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Merge remote-tracking branch 'origin/bug/JAL-3082selectRegex' into merge/JAL-3082
[jalview.git]
/
src
/
jalview
/
gui
/
AlignFrame.java
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
268139d
..
b080a25
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-734,9
+734,9
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
int aSize = alignPanels.size();
int aSize = alignPanels.size();
- tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
+ tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
- if (aSize == 1 && ap.av.viewName == null)
+ if (aSize == 1 && ap.av.getViewName() == null)
{
this.getContentPane().add(ap, BorderLayout.CENTER);
}
{
this.getContentPane().add(ap, BorderLayout.CENTER);
}
@@
-749,7
+749,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
expandViews.setEnabled(true);
gatherViews.setEnabled(true);
expandViews.setEnabled(true);
gatherViews.setEnabled(true);
- tabbedPane.addTab(ap.av.viewName, ap);
+ tabbedPane.addTab(ap.av.getViewName(), ap);
ap.setVisible(false);
}
ap.setVisible(false);
}
@@
-772,7
+772,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
gatherViews.setEnabled(true);
tabbedPane.setVisible(true);
AlignmentPanel first = alignPanels.get(0);
gatherViews.setEnabled(true);
tabbedPane.setVisible(true);
AlignmentPanel first = alignPanels.get(0);
- tabbedPane.addTab(first.av.viewName, first);
+ tabbedPane.addTab(first.av.getViewName(), first);
this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
}
this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
}
@@
-873,7
+873,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param av
* AlignViewport
*/
* @param av
* AlignViewport
*/
- void setMenusFromViewport(AlignViewport av)
+ public void setMenusFromViewport(AlignViewport av)
{
padGapsMenuitem.setSelected(av.isPadGaps());
colourTextMenuItem.setSelected(av.isShowColourText());
{
padGapsMenuitem.setSelected(av.isPadGaps());
colourTextMenuItem.setSelected(av.isShowColourText());
@@
-964,6
+964,11
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
return progressBar.operationInProgress();
}
return progressBar.operationInProgress();
}
+ /**
+ * Sets the text of the status bar. Note that setting a null or empty value
+ * will cause the status bar to be hidden, with possibly undesirable flicker
+ * of the screen layout.
+ */
@Override
public void setStatus(String text)
{
@Override
public void setStatus(String text)
{
@@
-1155,7
+1160,8
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
shortName.lastIndexOf(java.io.File.separatorChar) + 1);
}
shortName.lastIndexOf(java.io.File.separatorChar) + 1);
}
- success = new Jalview2XML().saveAlignment(this, file, shortName);
+ success = new jalview.project.Jalview2XML().saveAlignment(this, file,
+ shortName);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
@@
-2407,15
+2413,12
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
@Override
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
- SequenceGroup sg = new SequenceGroup();
-
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
- {
- sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
- }
+ SequenceGroup sg = new SequenceGroup(
+ viewport.getAlignment().getSequences());
sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
+ viewport.isSelectionGroupChanged(true);
viewport.sendSelection();
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
viewport.sendSelection();
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
@@
-2711,7
+2714,8
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* Create a new AlignmentPanel (with its own, new Viewport)
*/
/*
* Create a new AlignmentPanel (with its own, new Viewport)
*/
- AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
+ AlignmentPanel newap = new jalview.project.Jalview2XML()
+ .copyAlignPanel(alignPanel);
if (!copyAnnotation)
{
/*
if (!copyAnnotation)
{
/*
@@
-2723,10
+2727,10
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
newap.av.setGatherViewsHere(false);
newap.av.setGatherViewsHere(false);
- if (viewport.viewName == null)
+ if (viewport.getViewName() == null)
{
{
- viewport.viewName = MessageManager
- .getString("label.view_name_original");
+ viewport.setViewName(MessageManager
+ .getString("label.view_name_original"));
}
/*
}
/*
@@
-2750,7
+2754,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
newap.refresh(true); // adjust layout of annotations
}
newap.refresh(true); // adjust layout of annotations
}
- newap.av.viewName = getNewViewName(viewTitle);
+ newap.av.setViewName(getNewViewName(viewTitle));
addAlignmentPanel(newap, true);
newap.alignmentChanged();
addAlignmentPanel(newap, true);
newap.alignmentChanged();
@@
-2813,9
+2817,9
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (comp instanceof AlignmentPanel)
{
AlignmentPanel ap = (AlignmentPanel) comp;
if (comp instanceof AlignmentPanel)
{
AlignmentPanel ap = (AlignmentPanel) comp;
- if (!existingNames.contains(ap.av.viewName))
+ if (!existingNames.contains(ap.av.getViewName()))
{
{
- existingNames.add(ap.av.viewName);
+ existingNames.add(ap.av.getViewName());
}
}
}
}
}
}
@@
-2898,7
+2902,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.setFollowHighlight(state);
if (state)
{
viewport.setFollowHighlight(state);
if (state)
{
- alignPanel.scrollToPosition(viewport.getSearchResults(), false);
+ alignPanel.scrollToPosition(viewport.getSearchResults());
}
}
}
}
@@
-3045,6
+3049,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
@@
-3069,6
+3074,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
@@
-3607,9
+3613,9
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
frameTitle += " from ";
frameTitle += " from ";
- if (viewport.viewName != null)
+ if (viewport.getViewName() != null)
{
{
- frameTitle += viewport.viewName + " of ";
+ frameTitle += viewport.getViewName() + " of ";
}
frameTitle += this.title;
}
frameTitle += this.title;
@@
-4777,7
+4783,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (reply != null)
{
if (reply != null)
{
- viewport.viewName = reply;
+ viewport.setViewName(reply);
// TODO warn if reply is in getExistingViewNames()?
tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
}
// TODO warn if reply is in getExistingViewNames()?
tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
}
@@
-5409,7
+5415,9
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
public List<? extends AlignmentViewPanel> getAlignPanels()
{
*/
public List<? extends AlignmentViewPanel> getAlignPanels()
{
- return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+ // alignPanels is never null
+ // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+ return alignPanels;
}
/**
}
/**