);
+    SequenceI gappedseq = new Sequence(profileseq);
+    gappedseq.insertCharAt(5, al.getGapCharacter());
+    gappedseq.insertCharAt(6, al.getGapCharacter());
+    gappedseq.insertCharAt(7, al.getGapCharacter());
+    gappedseq.insertCharAt(8, al.getGapCharacter());
+    
+    // create an alignment view with the gapped sequence
+    SequenceI[] seqs = new SequenceI[1];
+    seqs[0] = gappedseq;
+    AlignmentI newal = new Alignment(seqs);
+    HiddenColumns hidden = new HiddenColumns();
+    hidden.hideColumns(15, 17);
+
+    AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
+            false);
+
+    // confirm that original contigs are as expected
+    int[] oldcontigs = hidden.getVisibleContigs(0, 20);
+    int[] testcontigs = { 0, 14, 18, 19 };
+    assertTrue(Arrays.equals(oldcontigs, testcontigs));
+            
+    // propagate insertions
+    HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
+            view);
+
+    // confirm that the contigs have changed to account for the gaps
+    int[] newcontigs = result.getVisibleContigs(0, 20);
+    testcontigs[1] = 10;
+    testcontigs[2] = 14;
+    assertTrue(Arrays.equals(newcontigs, testcontigs));
+    
+  }
 }