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JAL-4020 Added search for PyMOLWinWithConsole.bat (and PyMOLWin.exe) in likely places...
[jalview.git]
/
src
/
jalview
/
appletgui
/
AlignmentPanel.java
diff --git
a/src/jalview/appletgui/AlignmentPanel.java
b/src/jalview/appletgui/AlignmentPanel.java
index
bb26caa
..
fd75296
100644
(file)
--- a/
src/jalview/appletgui/AlignmentPanel.java
+++ b/
src/jalview/appletgui/AlignmentPanel.java
@@
-46,6
+46,7
@@
import java.awt.event.ComponentEvent;
import java.beans.PropertyChangeEvent;
import java.util.List;
import java.beans.PropertyChangeEvent;
import java.util.List;
+@SuppressWarnings("serial")
public class AlignmentPanel extends Panel
implements AdjustmentListener, AlignmentViewPanel, ViewportListenerI
{
public class AlignmentPanel extends Panel
implements AdjustmentListener, AlignmentViewPanel, ViewportListenerI
{
@@
-344,7
+345,7
@@
public class AlignmentPanel extends Panel
int verticalOffset, boolean redrawOverview, boolean centre)
{
// do we need to scroll the panel?
int verticalOffset, boolean redrawOverview, boolean centre)
{
// do we need to scroll the panel?
- if (results != null && results.getSize() > 0)
+ if (results != null && results.getCount() > 0)
{
AlignmentI alignment = av.getAlignment();
int seqIndex = alignment.findIndex(results);
{
AlignmentI alignment = av.getAlignment();
int seqIndex = alignment.findIndex(results);
@@
-415,14
+416,14
@@
public class AlignmentPanel extends Panel
public boolean scrollTo(int ostart, int end, int seqIndex,
boolean scrollToNearest, boolean redrawOverview)
{
public boolean scrollTo(int ostart, int end, int seqIndex,
boolean scrollToNearest, boolean redrawOverview)
{
- int startv, endv, starts, ends, width;
+ int startv, endv, starts, ends;// , width;
int start = -1;
if (av.hasHiddenColumns())
{
AlignmentI al = av.getAlignment();
int start = -1;
if (av.hasHiddenColumns())
{
AlignmentI al = av.getAlignment();
- start = al.getHiddenColumns().findColumnPosition(ostart);
- end = al.getHiddenColumns().findColumnPosition(end);
+ start = al.getHiddenColumns().absoluteToVisibleColumn(ostart);
+ end = al.getHiddenColumns().absoluteToVisibleColumn(end);
if (start == end)
{
if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart))
if (start == end)
{
if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart))
@@
-513,7
+514,7
@@
public class AlignmentPanel extends Panel
vpRanges.scrollToWrappedVisible(start);
}
vpRanges.scrollToWrappedVisible(start);
}
- paintAlignment(redrawOverview);
+ paintAlignment(redrawOverview, false);
return true;
}
return true;
}
@@
-562,7
+563,7
@@
public class AlignmentPanel extends Panel
apvscroll.addNotify();
hscroll.addNotify();
validate();
apvscroll.addNotify();
hscroll.addNotify();
validate();
- paintAlignment(true);
+ paintAlignment(true, false);
}
/**
}
/**
@@
-669,14
+670,9
@@
public class AlignmentPanel extends Panel
}
else
{
}
else
{
- int width = av.getAlignment().getWidth();
+ int width = av.getAlignment().getVisibleWidth();
int height = av.getAlignment().getHeight();
int height = av.getAlignment().getHeight();
- if (av.hasHiddenColumns())
- {
- width = av.getAlignment().getHiddenColumns()
- .findColumnPosition(width);
- }
if (x < 0)
{
x = 0;
if (x < 0)
{
x = 0;
@@
-913,7
+909,8
@@
public class AlignmentPanel extends Panel
* Repaint the alignment and annotations, and, optionally, any overview window
*/
@Override
* Repaint the alignment and annotations, and, optionally, any overview window
*/
@Override
- public void paintAlignment(boolean updateOverview)
+ public void paintAlignment(boolean updateOverview,
+ boolean updateStructures)
{
final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
av.isShowAutocalculatedAbove());
{
final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
av.isShowAutocalculatedAbove());
@@
-921,13
+918,14
@@
public class AlignmentPanel extends Panel
av.getSortAnnotationsBy());
repaint();
av.getSortAnnotationsBy());
repaint();
- if (updateOverview)
+ if (updateStructures)
{
{
- // TODO: determine if this paintAlignment changed structure colours
jalview.structure.StructureSelectionManager
.getStructureSelectionManager(av.applet)
.sequenceColoursChanged(this);
jalview.structure.StructureSelectionManager
.getStructureSelectionManager(av.applet)
.sequenceColoursChanged(this);
-
+ }
+ if (updateOverview)
+ {
if (overviewPanel != null)
{
overviewPanel.updateOverviewImage();
if (overviewPanel != null)
{
overviewPanel.updateOverviewImage();