JAL-1601 Test getVisibleCongigMapFor

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

diff --git a/test/jalview/datamodel/AlignmentViewTest.java b/test/jalview/datamodel/AlignmentViewTest.java
index 594d6e6..21c9b78 100644 (file)
--- a/test/jalview/datamodel/AlignmentViewTest.java
+++ b/test/jalview/datamodel/AlignmentViewTest.java
@@ -20,13 +20,24 @@
  */
 package jalview.datamodel;
 
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.contains;
+import org.hamcrest.Matchers;
 import static org.testng.Assert.assertEquals;
 
+import java.util.Arrays;
+import java.util.List;
+
+import jalview.gui.AlignFrame;
 import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.viewmodel.AlignmentViewport;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+
 public class AlignmentViewTest
 {
 
@@ -50,4 +61,89 @@ public class AlignmentViewTest
     assertEquals(av.getVisibleAlignment('$').getSequenceAt(0)
             .getSequenceAsString(), "A$$CDE");
   }
+
+  @Test
+  public void testGetVisibleContigMapFor()
+  {
+    AlignFrame af = new FileLoader()
+        .LoadFileWaitTillLoaded(">seq\nAAA-AAAA---AA--\n",
+            DataSourceType.PASTE);
+    var av = af.getViewport();
+    var seq = av.getAlignment().getSequenceAt(0);
+    var gapMap = seq.gapMap();
+    assertThat(Arrays.stream(gapMap).boxed().toArray(Integer[]::new),
+        Matchers.arrayContaining(0, 1, 2, 4, 5, 6, 7, 11, 12));
+
+    av.hideColumns(0, 1);
+    av.hideColumns(6, 7);
+    AlignmentView view = av.getAlignmentView(true);
+    var delMap = view.getVisibleContigMapFor(gapMap);
+    assertThat(Arrays.stream(delMap).boxed().toArray(Integer[]::new),
+        Matchers.arrayContaining(2, 3, 4, 7, 8));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetVisibleContigs()
+  {
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            ">s1\n0123456789\n", DataSourceType.PASTE);
+    AlignmentViewport av = af.getViewport();
+    AlignmentView view = av.getAlignmentView(true);
+
+    /*
+     * verify getVisibleContigs returns inclusive [start, end] ranges
+     * 
+     * no columns hidden
+     */
+    int[] contigs = view.getVisibleContigs();
+    assertEquals(contigs, new int[] { 0, 9 });
+
+    /*
+     * hide 3 internal columns
+     */
+    av.hideColumns(5, 7);
+    // the old AlignmentView is now stale!
+    contigs = view.getVisibleContigs();
+    assertEquals(contigs, new int[] { 0, 9 });
+    // get a fresh AlignmentView
+    view = av.getAlignmentView(true);
+    contigs = view.getVisibleContigs();
+    assertEquals(contigs, new int[] { 0, 4, 8, 9 });
+
+    // hide first 2 columns
+    av.hideColumns(0, 1);
+    view = av.getAlignmentView(true);
+    contigs = view.getVisibleContigs();
+    assertEquals(contigs, new int[] { 2, 4, 8, 9 });
+
+    // hide last column
+    av.hideColumns(9, 9);
+    view = av.getAlignmentView(true);
+    contigs = view.getVisibleContigs();
+    assertEquals(contigs, new int[] { 2, 4, 8, 8 });
+
+    // unhide columns 5-7
+    av.showColumn(5);
+    view = av.getAlignmentView(true);
+    contigs = view.getVisibleContigs();
+    assertEquals(contigs, new int[] { 2, 8 });
+
+    // hide columns 2-7
+    av.hideColumns(2, 7);
+    view = av.getAlignmentView(true);
+    contigs = view.getVisibleContigs();
+    assertEquals(contigs, new int[] { 8, 8 });
+
+    // hide column 8
+    av.hideColumns(8, 8);
+    view = av.getAlignmentView(true);
+    contigs = view.getVisibleContigs();
+    assertEquals(contigs, new int[] {});
+
+    // unhide all
+    av.showAllHiddenColumns();
+    view = av.getAlignmentView(true);
+    contigs = view.getVisibleContigs();
+    assertEquals(contigs, new int[] { 0, 9 });
+  }
 }