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JAL-3416 Use JalviewInternalFrame instead of new JInternalFrame
test/JAL-3416_setOpaque_true_test_with_JalviewInternalFrame
author
Ben Soares
<b.soares@dundee.ac.uk>
Thu, 15 Jun 2023 15:59:03 +0000
(16:59 +0100)
committer
Ben Soares
<b.soares@dundee.ac.uk>
Thu, 15 Jun 2023 15:59:03 +0000
(16:59 +0100)
42 files changed:
src/jalview/bin/Jalview.java
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src/jalview/fts/core/GFTSPanel.java
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src/jalview/gui/AlignFrame.java
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src/jalview/gui/AlignViewport.java
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src/jalview/gui/AnnotationChooser.java
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src/jalview/gui/AnnotationColourChooser.java
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src/jalview/gui/AnnotationColumnChooser.java
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src/jalview/gui/AnnotationExporter.java
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src/jalview/gui/AnnotationRowFilter.java
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src/jalview/gui/AppVarna.java
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src/jalview/gui/CalculationChooser.java
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src/jalview/gui/ChimeraViewFrame.java
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src/jalview/gui/Desktop.java
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src/jalview/gui/FeatureSettings.java
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src/jalview/gui/Finder.java
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src/jalview/gui/FontChooser.java
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src/jalview/gui/JalviewInternalFrame.java
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src/jalview/gui/JvOptionPane.java
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src/jalview/gui/OverviewPanel.java
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src/jalview/gui/PopupMenu.java
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src/jalview/gui/Preferences.java
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src/jalview/gui/PymolViewer.java
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src/jalview/gui/RedundancyPanel.java
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src/jalview/gui/SequenceFetcher.java
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src/jalview/gui/SliderPanel.java
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src/jalview/gui/SplashScreen.java
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src/jalview/gui/SplitFrame.java
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src/jalview/gui/UserDefinedColours.java
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src/jalview/gui/VamsasApplication.java
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src/jalview/gui/WebserviceInfo.java
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src/jalview/io/VamsasAppDatastore.java
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src/jalview/jbgui/GAlignFrame.java
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src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
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src/jalview/jbgui/GCutAndPasteTransfer.java
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src/jalview/jbgui/GPCAPanel.java
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src/jalview/jbgui/GRnaStructureViewer.java
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src/jalview/jbgui/GSplitFrame.java
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src/jalview/jbgui/GStructureChooser.java
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src/jalview/jbgui/GStructureViewer.java
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src/jalview/jbgui/GTreePanel.java
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src/jalview/project/Jalview2XML.java
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src/jalview/ws/jws2/MsaWSThread.java
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diff --git
a/src/jalview/bin/Jalview.java
b/src/jalview/bin/Jalview.java
index
6d2866a
..
eeac532
100755
(executable)
--- a/
src/jalview/bin/Jalview.java
+++ b/
src/jalview/bin/Jalview.java
@@
-1403,6
+1403,7
@@
public class Jalview
private static boolean setFlatLookAndFeel()
{
boolean set = false;
private static boolean setFlatLookAndFeel()
{
boolean set = false;
+ UIManager.put("InternalFrame.dropShadowPainted", false);
if (SystemInfo.isMacOS)
{
try
if (SystemInfo.isMacOS)
{
try
diff --git
a/src/jalview/fts/core/GFTSPanel.java
b/src/jalview/fts/core/GFTSPanel.java
index
dd7fd94
..
ba5f123
100644
(file)
--- a/
src/jalview/fts/core/GFTSPanel.java
+++ b/
src/jalview/fts/core/GFTSPanel.java
@@
-50,7
+50,7
@@
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JFrame;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JFrame;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
@@
-90,7
+90,7
@@
public abstract class GFTSPanel extends JPanel implements GFTSPanelI
{
private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
{
private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
- protected JInternalFrame mainFrame = new JInternalFrame(
+ protected JalviewInternalFrame mainFrame = new JalviewInternalFrame(
getFTSFrameTitle());
protected JTabbedPane tabs = new JTabbedPane();
getFTSFrameTitle());
protected JTabbedPane tabs = new JTabbedPane();
@@
-826,7
+826,7
@@
public abstract class GFTSPanel extends JPanel implements GFTSPanelI
return cmb_searchTarget;
}
return cmb_searchTarget;
}
- public JInternalFrame getMainFrame()
+ public JalviewInternalFrame getMainFrame()
{
return mainFrame;
}
{
return mainFrame;
}
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
5c2f2f6
..
41777d8
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-3496,7
+3496,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
pane = editPane;
}
pane = editPane;
}
- JInternalFrame frame = new JInternalFrame();
+ JalviewInternalFrame frame = new JalviewInternalFrame();
frame.setFrameIcon(null);
frame.getContentPane().add(new JScrollPane(pane));
frame.setFrameIcon(null);
frame.getContentPane().add(new JScrollPane(pane));
@@
-3524,7
+3524,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
return alignPanel.overviewPanel;
}
{
return alignPanel.overviewPanel;
}
- JInternalFrame frame = new JInternalFrame();
+ JalviewInternalFrame frame = new JalviewInternalFrame();
frame.setFrameIcon(null);
final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
showHidden);
frame.setFrameIcon(null);
final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
showHidden);
@@
-3803,7
+3803,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
else
{
}
else
{
- JInternalFrame frame = new JInternalFrame();
+ JalviewInternalFrame frame = new JalviewInternalFrame();
frame.setFrameIcon(null);
frame.setContentPane(new PairwiseAlignPanel(viewport));
Desktop.addInternalFrame(frame,
frame.setFrameIcon(null);
frame.setContentPane(new PairwiseAlignPanel(viewport));
Desktop.addInternalFrame(frame,
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
5613f16
..
f45455e
100644
(file)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-30,7
+30,7
@@
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
import java.util.Hashtable;
import java.util.List;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
@@
-915,7
+915,7
@@
public class AlignViewport extends AlignmentViewport
/*
* Open in split pane. DNA sequence above, protein below.
