import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
private FeatureRenderer fr;
- private List<int[]> hiddenColumns;
+ private List<int[]> hiddenColumnsList;
- private ColumnSelection columnSelection;
+ private HiddenColumns hiddenColumns;
private List<String> hiddenSeqRefs;
// hidden column business
if (getViewport().hasHiddenColumns())
{
- List<int[]> hiddenCols = getViewport().getColumnSelection()
- .getHiddenColumns();
+ List<int[]> hiddenCols = getViewport().getAlignment()
+ .getHiddenColumns()
+ .getListOfCols();
StringBuilder hiddenColsBuilder = new StringBuilder();
for (int[] range : hiddenCols)
{
String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
if (hiddenCols != null && !hiddenCols.isEmpty())
{
- columnSelection = new ColumnSelection();
+ HiddenColumns hidden = new HiddenColumns();
String[] rangeStrings = hiddenCols.split(";");
for (String rangeString : rangeStrings)
{
String[] range = rangeString.split("-");
- columnSelection.hideColumns(Integer.valueOf(range[0]),
+ hidden.hideColumns(Integer.valueOf(range[0]),
Integer.valueOf(range[1]));
}
}
return annotations;
}
- public List<int[]> getHiddenColumns()
- {
- return hiddenColumns;
- }
-
@Override
- public ColumnSelection getColumnSelection()
+ public HiddenColumns getHiddenColumns()
{
- return columnSelection;
+ return hiddenColumns;
}
- public void setColumnSelection(ColumnSelection columnSelection)
+ public void setHiddenColumns(HiddenColumns hidden)
{
- this.columnSelection = columnSelection;
+ this.hiddenColumns = hidden;
}
@Override