+ @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));
+ }
+