*/
/*
* Open in split pane. DNA sequence above, protein below.
*/
- JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
+ JalviewInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
return proteinFrame.viewport.getAlignment();
Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
return proteinFrame.viewport.getAlignment();
diff --git
a/src/jalview/gui/AnnotationChooser.java
b/src/jalview/gui/AnnotationChooser.java
index
d976815
..
fbfb6e0
100644
(file)
--- a/
src/jalview/gui/AnnotationChooser.java
+++ b/
src/jalview/gui/AnnotationChooser.java
@@
-36,7
+36,7
@@
import java.util.List;
import java.util.Map;
import javax.swing.JButton;
import java.util.Map;
import javax.swing.JButton;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
@@
-63,7
+63,7
@@
public class AnnotationChooser extends JPanel
private static final int MY_FRAME_HEIGHT = 250;
private static final int MY_FRAME_HEIGHT = 250;
- private JInternalFrame frame;
+ private JalviewInternalFrame frame;
private AlignmentPanel ap;
private AlignmentPanel ap;
@@
-601,7
+601,7
@@
public class AnnotationChooser extends JPanel
*/
private void showFrame()
{
*/
private void showFrame()
{
- frame = new JInternalFrame();
+ frame = new JalviewInternalFrame();
frame.setFrameIcon(null);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.setFrameIcon(null);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
diff --git
a/src/jalview/gui/AnnotationColourChooser.java
b/src/jalview/gui/AnnotationColourChooser.java
index
d898398
..
7e6a198
100644
(file)
--- a/
src/jalview/gui/AnnotationColourChooser.java
+++ b/
src/jalview/gui/AnnotationColourChooser.java
@@
-35,7
+35,7
@@
import javax.swing.BorderFactory;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
@@
-90,7
+90,7
@@
public class AnnotationColourChooser extends AnnotationRowFilter
}
}
}
}
}
}
- frame = new JInternalFrame();
+ frame = new JalviewInternalFrame();
frame.setFrameIcon(null);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.setFrameIcon(null);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
diff --git
a/src/jalview/gui/AnnotationColumnChooser.java
b/src/jalview/gui/AnnotationColumnChooser.java
index
0483aa6
..
a7b9149
100644
(file)
--- a/
src/jalview/gui/AnnotationColumnChooser.java
+++ b/
src/jalview/gui/AnnotationColumnChooser.java
@@
-36,7
+36,7
@@
import java.awt.event.KeyEvent;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
@@
-101,7
+101,7
@@
public class AnnotationColumnChooser extends AnnotationRowFilter
public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap, AlignmentAnnotation selectedAnnotation)
{
super(av, ap);
public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap, AlignmentAnnotation selectedAnnotation)
{
super(av, ap);
- frame = new JInternalFrame();
+ frame = new JalviewInternalFrame();
frame.setFrameIcon(null);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.setFrameIcon(null);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
diff --git
a/src/jalview/gui/AnnotationExporter.java
b/src/jalview/gui/AnnotationExporter.java
index
894db79
..
4881176
100644
(file)
--- a/
src/jalview/gui/AnnotationExporter.java
+++ b/
src/jalview/gui/AnnotationExporter.java
@@
-32,7
+32,7
@@
import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.ButtonGroup;
import javax.swing.JButton;
import javax.swing.JCheckBox;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
import javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
@@
-59,7
+59,7
@@
import jalview.util.MessageManager;
*/
public class AnnotationExporter extends JPanel
{
*/
public class AnnotationExporter extends JPanel
{
- private JInternalFrame frame;
+ private JalviewInternalFrame frame;
private AlignmentPanel ap;
private AlignmentPanel ap;
@@
-106,7
+106,7
@@
public class AnnotationExporter extends JPanel
ex.printStackTrace();
}
ex.printStackTrace();
}
- frame = new JInternalFrame();
+ frame = new JalviewInternalFrame();
frame.setFrameIcon(null);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.setFrameIcon(null);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
diff --git
a/src/jalview/gui/AnnotationRowFilter.java
b/src/jalview/gui/AnnotationRowFilter.java
index
44a1668
..
a9806fe
100644
(file)
--- a/
src/jalview/gui/AnnotationRowFilter.java
+++ b/
src/jalview/gui/AnnotationRowFilter.java
@@
-44,7
+44,7
@@
import java.util.Vector;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JPanel;
import javax.swing.JTextField;
import javax.swing.event.ChangeEvent;
import javax.swing.JPanel;
import javax.swing.JTextField;
import javax.swing.event.ChangeEvent;
@@
-73,7
+73,7
@@
public abstract class AnnotationRowFilter extends JPanel
protected JTextField thresholdValue = new JTextField(20);
protected JTextField thresholdValue = new JTextField(20);
- protected JInternalFrame frame;
+ protected JalviewInternalFrame frame;
protected JButton ok = new JButton();
protected JButton ok = new JButton();
diff --git
a/src/jalview/gui/AppVarna.java
b/src/jalview/gui/AppVarna.java
index
6fac8fc
..
