AlignedCodonFrame acf3 = new AlignedCodonFrame();
acf3.addMap(seq3.getDatasetSequence(), seq1.getDatasetSequence(), map);
- List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings = new ArrayList<>();
mappings.add(acf1);
mappings.add(acf2);
mappings.add(acf3);
AlignedCodonFrame acf4 = new AlignedCodonFrame();
acf4.addMap(seq3.getDatasetSequence(), seq4.getDatasetSequence(), map);
- List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings = new ArrayList<>();
mappings.add(acf1);
mappings.add(acf2);
mappings.add(acf3);
AlignedCodonFrame acf = new AlignedCodonFrame();
MapList map = new MapList(new int[] { 8, 16 }, new int[] { 5, 7 }, 3, 1);
acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
- List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings = new ArrayList<>();
mappings.add(acf);
AlignmentI prot = new Alignment(new SequenceI[] { protein });
MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
proteinView, dnaView, dnaSelection, dnaHidden);
assertEquals("[]", dnaSelection.getSelected().toString());
- List<int[]> hidden = dnaHidden.getListOfCols();
+ List<int[]> hidden = dnaHidden.getHiddenColumnsCopy();
assertEquals(1, hidden.size());
assertEquals("[0, 4]", Arrays.toString(hidden.get(0)));
proteinSelection.hideSelectedColumns(1, hiddenCols);
MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
proteinView, dnaView, dnaSelection, dnaHidden);
- hidden = dnaHidden.getListOfCols();
+ hidden = dnaHidden.getHiddenColumnsCopy();
assertEquals(1, hidden.size());
assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
proteinSelection.hideSelectedColumns(2, hiddenCols);
MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
proteinView, dnaView, dnaSelection, dnaHidden);
- assertTrue(dnaHidden.getListOfCols().isEmpty());
+ assertTrue(dnaHidden.getHiddenColumnsCopy().isEmpty());
/*
* Column 3 in protein picks up Seq1/P, Seq2/Q, Seq3/S which map to columns
MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
proteinView, dnaView, dnaSelection, dnaHidden);
assertEquals("[0, 1, 2, 3]", dnaSelection.getSelected().toString());
- hidden = dnaHidden.getListOfCols();
+ hidden = dnaHidden.getHiddenColumnsCopy();
assertEquals(1, hidden.size());
assertEquals("[5, 10]", Arrays.toString(hidden.get(0)));
proteinSelection.hideSelectedColumns(3, hiddenCols);
MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
proteinView, dnaView, dnaSelection, dnaHidden);
- hidden = dnaHidden.getListOfCols();
+ hidden = dnaHidden.getHiddenColumnsCopy();
assertEquals(2, hidden.size());
assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
assertEquals("[5, 10]", Arrays.toString(hidden.get(1)));
/*
* [start, end] ranges
*/
- List<int[]> ranges = new ArrayList<int[]>();
+ List<int[]> ranges = new ArrayList<>();
assertEquals(0, MappingUtils.getLength(ranges));
ranges.add(new int[] { 1, 1 });
assertEquals(1, MappingUtils.getLength(ranges));
public void testContains()
{
assertFalse(MappingUtils.contains(null, 1));
- List<int[]> ranges = new ArrayList<int[]>();
+ List<int[]> ranges = new ArrayList<>();
assertFalse(MappingUtils.contains(ranges, 1));
ranges.add(new int[] { 1, 4 });