JAL-2050 hide introns also when fetching Ensembl xrefs for Uniprot

[jalview.git] / test / jalview / gui / AlignFrameTest.java

diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
new file mode 100644 (file)
index 0000000..80e3d5a
--- /dev/null
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -0,0 +1,71 @@
+package jalview.gui;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class AlignFrameTest
+{
+
+  @Test
+  public void testHideFeatureColumns()
+  {
+    SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
+    SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
+    seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5,
+            Float.NaN, null));
+    seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10,
+            Float.NaN, null));
+    seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
+            Float.NaN, null));
+    seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
+            Float.NaN, null));
+    AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
+    AlignFrame af = new AlignFrame(al, al.getWidth(), al.getHeight());
+
+    /*
+     * hiding a feature not present does nothing
+     */
+    assertFalse(af.hideFeatureColumns("exon", true));
+    assertTrue(af.getViewport().getColumnSelection().isEmpty());
+    assertTrue(af.getViewport().getColumnSelection().getHiddenColumns()
+            .isEmpty());
+    assertFalse(af.hideFeatureColumns("exon", false));
+    assertTrue(af.getViewport().getColumnSelection().isEmpty());
+    assertTrue(af.getViewport().getColumnSelection().getHiddenColumns()
+            .isEmpty());
+
+    /*
+     * hiding a feature in all columns does nothing
+     */
+    assertFalse(af.hideFeatureColumns("Metal", true));
+    assertTrue(af.getViewport().getColumnSelection().isEmpty());
+    List<int[]> hidden = af.getViewport().getColumnSelection()
+            .getHiddenColumns();
+    assertTrue(hidden.isEmpty());
+
+    /*
+     * hide a feature present in some columns
+     * sequence positions [2-4], [7-9] are column positions
+     * [1-3], [6-8] base zero
+     */
+    assertTrue(af.hideFeatureColumns("Turn", true));
+    hidden = af.getViewport().getColumnSelection()
+            .getHiddenColumns();
+    assertEquals(2, hidden.size());
+    assertEquals(1, hidden.get(0)[0]);
+    assertEquals(3, hidden.get(0)[1]);
+    assertEquals(6, hidden.get(1)[0]);
+    assertEquals(8, hidden.get(1)[1]);
+  }
+}