02fdd7b
100644
(file)
--- a/
src/jalview/gui/AppVarna.java
+++ b/
src/jalview/gui/AppVarna.java
@@
-28,7
+28,7
@@
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.List;
import java.util.Map;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JSplitPane;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
import javax.swing.JSplitPane;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
@@
-60,7
+60,7
@@
import jalview.util.Comparison;
import jalview.util.MessageManager;
import jalview.util.ShiftList;
import jalview.util.MessageManager;
import jalview.util.ShiftList;
-public class AppVarna extends JInternalFrame
+public class AppVarna extends JalviewInternalFrame
implements SelectionListener, SecondaryStructureListener,
InterfaceVARNASelectionListener, VamsasSource
{
implements SelectionListener, SecondaryStructureListener,
InterfaceVARNASelectionListener, VamsasSource
{
diff --git
a/src/jalview/gui/CalculationChooser.java
b/src/jalview/gui/CalculationChooser.java
index
af41e58
..
e3af388
100644
(file)
--- a/
src/jalview/gui/CalculationChooser.java
+++ b/
src/jalview/gui/CalculationChooser.java
@@
-44,7
+44,7
@@
import javax.swing.DefaultComboBoxModel;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
import javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
@@
-92,7
+92,7
@@
public class CalculationChooser extends JPanel
JButton calculate;
JButton calculate;
- private JInternalFrame frame;
+ private JalviewInternalFrame frame;
private JCheckBox includeGaps;
private JCheckBox includeGaps;
@@
-129,7
+129,7
@@
public class CalculationChooser extends JPanel
void init()
{
setLayout(new BorderLayout());
void init()
{
setLayout(new BorderLayout());
- frame = new JInternalFrame();
+ frame = new JalviewInternalFrame();
frame.setFrameIcon(null);
frame.setContentPane(this);
this.setBackground(Color.white);
frame.setFrameIcon(null);
frame.setContentPane(this);
this.setBackground(Color.white);
diff --git
a/src/jalview/gui/ChimeraViewFrame.java
b/src/jalview/gui/ChimeraViewFrame.java
index
cc6a785
..
3f926e3
100644
(file)
--- a/
src/jalview/gui/ChimeraViewFrame.java
+++ b/
src/jalview/gui/ChimeraViewFrame.java
@@
-30,7
+30,7
@@
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.List;
import java.util.Map;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.event.InternalFrameAdapter;
@@
-312,7
+312,7
@@
public class ChimeraViewFrame extends StructureViewerBase
* closeViewer will decide whether or not to close this frame
* depending on whether user chooses to Cancel or not
*/
* closeViewer will decide whether or not to close this frame
* depending on whether user chooses to Cancel or not
*/
- setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE);
+ setDefaultCloseOperation(JalviewInternalFrame.DO_NOTHING_ON_CLOSE);
}
/**
}
/**
diff --git
a/src/jalview/gui/Desktop.java
b/src/jalview/gui/Desktop.java
index
6fd70a9
..
d308f62
100644
(file)
--- a/
src/jalview/gui/Desktop.java
+++ b/
src/jalview/gui/Desktop.java
@@
-890,7
+890,7
@@
public class Desktop extends jalview.jbgui.GDesktop
* height
*/
public static synchronized void addInternalFrame(
* height
*/
public static synchronized void addInternalFrame(
- final JInternalFrame frame, String title, int w, int h)
+ final JalviewInternalFrame frame, String title, int w, int h)
{
addInternalFrame(frame, title, true, w, h, true, false);
}
{
addInternalFrame(frame, title, true, w, h, true, false);
}
@@
-911,8
+911,8
@@
public class Desktop extends jalview.jbgui.GDesktop
* height
*/
public static synchronized void addInternalFrame(
* height
*/
public static synchronized void addInternalFrame(
- final JInternalFrame frame, String title, boolean makeVisible,
- int w, int h)
+ final JalviewInternalFrame frame, String title,
+ boolean makeVisible, int w, int h)
{
addInternalFrame(frame, title, makeVisible, w, h, true, false);
}
{
addInternalFrame(frame, title, makeVisible, w, h, true, false);
}
@@
-932,7
+932,7
@@
public class Desktop extends jalview.jbgui.GDesktop
* Allow resize
*/
public static synchronized void addInternalFrame(
* Allow resize
*/
public static synchronized void addInternalFrame(
- final JInternalFrame frame, String title, int w, int h,
+ final JalviewInternalFrame frame, String title, int w, int h,
boolean resizable)
{
addInternalFrame(frame, title, true, w, h, resizable, false);
boolean resizable)
{
addInternalFrame(frame, title, true, w, h, resizable, false);
@@
-958,8
+958,9
@@
public class Desktop extends jalview.jbgui.GDesktop
* Do not set the default minimum size for frame
*/
public static synchronized void addInternalFrame(
* Do not set the default minimum size for frame
*/
public static synchronized void addInternalFrame(
- final JInternalFrame frame, String title, boolean makeVisible,
- int w, int h, boolean resizable, boolean ignoreMinSize)
+ final JalviewInternalFrame frame, String title,
+ boolean makeVisible, int w, int h, boolean resizable,
+ boolean ignoreMinSize)
{
// TODO: allow callers to determine X and Y position of frame (eg. via
{
// TODO: allow callers to determine X and Y position of frame (eg. via
@@
-1096,12
+1097,12
@@
public class Desktop extends jalview.jbgui.GDesktop
}
/**
}
/**
- * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close
- * the window
+ * Add key bindings to a JalviewInternalFrame so that Ctrl-W and Cmd-W will
+ * close the window
*
* @param frame
*/
*
* @param frame
*/
- private static void setKeyBindings(JInternalFrame frame)
+ private static void setKeyBindings(JalviewInternalFrame frame)
{
@SuppressWarnings("serial")
final Action closeAction = new AbstractAction()
{
@SuppressWarnings("serial")
final Action closeAction = new AbstractAction()
@@
-3213,7
+3214,7
@@
public class Desktop extends jalview.jbgui.GDesktop
topPanel.av.setGatherViewsHere(false);
bottomPanel.av.setGatherViewsHere(false);
topPanel.av.setGatherViewsHere(false);
bottomPanel.av.setGatherViewsHere(false);
- JInternalFrame splitFrame = new SplitFrame(newTopFrame,
+ JalviewInternalFrame splitFrame = new SplitFrame(newTopFrame,
newBottomFrame);
if (geometry != null)
{
newBottomFrame);
if (geometry != null)
{
diff --git
a/src/jalview/gui/FeatureSettings.java
b/src/jalview/gui/FeatureSettings.java
index
2e9731d
..
