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Merge branch 'develop' into features/JAL-2446NCList
[jalview.git]
/
src
/
jalview
/
appletgui
/
AlignFrame.java
diff --git
a/src/jalview/appletgui/AlignFrame.java
b/src/jalview/appletgui/AlignFrame.java
index
24f882e
..
fb1ee92
100644
(file)
--- a/
src/jalview/appletgui/AlignFrame.java
+++ b/
src/jalview/appletgui/AlignFrame.java
@@
-1811,7
+1811,7
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
synchronized void slideSequences(boolean right, int size)
{
synchronized void slideSequences(boolean right, int size)
{
- List<SequenceI> sg = new Vector<SequenceI>();
+ List<SequenceI> sg = new Vector<>();
if (viewport.cursorMode)
{
sg.add(viewport.getAlignment().getSequenceAt(
if (viewport.cursorMode)
{
sg.add(viewport.getAlignment().getSequenceAt(
@@
-1913,7
+1913,7
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
static StringBuffer copiedSequences;
static StringBuffer copiedSequences;
- static Vector copiedHiddenColumns;
+ static Vector<int[]> copiedHiddenColumns;
protected void copy_actionPerformed()
{
protected void copy_actionPerformed()
{
@@
-1924,7
+1924,7
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
SequenceGroup sg = viewport.getSelectionGroup();
copiedSequences = new StringBuffer();
SequenceGroup sg = viewport.getSelectionGroup();
copiedSequences = new StringBuffer();
- Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
+ Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
for (int i = 0; i < sg.getSize(); i++)
{
SequenceI seq = sg.getSequenceAt(i);
for (int i = 0; i < sg.getSize(); i++)
{
SequenceI seq = sg.getSequenceAt(i);
@@
-1937,13
+1937,13
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
{
if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
{
- copiedHiddenColumns = new Vector();
+ copiedHiddenColumns = new Vector<>(viewport.getAlignment()
+ .getHiddenColumns().getHiddenColumnsCopy());
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
- for (int[] region : viewport.getAlignment().getHiddenColumns()
- .getHiddenRegions())
+ for (int[] region : copiedHiddenColumns)
{
{
- copiedHiddenColumns.addElement(new int[] {
- region[0] - hiddenOffset, region[1] - hiddenOffset });
+ region[0] = region[0] - hiddenOffset;
+ region[1] = region[1] - hiddenOffset;
}
}
else
}
}
else
@@
-2058,7
+2058,7
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
for (int i = 0; i < copiedHiddenColumns.size(); i++)
{
{
for (int i = 0; i < copiedHiddenColumns.size(); i++)
{
- int[] region = (int[]) copiedHiddenColumns.elementAt(i);
+ int[] region = copiedHiddenColumns.elementAt(i);
af.viewport.hideColumns(region[0], region[1]);
}
}
af.viewport.hideColumns(region[0], region[1]);
}
}