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JAL-2321 use configured values for structure derived annotation
[jalview.git]
/
src
/
jalview
/
appletgui
/
ScalePanel.java
diff --git
a/src/jalview/appletgui/ScalePanel.java
b/src/jalview/appletgui/ScalePanel.java
index
4e44888
..
c91449f
100755
(executable)
--- a/
src/jalview/appletgui/ScalePanel.java
+++ b/
src/jalview/appletgui/ScalePanel.java
@@
-87,7
+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
{
@@
-235,7
+235,7
@@
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)
@@
-276,7
+276,7
@@
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);
@@
-378,7
+378,7
@@
public class ScalePanel extends Panel
{
if (hidden.isVisible(sel))
{
{
if (hidden.isVisible(sel))
{
- sel = hidden.findColumnPosition(sel);
+ sel = hidden.absoluteToVisibleColumn(sel);
}
else
{
}
else
{
@@
-437,7
+437,7
@@
public class ScalePanel extends Panel
if (av.getShowHiddenMarkers())
{
int widthx = 1 + endx - startx;
if (av.getShowHiddenMarkers())
{
int widthx = 1 + endx - startx;
- Iterator<Integer> it = hidden.getBoundedStartIterator(startx,
+ Iterator<Integer> it = hidden.getStartRegionIterator(startx,
startx + widthx + 1);
while (it.hasNext())
{
startx + widthx + 1);
while (it.hasNext())
{