a90ce59
100644
(file)
--- a/
src/jalview/gui/FeatureSettings.java
+++ b/
src/jalview/gui/FeatureSettings.java
@@
-62,7
+62,7
@@
import javax.swing.BorderFactory;
import javax.swing.Icon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.Icon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JMenuItem;
import javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JMenuItem;
@@
-156,7
+156,7
@@
public class FeatureSettings extends JPanel
private Map<String, FeatureMatcherSetI> originalFilters;
private Map<String, FeatureMatcherSetI> originalFilters;
- final JInternalFrame frame;
+ final JalviewInternalFrame frame;
JScrollPane scrollPane = new JScrollPane();
JScrollPane scrollPane = new JScrollPane();
@@
-409,7
+409,7
@@
public class FeatureSettings extends JPanel
}
else
{
}
else
{
- frame = new JInternalFrame();
+ frame = new JalviewInternalFrame();
frame.setContentPane(this);
frame.setFrameIcon(null);
Rectangle bounds = af.getFeatureSettingsGeometry();
frame.setContentPane(this);
frame.setFrameIcon(null);
Rectangle bounds = af.getFeatureSettingsGeometry();
diff --git
a/src/jalview/gui/Finder.java
b/src/jalview/gui/Finder.java
index
2756b14
..
f641f4b
100755
(executable)
--- a/
src/jalview/gui/Finder.java
+++ b/
src/jalview/gui/Finder.java
@@
-75,7
+75,7
@@
public class Finder extends GFinder
private AlignmentPanel ap;
private AlignmentPanel ap;
- private JInternalFrame frame;
+ private JalviewInternalFrame frame;
/*
* Finder agent per viewport searched
/*
* Finder agent per viewport searched
@@
-107,7
+107,7
@@
public class Finder extends GFinder
ap = alignPanel;
focusFixed = fixedFocus;
finders = new HashMap<>();
ap = alignPanel;
focusFixed = fixedFocus;
finders = new HashMap<>();
- frame = new JInternalFrame();
+ frame = new JalviewInternalFrame();
frame.setFrameIcon(null);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.setFrameIcon(null);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
diff --git
a/src/jalview/gui/FontChooser.java
b/src/jalview/gui/FontChooser.java
index
f532706
..
6e5d7de
100755
(executable)
--- a/
src/jalview/gui/FontChooser.java
+++ b/
src/jalview/gui/FontChooser.java
@@
-24,7
+24,7
@@
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.geom.Rectangle2D;
import java.awt.FontMetrics;
import java.awt.geom.Rectangle2D;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JLayeredPane;
import jalview.bin.Cache;
import javax.swing.JLayeredPane;
import jalview.bin.Cache;
@@
-66,7
+66,7
@@
public class FontChooser extends GFontChooser
boolean init = true;
boolean init = true;
- JInternalFrame frame;
+ JalviewInternalFrame frame;
/*
* The last font settings selected in the dialog
/*
* The last font settings selected in the dialog
@@
-111,7
+111,7
@@
public class FontChooser extends GFontChooser
void init()
{
void init()
{
- frame = new JInternalFrame();
+ frame = new JalviewInternalFrame();
frame.setFrameIcon(null);
frame.setContentPane(this);
frame.setFrameIcon(null);
frame.setContentPane(this);
diff --git a/src/jalview/gui/JalviewInternalFrame.java
b/src/jalview/gui/JalviewInternalFrame.java
new file mode 100644
(file)
index 0000000..
c019629
--- /dev/null
+++ b/
src/jalview/gui/JalviewInternalFrame.java
@@ -0,0
+1,25
@@
+package jalview.gui;
+
+import javax.swing.JInternalFrame;
+
+public class JalviewInternalFrame extends JInternalFrame
+{
+ public JalviewInternalFrame()
+ {
+ super();
+ init();
+ }
+
+ public JalviewInternalFrame(String title)
+ {
+ super(title);
+ init();
+ }
+
+ private void init()
+ {
+ this.setFrameIcon(null);
+ this.setOpaque(true);
+ }
+
+}
diff --git
a/src/jalview/gui/JvOptionPane.java
b/src/jalview/gui/JvOptionPane.java
index
c0efd4a
..
