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JAL-4366 compute coverage on each side of the pairwise alignment
[jalview.git]
/
src
/
jalview
/
appletgui
/
ScalePanel.java
diff --git
a/src/jalview/appletgui/ScalePanel.java
b/src/jalview/appletgui/ScalePanel.java
index
e00db7c
..
ccb6d94
100755
(executable)
--- a/
src/jalview/appletgui/ScalePanel.java
+++ b/
src/jalview/appletgui/ScalePanel.java
@@
-42,6
+42,7
@@
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.beans.PropertyChangeEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.beans.PropertyChangeEvent;
+import java.util.Iterator;
import java.util.List;
public class ScalePanel extends Panel
import java.util.List;
public class ScalePanel extends Panel
@@
-86,7
+87,7
@@
public class ScalePanel extends Panel
if (av.hasHiddenColumns())
{
if (av.hasHiddenColumns())
{
- res = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(x);
+ res = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(x);
}
else
{
}
else
{
@@
-95,8
+96,8
@@
public class ScalePanel extends Panel
min = res;
max = res;
min = res;
max = res;
- if ((evt.getModifiers()
- & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ if ((evt.getModifiersEx()
+ & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
{
rightMouseButtonPressed(evt, res);
}
{
rightMouseButtonPressed(evt, res);
}
@@
-141,7
+142,7
@@
public class ScalePanel extends Panel
sg.setStartRes(min);
sg.setEndRes(max);
}
sg.setStartRes(min);
sg.setEndRes(max);
}
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
av.sendSelection();
}
av.sendSelection();
}
@@
-167,13
+168,14
@@
public class ScalePanel extends Panel
{
av.showColumn(reveal[0]);
reveal = null;
{
av.showColumn(reveal[0]);
reveal = null;
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
av.sendSelection();
}
});
pop.add(item);
av.sendSelection();
}
});
pop.add(item);
- if (av.getAlignment().getHiddenColumns().hasManyHiddenColumns())
+ if (av.getAlignment().getHiddenColumns()
+ .hasMultiHiddenColumnRegions())
{
item = new MenuItem(MessageManager.getString("action.reveal_all"));
item.addActionListener(new ActionListener()
{
item = new MenuItem(MessageManager.getString("action.reveal_all"));
item.addActionListener(new ActionListener()
@@
-183,7
+185,7
@@
public class ScalePanel extends Panel
{
av.showAllHiddenColumns();
reveal = null;
{
av.showAllHiddenColumns();
reveal = null;
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
av.sendSelection();
}
});
av.sendSelection();
}
});
@@
-208,7
+210,7
@@
public class ScalePanel extends Panel
av.setSelectionGroup(null);
}
av.setSelectionGroup(null);
}
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
av.sendSelection();
}
});
av.sendSelection();
}
});
@@
-234,12
+236,12
@@
public class ScalePanel extends Panel
if (av.hasHiddenColumns())
{
res = av.getAlignment().getHiddenColumns()
if (av.hasHiddenColumns())
{
res = av.getAlignment().getHiddenColumns()
- .adjustForHiddenColumns(res);
+ .visibleToAbsoluteColumn(res);
}
if (!stretchingGroup)
{
}
if (!stretchingGroup)
{
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
return;
}
return;
}
@@
-256,7
+258,7
@@
public class ScalePanel extends Panel
}
stretchingGroup = false;
}
stretchingGroup = false;
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
av.sendSelection();
}
av.sendSelection();
}
@@
-275,7
+277,7
@@
public class ScalePanel extends Panel
int res = (evt.getX() / av.getCharWidth())
+ av.getRanges().getStartRes();
res = Math.max(0, res);
int res = (evt.getX() / av.getCharWidth())
+ av.getRanges().getStartRes();
res = Math.max(0, res);
- res = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(res);
+ res = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(res);
res = Math.min(res, av.getAlignment().getWidth() - 1);
min = Math.min(res, min);
max = Math.max(res, max);
res = Math.min(res, av.getAlignment().getWidth() - 1);
min = Math.min(res, min);
max = Math.max(res, max);
@@
-285,7
+287,7
@@
public class ScalePanel extends Panel
{
stretchingGroup = true;
cs.stretchGroup(res, sg, min, max);
{
stretchingGroup = true;
cs.stretchGroup(res, sg, min, max);
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
}
}
}
@@
-377,7
+379,7
@@
public class ScalePanel extends Panel
{
if (hidden.isVisible(sel))
{
{
if (hidden.isVisible(sel))
{
- sel = hidden.findColumnPosition(sel);
+ sel = hidden.absoluteToVisibleColumn(sel);
}
else
{
}
else
{
@@
-436,11
+438,11
@@
public class ScalePanel extends Panel
if (av.getShowHiddenMarkers())
{
int widthx = 1 + endx - startx;
if (av.getShowHiddenMarkers())
{
int widthx = 1 + endx - startx;
- List<Integer> positions = hidden.findHiddenRegionPositions(startx,
+ Iterator<Integer> it = hidden.getStartRegionIterator(startx,
startx + widthx + 1);
startx + widthx + 1);
- for (int pos : positions)
+ while (it.hasNext())
{
{
- res = pos - startx;
+ res = it.next() - startx;
gg.fillPolygon(
new int[]
gg.fillPolygon(
new int[]
@@
-463,7
+465,9
@@
public class ScalePanel extends Panel
// Here we only want to fastpaint on a scroll, with resize using a normal
// paint, so scroll events are identified as changes to the horizontal or
// vertical start value.
// Here we only want to fastpaint on a scroll, with resize using a normal
// paint, so scroll events are identified as changes to the horizontal or
// vertical start value.
- if (evt.getPropertyName().equals(ViewportRanges.STARTRES))
+ if (evt.getPropertyName().equals(ViewportRanges.STARTRES)
+ || evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ)
+ || evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
{
// scroll event, repaint panel
repaint();
{
// scroll event, repaint panel
repaint();