package jalview.gui;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
if (av.hasHiddenColumns())
{
- startx = av.getColumnSelection().adjustForHiddenColumns(startx);
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ startx = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(startx);
+ endx = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(endx);
}
int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth) - 1;
}
// WEST SCALE
if (av.hasHiddenColumns())
{
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ endx = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(endx);
}
SequenceI seq;
if (av.hasHiddenColumns())
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth) - 1;
}
while ((ypos <= canvasHeight) && (startRes < maxwidth))
{
g.setColor(Color.blue);
int res;
- for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
- .size(); i++)
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ for (int i = 0; i < hidden.getListOfCols().size(); i++)
{
- res = av.getColumnSelection().findHiddenRegionPosition(i)
- - startRes;
+ res = hidden.findHiddenRegionPosition(i) - startRes;
if (res < 0 || res > endx - startRes)
{
}
else
{
- List<int[]> regions = av.getColumnSelection().getHiddenColumns();
+ List<int[]> regions = av.getAlignment().getHiddenColumns()
+ .getListOfCols();
int screenY = 0;
int blockStart = startRes;