703958b
100644
(file)
--- a/
src/jalview/gui/JvOptionPane.java
+++ b/
src/jalview/gui/JvOptionPane.java
@@
-901,9
+901,9
@@
public class JvOptionPane extends JOptionPane
if (raiseParent)
{
parentComponent.requestFocus();
if (raiseParent)
{
parentComponent.requestFocus();
- if (parentComponent instanceof JInternalFrame)
+ if (parentComponent instanceof JalviewInternalFrame)
{
{
- JInternalFrame jif = (JInternalFrame) parentComponent;
+ JalviewInternalFrame jif = (JalviewInternalFrame) parentComponent;
jif.show();
jif.moveToFront();
jif.grabFocus();
jif.show();
jif.moveToFront();
jif.grabFocus();
@@
-1009,9
+1009,9
@@
public class JvOptionPane extends JOptionPane
if (raiseParent)
{
parentComponent.requestFocus();
if (raiseParent)
{
parentComponent.requestFocus();
- if (parentComponent instanceof JInternalFrame)
+ if (parentComponent instanceof JalviewInternalFrame)
{
{
- JInternalFrame jif = (JInternalFrame) parentComponent;
+ JalviewInternalFrame jif = (JalviewInternalFrame) parentComponent;
jif.show();
jif.moveToFront();
jif.grabFocus();
jif.show();
jif.moveToFront();
jif.grabFocus();
@@
-1421,9
+1421,9
@@
public class JvOptionPane extends JOptionPane
if (raiseParent)
{
parentComponent.requestFocus();
if (raiseParent)
{
parentComponent.requestFocus();
- if (parentComponent instanceof JInternalFrame)
+ if (parentComponent instanceof JalviewInternalFrame)
{
{
- JInternalFrame jif = (JInternalFrame) parentComponent;
+ JalviewInternalFrame jif = (JalviewInternalFrame) parentComponent;
jif.show();
jif.moveToFront();
jif.grabFocus();
jif.show();
jif.moveToFront();
jif.grabFocus();
@@
-1472,13
+1472,13
@@
public class JvOptionPane extends JOptionPane
}
/**
}
/**
- * This helper method makes the JInternalFrame wait until it is notified by an
- * InternalFrameClosing event. This method also adds the given JOptionPane to
- * the JInternalFrame and sizes it according to the JInternalFrame's preferred
- * size.
+ * This helper method makes the JalviewInternalFrame wait until it is notified
+ * by an InternalFrameClosing event. This method also adds the given
+ * JOptionPane to the JalviewInternalFrame and sizes it according to the
+ * JalviewInternalFrame's preferred size.
*
* @param f
*
* @param f
- * The JInternalFrame to make modal.
+ * The JalviewInternalFrame to make modal.
*/
private static void startModal(JInternalFrame f)
{
*/
private static void startModal(JInternalFrame f)
{
diff --git
a/src/jalview/gui/OverviewPanel.java
b/src/jalview/gui/OverviewPanel.java
index
872d142
..
cde4ea9
100755
(executable)
--- a/
src/jalview/gui/OverviewPanel.java
+++ b/
src/jalview/gui/OverviewPanel.java
@@
-35,7
+35,7
@@
import java.beans.PropertyChangeEvent;
import java.beans.PropertyVetoException;
import javax.swing.JCheckBoxMenuItem;
import java.beans.PropertyVetoException;
import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.SwingUtilities;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.SwingUtilities;
@@
-67,7
+67,7
@@
public class OverviewPanel extends JPanel
private AlignmentPanel ap;
private AlignmentPanel ap;
- private JInternalFrame internalFrame;
+ private JalviewInternalFrame internalFrame;
protected JCheckBoxMenuItem displayToggle;
protected JCheckBoxMenuItem displayToggle;
@@
-86,7
+86,7
@@
public class OverviewPanel extends JPanel
* @param isShowHidden
* TODO
*/
* @param isShowHidden
* TODO
*/
- public OverviewPanel(AlignmentPanel alPanel, JInternalFrame frame,
+ public OverviewPanel(AlignmentPanel alPanel, JalviewInternalFrame frame,
boolean isShowHidden)
{
this.av = alPanel.av;
boolean isShowHidden)
{
this.av = alPanel.av;
@@
-413,8
+413,8
@@
public class OverviewPanel extends JPanel
* close the parent frame (which also removes it from the
* Desktop Windows menu)
*/
* close the parent frame (which also removes it from the
* Desktop Windows menu)
*/
- ((JInternalFrame) SwingUtilities
- .getAncestorOfClass(JInternalFrame.class, (this)))
+ ((JalviewInternalFrame) SwingUtilities
+ .getAncestorOfClass(JalviewInternalFrame.class, (this)))
.setClosed(true);
} catch (PropertyVetoException e)
{
.setClosed(true);
} catch (PropertyVetoException e)
{
diff --git
a/src/jalview/gui/PopupMenu.java
b/src/jalview/gui/PopupMenu.java
index
57a2fa0
..
