git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-2602 same fix for applet
[jalview.git]
/
src
/
jalview
/
appletgui
/
AlignFrame.java
diff --git
a/src/jalview/appletgui/AlignFrame.java
b/src/jalview/appletgui/AlignFrame.java
index
cd1e1a9
..
8f28658
100644
(file)
--- a/
src/jalview/appletgui/AlignFrame.java
+++ b/
src/jalview/appletgui/AlignFrame.java
@@
-46,6
+46,7
@@
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
@@
-172,14
+173,14
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
}
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
- ColumnSelection columnSelection, JalviewLite applet,
+ HiddenColumns hidden, JalviewLite applet,
String title, boolean embedded)
{
String title, boolean embedded)
{
- this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
+ this(al, hiddenSeqs, hidden, applet, title, embedded, true);
}
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
}
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
- ColumnSelection columnSelection, JalviewLite applet,
+ HiddenColumns hidden, JalviewLite applet,
String title, boolean embedded, boolean addToDisplay)
{
if (applet != null)
String title, boolean embedded, boolean addToDisplay)
{
if (applet != null)
@@
-222,9
+223,9
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
viewport.hideSequence(hiddenSeqs);
}
{
viewport.hideSequence(hiddenSeqs);
}
- if (columnSelection != null)
+ if (hidden != null)
{
{
- viewport.setColumnSelection(columnSelection);
+ viewport.getAlignment().setHiddenColumns(hidden);
}
viewport.setScaleAboveWrapped(scaleAbove.getState());
}
viewport.setScaleAboveWrapped(scaleAbove.getState());
@@
-600,24
+601,22
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
case KeyEvent.VK_PAGE_UP:
if (viewport.getWrapAlignment())
{
case KeyEvent.VK_PAGE_UP:
if (viewport.getWrapAlignment())
{
- alignPanel.scrollUp(true);
+ ranges.scrollUp(true);
}
else
{
}
else
{
- alignPanel.setScrollValues(ranges.getStartRes(),
- 2 * ranges.getStartSeq() - ranges.getEndSeq());
+ ranges.pageUp();
}
break;
case KeyEvent.VK_PAGE_DOWN:
if (viewport.getWrapAlignment())
{
}
break;
case KeyEvent.VK_PAGE_DOWN:
if (viewport.getWrapAlignment())
{
- alignPanel.scrollUp(false);
+ ranges.scrollUp(false);
}
else
{
}
else
{
- alignPanel
- .setScrollValues(ranges.getStartRes(), ranges.getEndSeq());
+ ranges.pageDown();
}
break;
}
break;
@@
-1799,7
+1798,7
@@
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(
@@
-1901,7
+1900,7
@@
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()
{
@@
-1912,7
+1911,7
@@
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);
@@
-1925,12
+1924,13
@@
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.getColumnSelection().getHiddenColumns())
+ 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
@@
-2045,7
+2045,7
@@
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]);
}
}
@@
-4207,9
+4207,10
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
* @param csel
* - columns to be selected on the alignment
*/
* @param csel
* - columns to be selected on the alignment
*/
- public void select(SequenceGroup sel, ColumnSelection csel)
+ public void select(SequenceGroup sel, ColumnSelection csel,
+ HiddenColumns hidden)
{
{
- alignPanel.seqPanel.selection(sel, csel, null);
+ alignPanel.seqPanel.selection(sel, csel, hidden, null);
}
public void scrollTo(int row, int column)
}
public void scrollTo(int row, int column)