import jalview.datamodel.AlignedCodon;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
AlignmentI alf = new FormatAdapter().readFile(
JAL_1312_example_align_fasta, DataSourceType.PASTE,
FileFormat.Fasta);
- ColumnSelection cs = new ColumnSelection();
+ HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(alf, cs);
Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
AlignmentI translated = dna.translateCdna();
int vwidth = 15;
for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
{
- ColumnSelection cs = new ColumnSelection();
+ HiddenColumns cs = new HiddenColumns();
if (ipos > 0)
{
cs.hideColumns(0, ipos - 1);
{
AlignmentI alf = new FormatAdapter().readFile(fasta,
DataSourceType.PASTE, FileFormat.Fasta);
- ColumnSelection cs = new ColumnSelection();
+ HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(alf, cs);
Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
AlignmentI translated = dna.translateCdna();
{
AlignmentI alf = new FormatAdapter().readFile(fasta,
DataSourceType.PASTE, FileFormat.Fasta);
- ColumnSelection cs = new ColumnSelection();
+ HiddenColumns cs = new HiddenColumns();
cs.hideColumns(6, 14); // hide codons 3/4/5
cs.hideColumns(24, 35); // hide codons 9-12
cs.hideColumns(177, 191); // hide codons 60-64
*/
AlignmentI cdna = new AlignmentGenerator(true)
.generate(12, 8, 97, 5, 5);
- ColumnSelection cs = new ColumnSelection();
+ HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(cdna, cs);
Dna dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 });
AlignmentI translated = dna.translateCdna();
assertEquals(seqDs, al.getSequenceAt(0).getDatasetSequence()
.getSequenceAsString());
- ColumnSelection cs = new ColumnSelection();
+ HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(al, cs);
Dna testee = new Dna(av, new int[] { 0, al.getWidth() - 1 });
AlignmentI reversed = testee.reverseCdna(false);