c8708bf
100644
(file)
--- a/
src/jalview/gui/PopupMenu.java
+++ b/
src/jalview/gui/PopupMenu.java
@@
-41,7
+41,7
@@
import java.util.Vector;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
@@
-902,10
+902,10
@@
public class PopupMenu extends JPopupMenu implements ColourChangeListener
protected void showFeatureDetails(SequenceFeature sf, String seqName,
MappedFeatures mf)
{
protected void showFeatureDetails(SequenceFeature sf, String seqName,
MappedFeatures mf)
{
- JInternalFrame details;
+ JalviewInternalFrame details;
if (Platform.isJS())
{
if (Platform.isJS())
{
- details = new JInternalFrame();
+ details = new JalviewInternalFrame();
details.setFrameIcon(null);
JPanel panel = new JPanel(new BorderLayout());
panel.setOpaque(true);
details.setFrameIcon(null);
JPanel panel = new JPanel(new BorderLayout());
panel.setOpaque(true);
@@
-1825,7
+1825,7
@@
public class PopupMenu extends JPopupMenu implements ColourChangeListener
contents.append("</body></html>");
String report = contents.toString();
contents.append("</body></html>");
String report = contents.toString();
- JInternalFrame frame;
+ JalviewInternalFrame frame;
if (Platform.isJS())
{
JLabel textLabel = new JLabel();
if (Platform.isJS())
{
JLabel textLabel = new JLabel();
@@
-1835,7
+1835,7
@@
public class PopupMenu extends JPopupMenu implements ColourChangeListener
pane.setOpaque(true);
pane.setBackground(Color.WHITE);
pane.add(textLabel, BorderLayout.NORTH);
pane.setOpaque(true);
pane.setBackground(Color.WHITE);
pane.add(textLabel, BorderLayout.NORTH);
- frame = new JInternalFrame();
+ frame = new JalviewInternalFrame();
frame.setFrameIcon(null);
frame.getContentPane().add(new JScrollPane(pane));
}
frame.setFrameIcon(null);
frame.getContentPane().add(new JScrollPane(pane));
}
diff --git
a/src/jalview/gui/Preferences.java
b/src/jalview/gui/Preferences.java
index
c4f32c3
..
5769bb7
100755
(executable)
--- a/
src/jalview/gui/Preferences.java
+++ b/
src/jalview/gui/Preferences.java
@@
-34,7
+34,7
@@
import java.util.concurrent.CompletableFuture;
import javax.help.HelpSetException;
import javax.swing.JComboBox;
import javax.help.HelpSetException;
import javax.swing.JComboBox;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JPanel;
import javax.swing.ListSelectionModel;
import javax.swing.RowFilter;
import javax.swing.JPanel;
import javax.swing.ListSelectionModel;
import javax.swing.RowFilter;
@@
-188,7
+188,7
@@
public class Preferences extends GPreferences
Cache.enableSessionProperties();
}
Cache.enableSessionProperties();
}
- JInternalFrame frame;
+ JalviewInternalFrame frame;
private WsPreferences wsPrefs;
private WsPreferences wsPrefs;
@@
-257,7
+257,7
@@
public class Preferences extends GPreferences
// don't populate with session properties
Cache.disableSessionProperties();
// don't populate with session properties
Cache.disableSessionProperties();
- frame = new JInternalFrame();
+ frame = new JalviewInternalFrame();
frame.setFrameIcon(null);
frame.setContentPane(this);
if (!Platform.isJS())
frame.setFrameIcon(null);
frame.setContentPane(this);
if (!Platform.isJS())
diff --git
a/src/jalview/gui/PymolViewer.java
b/src/jalview/gui/PymolViewer.java
index
52c253d
..
f68e503
100644
(file)
--- a/
src/jalview/gui/PymolViewer.java
+++ b/
src/jalview/gui/PymolViewer.java
@@
-27,7
+27,7
@@
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.List;
import java.util.Map;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JMenuItem;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
import javax.swing.JMenuItem;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
@@
-63,7
+63,7
@@
public class PymolViewer extends StructureViewerBase
* closeViewer will decide whether or not to close this frame
* depending on whether user chooses to Cancel or not
*/
* closeViewer will decide whether or not to close this frame
* depending on whether user chooses to Cancel or not
*/
- setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE);
+ setDefaultCloseOperation(JalviewInternalFrame.DO_NOTHING_ON_CLOSE);
}
public PymolViewer(PDBEntry pdb, SequenceI[] seqs, Object object,
}
public PymolViewer(PDBEntry pdb, SequenceI[] seqs, Object object,
diff --git
a/src/jalview/gui/RedundancyPanel.java
b/src/jalview/gui/RedundancyPanel.java
index
8d66a44
..
