import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
import jalview.renderer.ScaleRenderer;
import jalview.renderer.ScaleRenderer.ScaleMark;
import jalview.util.MessageManager;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.beans.PropertyChangeEvent;
+import java.util.Iterator;
import java.util.List;
import javax.swing.JMenuItem;
if (av.hasHiddenColumns())
{
- x = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(x);
+ x = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(x);
}
if (x >= av.getAlignment().getWidth())
});
pop.add(item);
- if (av.getAlignment().getHiddenColumns().hasHiddenColumns())
+ if (av.getAlignment().getHiddenColumns().hasMultiHiddenColumnRegions())
{
item = new JMenuItem(MessageManager.getString("action.reveal_all"));
item.addActionListener(new ActionListener()
}
av.getColumnSelection().addElement(res);
- SequenceGroup sg = new SequenceGroup();
- // try to be as quick as possible
- SequenceI[] iVec = av.getAlignment().getSequencesArray();
- for (int i = 0; i < iVec.length; i++)
- {
- sg.addSequence(iVec[i], false);
- iVec[i] = null;
- }
- iVec = null;
+ SequenceGroup sg = new SequenceGroup(av.getAlignment().getSequences());
sg.setStartRes(res);
sg.setEndRes(res);
{
mouseDragging = false;
- int res = (evt.getX() / av.getCharWidth())
+ int xCords = Math.max(0, evt.getX()); // prevent negative X coordinates
+
+ int res = (xCords / av.getCharWidth())
+ av.getRanges().getStartRes();
if (av.hasHiddenColumns())
{
res = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(res);
+ .visibleToAbsoluteColumn(res);
}
if (res >= av.getAlignment().getWidth())
int res = (evt.getX() / av.getCharWidth())
+ av.getRanges().getStartRes();
res = Math.max(0, res);
- res = hidden.adjustForHiddenColumns(res);
+ res = hidden.visibleToAbsoluteColumn(res);
res = Math.min(res, av.getAlignment().getWidth() - 1);
min = Math.min(res, min);
max = Math.max(res, max);
reveal = av.getAlignment().getHiddenColumns()
.getRegionWithEdgeAtRes(res);
- res = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(res);
+ res = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(res);
ToolTipManager.sharedInstance().registerComponent(this);
this.setToolTipText(
@Override
public void paintComponent(Graphics g)
{
+ super.paintComponent(g);
+
/*
* shouldn't get called in wrapped mode as the scale above is
* drawn instead by SeqCanvas.drawNorthScale
{
if (hidden.isVisible(sel))
{
- sel = hidden.findColumnPosition(sel);
+ sel = hidden.absoluteToVisibleColumn(sel);
}
else
{
if (av.getShowHiddenMarkers())
{
- List<Integer> positions = hidden.findHiddenRegionPositions();
- for (int pos : positions)
+ Iterator<Integer> it = hidden.getStartRegionIterator(startx,
+ startx + widthx + 1);
+ while (it.hasNext())
{
- res = pos - startx;
-
- if (res < 0 || res > widthx)
- {
- continue;
- }
+ res = it.next() - startx;
gg.fillPolygon(
new int[]
- { -1 + res * avCharWidth - avCharHeight / 4,
- -1 + res * avCharWidth + avCharHeight / 4,
- -1 + res * avCharWidth },
- new int[]
- { y, y, y + 2 * yOf }, 3);
+ { -1 + res * avCharWidth - avCharHeight / 4,
+ -1 + res * avCharWidth + avCharHeight / 4,
+ -1 + res * avCharWidth }, new int[]
+ { y, y, y + 2 * yOf }, 3);
}
}
}
// paint, so scroll events are identified as changes to the horizontal or
// vertical start value.
if (evt.getPropertyName().equals(ViewportRanges.STARTRES)
- || evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ))
+ || evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ)
+ || evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
{
// scroll event, repaint panel
- repaint();
+
+ // Call repaint on alignment panel so that repaints from other alignment
+ // panel components can be aggregated. Otherwise performance of the overview
+ // window and others may be adversely affected.
+ av.getAlignPanel().repaint();
}
}