import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
{
for (int index : av.getColumnSelection().getSelected())
{
- if (av.getColumnSelection().isVisible(index))
+ if (av.getAlignment().getHiddenColumns().isVisible(index))
{
anot[index] = null;
}
for (int index : av.getColumnSelection().getSelected())
{
- if (!av.getColumnSelection().isVisible(index))
+ if (!av.getAlignment().getHiddenColumns().isVisible(index))
{
continue;
}
for (int index : av.getColumnSelection().getSelected())
{
- if (!av.getColumnSelection().isVisible(index))
+ if (!av.getAlignment().getHiddenColumns().isVisible(index))
{
continue;
}
}
for (int index : av.getColumnSelection().getSelected())
{
- if (!av.getColumnSelection().isVisible(index))
+ if (!av.getAlignment().getHiddenColumns().isVisible(index))
{
continue;
}
StringBuilder collatedInput = new StringBuilder(64);
String last = "";
ColumnSelection viscols = av.getColumnSelection();
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
/*
* the selection list (read-only view) is in selection order, not
* column order; make a copy so we can sort it
*/
- List<Integer> selected = new ArrayList<Integer>(viscols.getSelected());
+ List<Integer> selected = new ArrayList<>(viscols.getSelected());
Collections.sort(selected);
for (int index : selected)
{
// always check for current display state - just in case
- if (!viscols.isVisible(index))
+ if (!hidden.isVisible(index))
{
continue;
}
if (av.hasHiddenColumns())
{
- column = av.getColumnSelection().adjustForHiddenColumns(column);
+ column = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(column);
}
AlignmentAnnotation ann = aa[row];
repaint();
return;
}
+
+ int sr = av.getRanges().getStartRes();
+ int er = av.getRanges().getEndRes() + 1;
+ int transX = 0;
+
long stime = System.currentTimeMillis();
gg.copyArea(0, 0, imgWidth, getHeight(),
-horizontal * av.getCharWidth(), 0);
long mtime = System.currentTimeMillis();
- int sr = av.getRanges().getStartRes();
- int er = av.getRanges().getEndRes() + 1;
- int transX = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
public void propertyChange(PropertyChangeEvent evt)
{
// Respond to viewport range changes (e.g. alignment panel was scrolled)
- if (evt.getPropertyName().equals("startres")
- || evt.getPropertyName().equals("endres"))
+ if (evt.getPropertyName().equals("startres"))
{
fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
}
+ else if (evt.getPropertyName().equals("endres"))
+ {
+ // resize - do nothing
+ }
}
}