0bf7477
100755
(executable)
--- a/
src/jalview/gui/RedundancyPanel.java
+++ b/
src/jalview/gui/RedundancyPanel.java
@@
-26,7
+26,7
@@
import java.util.List;
import java.util.Stack;
import java.util.Vector;
import java.util.Stack;
import java.util.Vector;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JProgressBar;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.JProgressBar;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
@@
-62,7
+62,7
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
SequenceI[] originalSequences;
SequenceI[] originalSequences;
- JInternalFrame frame;
+ JalviewInternalFrame frame;
Vector redundantSeqs;
Vector redundantSeqs;
@@
-99,7
+99,7
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
Thread worker = new Thread(this);
worker.start();
Thread worker = new Thread(this);
worker.start();
- frame = new JInternalFrame();
+ frame = new JalviewInternalFrame();
frame.setFrameIcon(null);
frame.setContentPane(this);
Desktop.addInternalFrame(frame,
frame.setFrameIcon(null);
frame.setContentPane(this);
Desktop.addInternalFrame(frame,
diff --git
a/src/jalview/gui/SequenceFetcher.java
b/src/jalview/gui/SequenceFetcher.java
index
6b4c74a
..
cae7c02
100755
(executable)
--- a/
src/jalview/gui/SequenceFetcher.java
+++ b/
src/jalview/gui/SequenceFetcher.java
@@
-35,7
+35,7
@@
import java.util.List;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
@@
-125,7
+125,7
@@
public class SequenceFetcher extends JPanel implements Runnable
JTextArea textArea;
JTextArea textArea;
- JInternalFrame frame;
+ JalviewInternalFrame frame;
IProgressIndicator guiWindow;
IProgressIndicator guiWindow;
@@
-184,7
+184,7
@@
public class SequenceFetcher extends JPanel implements Runnable
jbInit(selectedDb);
textArea.setText(queryString);
jbInit(selectedDb);
textArea.setText(queryString);
- frame = new JInternalFrame();
+ frame = new JalviewInternalFrame();
frame.setContentPane(this);
frame.setFrameIcon(null);
Desktop.addInternalFrame(frame, getFrameTitle(), true, 400,
frame.setContentPane(this);
frame.setFrameIcon(null);
Desktop.addInternalFrame(frame, getFrameTitle(), true, 400,
diff --git
a/src/jalview/gui/SliderPanel.java
b/src/jalview/gui/SliderPanel.java
index
1d59853
..
2a198d9
100755
(executable)
--- a/
src/jalview/gui/SliderPanel.java
+++ b/
src/jalview/gui/SliderPanel.java
@@
-25,7
+25,7
@@
import java.awt.event.MouseEvent;
import java.beans.PropertyVetoException;
import java.util.List;
import java.beans.PropertyVetoException;
import java.util.List;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JLayeredPane;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.JLayeredPane;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
@@
-48,9
+48,9
@@
public class SliderPanel extends GSliderPanel
{
private static final String BACKGROUND = "Background";
{
private static final String BACKGROUND = "Background";
- static JInternalFrame conservationSlider;
+ static JalviewInternalFrame conservationSlider;
- static JInternalFrame PIDSlider;
+ static JalviewInternalFrame PIDSlider;
AlignmentPanel ap;
AlignmentPanel ap;
@@
-155,7
+155,7
@@
public class SliderPanel extends GSliderPanel
if (conservationSlider == null)
{
sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, rs);
if (conservationSlider == null)
{
sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, rs);
- conservationSlider = new JInternalFrame();
+ conservationSlider = new JalviewInternalFrame();
conservationSlider.setFrameIcon(null);
conservationSlider.setContentPane(sliderPanel);
conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
conservationSlider.setFrameIcon(null);
conservationSlider.setContentPane(sliderPanel);
conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
@@
-269,7
+269,7
@@
public class SliderPanel extends GSliderPanel
if (PIDSlider == null)
{
sliderPanel = new SliderPanel(ap, threshold, false, rs);
if (PIDSlider == null)
{
sliderPanel = new SliderPanel(ap, threshold, false, rs);
- PIDSlider = new JInternalFrame();
+ PIDSlider = new JalviewInternalFrame();
PIDSlider.setFrameIcon(null);
PIDSlider.setContentPane(sliderPanel);
PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
PIDSlider.setFrameIcon(null);
PIDSlider.setContentPane(sliderPanel);
PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
@@
-304,7
+304,7
@@
public class SliderPanel extends GSliderPanel
*
* @return
*/
*
* @return
*/
- public static JInternalFrame showPIDSlider()
+ public static JalviewInternalFrame showPIDSlider()
{
hideConservationSlider();
{
hideConservationSlider();
@@
-457,7
+457,7
@@
public class SliderPanel extends GSliderPanel
return getValue(conservationSlider);
}
return getValue(conservationSlider);
}
- static int getValue(JInternalFrame slider)
+ static int getValue(JalviewInternalFrame slider)
{
return slider == null ? 0
: ((SliderPanel) slider.getContentPane()).getValue();
{
return slider == null ? 0
: ((SliderPanel) slider.getContentPane()).getValue();
diff --git
a/src/jalview/gui/SplashScreen.java
b/src/jalview/gui/SplashScreen.java
index
61273c7
..
83cd0dc
100755
(executable)
--- a/
src/jalview/gui/SplashScreen.java
+++ b/
src/jalview/gui/SplashScreen.java
@@
-31,7
+31,7
@@
import java.awt.MediaTracker;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
import javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
@@
-72,7
+72,7
@@
public class SplashScreen extends JPanel
*/
private Component splashText;
*/
private Component splashText;
- private JInternalFrame iframe;
+ private JalviewInternalFrame iframe;
private Image image;
private Image image;
@@
-184,7
+184,7
@@
public class SplashScreen extends JPanel
this.setForeground(fg);
this.setFont(font);
this.setForeground(fg);
this.setFont(font);
- iframe = new JInternalFrame();
+ iframe = new JalviewInternalFrame();
iframe.setFrameIcon(null);
iframe.setClosable(true);
this.setLayout(new BorderLayout());
iframe.setFrameIcon(null);
iframe.setClosable(true);
this.setLayout(new BorderLayout());
diff --git
a/src/jalview/gui/SplitFrame.java
b/src/jalview/gui/SplitFrame.java
index
73744b3
..
