JAL-1989 map hidden column ranges

[jalview.git] / test / jalview / util / MappingUtilsTest.java

diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index 032af30..51c99af 100644 (file)
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -736,4 +736,75 @@ public class MappingUtilsTest
     assertEquals(12, e.getPosition());
     assertEquals(6, e.getNumber());
   }
+
+  /**
+   * Test mapping a column selection including hidden columns
+   * 
+   * @throws IOException
+   */
+  @Test(groups = { "Functional" })
+  public void testMapColumnSelection_hiddenColumns() throws IOException
+  {
+    setupMappedAlignments();
+  
+    ColumnSelection colsel = new ColumnSelection();
+
+    /*
+     * Column 0 in protein picks up Seq2/L, Seq3/G which map to cols 0-4 and 0-3
+     * in dna respectively, overall 0-4
+     */
+    colsel.hideColumns(0);
+    ColumnSelection cs = MappingUtils.mapColumnSelection(colsel,
+            proteinView, dnaView);
+    assertEquals("[]", cs.getSelected().toString());
+    List<int[]> hidden = cs.getHiddenColumns();
+    assertEquals(1, hidden.size());
+    assertEquals("[0, 4]", Arrays.toString(hidden.get(0)));
+
+    /*
+     * Column 1 in protein picks up Seq1/K which maps to cols 0-3 in dna
+     */
+    colsel.revealAllHiddenColumns();
+    colsel.hideColumns(1);
+    cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+    hidden = cs.getHiddenColumns();
+    assertEquals(1, hidden.size());
+    assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
+
+    /*
+     * Column 2 in protein picks up gaps only - no mapping
+     */
+    colsel.revealAllHiddenColumns();
+    colsel.clear();
+    colsel.hideColumns(2);
+    cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+    assertTrue(cs.getHiddenColumns().isEmpty());
+
+    /*
+     * Column 3 in protein picks up Seq1/P, Seq2/Q, Seq3/S which map to columns
+     * 6-9, 6-10, 5-8 respectively, overall to 5-10
+     */
+    colsel.revealAllHiddenColumns();
+    colsel.clear();
+    colsel.hideColumns(3); // 5-10 hidden in dna
+    colsel.addElement(1); // 0-3 selected in dna
+    cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+    assertEquals("[0, 1, 2, 3]", cs.getSelected().toString());
+    hidden = cs.getHiddenColumns();
+    assertEquals(1, hidden.size());
+    assertEquals("[5, 10]", Arrays.toString(hidden.get(0)));
+
+    /*
+     * Combine hiding columns 1 and 3 to get discontiguous hidden columns
+     */
+    colsel.revealAllHiddenColumns();
+    colsel.clear();
+    colsel.hideColumns(1);
+    colsel.hideColumns(3);
+    cs = MappingUtils.mapColumnSelection(colsel, proteinView, dnaView);
+    hidden = cs.getHiddenColumns();
+    assertEquals(2, hidden.size());
+    assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
+    assertEquals("[5, 10]", Arrays.toString(hidden.get(1)));
+  }
 }