b2de97b
100644
(file)
--- a/
src/jalview/gui/SplitFrame.java
+++ b/
src/jalview/gui/SplitFrame.java
@@
-861,7
+861,7
@@
public class SplitFrame extends GSplitFrame implements SplitContainerI
* holds the frame for feature settings, so Protein and DNA tabs can be
* managed
*/
* holds the frame for feature settings, so Protein and DNA tabs can be
* managed
*/
- JInternalFrame featureSettingsUI;
+ JalviewInternalFrame featureSettingsUI;
JTabbedPane featureSettingsPanels;
JTabbedPane featureSettingsPanels;
@@
-898,7
+898,7
@@
public class SplitFrame extends GSplitFrame implements SplitContainerI
getAlignFrames().get(tab).showFeatureSettingsUI();
}
});
getAlignFrames().get(tab).showFeatureSettingsUI();
}
});
- featureSettingsUI = new JInternalFrame(MessageManager.getString(
+ featureSettingsUI = new JalviewInternalFrame(MessageManager.getString(
"label.sequence_feature_settings_for_CDS_and_Protein"));
featureSettingsUI.setFrameIcon(null);
featureSettingsPanels.setOpaque(true);
"label.sequence_feature_settings_for_CDS_and_Protein"));
featureSettingsUI.setFrameIcon(null);
featureSettingsPanels.setOpaque(true);
diff --git
a/src/jalview/gui/UserDefinedColours.java
b/src/jalview/gui/UserDefinedColours.java
index
14f9adf
..
9569918
100755
(executable)
--- a/
src/jalview/gui/UserDefinedColours.java
+++ b/
src/jalview/gui/UserDefinedColours.java
@@
-34,7
+34,7
@@
import java.util.List;
import java.util.Locale;
import javax.swing.JButton;
import java.util.Locale;
import javax.swing.JButton;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.xml.bind.JAXBContext;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.xml.bind.JAXBContext;
@@
-94,7
+94,7
@@
public class UserDefinedColours extends GUserDefinedColours
*/
boolean changedButNotSaved;
*/
boolean changedButNotSaved;
- JInternalFrame frame;
+ JalviewInternalFrame frame;
List<JButton> upperCaseButtons;
List<JButton> upperCaseButtons;
@@
-147,7
+147,7
@@
public class UserDefinedColours extends GUserDefinedColours
void showFrame()
{
colorChooser.getSelectionModel().addChangeListener(this);
void showFrame()
{
colorChooser.getSelectionModel().addChangeListener(this);
- frame = new JInternalFrame();
+ frame = new JalviewInternalFrame();
frame.setFrameIcon(null);
frame.setContentPane(this);
Desktop.addInternalFrame(frame,
frame.setFrameIcon(null);
frame.setContentPane(this);
Desktop.addInternalFrame(frame,
diff --git
a/src/jalview/gui/VamsasApplication.java
b/src/jalview/gui/VamsasApplication.java
index
8a8ba8d
..
e49fcaa
100644
(file)
--- a/
src/jalview/gui/VamsasApplication.java
+++ b/
src/jalview/gui/VamsasApplication.java
@@
-20,6
+20,16
@@
*/
package jalview.gui;
*/
package jalview.gui;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+
+import javax.swing.JInternalFrame;
+
import jalview.bin.Cache;
import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.bin.Cache;
import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
@@
-35,17
+45,6
@@
import jalview.structure.VamsasListener;
import jalview.structure.VamsasSource;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.structure.VamsasSource;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
-
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.io.File;
-import java.io.IOException;
-import java.util.Hashtable;
-import java.util.IdentityHashMap;
-import java.util.Iterator;
-
-import javax.swing.JInternalFrame;
-
import uk.ac.vamsas.client.ClientHandle;
import uk.ac.vamsas.client.IClient;
import uk.ac.vamsas.client.IClientDocument;
import uk.ac.vamsas.client.ClientHandle;
import uk.ac.vamsas.client.IClient;
import uk.ac.vamsas.client.IClientDocument;
@@
-932,8
+931,8
@@
public class VamsasApplication implements SelectionSource, VamsasSource
jselection.setEndRes(prange[p + u] - 1);
}
// mark all the columns in the range.
jselection.setEndRes(prange[p + u] - 1);
}
// mark all the columns in the range.
- for (int sr = prange[p], er = prange[p + 1], de = er
- + d; sr != de; sr += d)
+ for (int sr = prange[p], er = prange[p + 1],
+ de = er + d; sr != de; sr += d)
{
colsel.addElement(sr - 1);
}
{
colsel.addElement(sr - 1);
}
diff --git
a/src/jalview/gui/WebserviceInfo.java
b/src/jalview/gui/WebserviceInfo.java
index
7eeee9a
..
20d5c34
100644
(file)
--- a/
src/jalview/gui/WebserviceInfo.java
+++ b/
src/jalview/gui/WebserviceInfo.java
@@
-36,7
+36,7
@@
import java.util.Vector;
import javax.swing.JComponent;
import javax.swing.JEditorPane;
import javax.swing.JComponent;
import javax.swing.JEditorPane;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTabbedPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTabbedPane;
@@
-94,7
+94,7
@@
public class WebserviceInfo extends GWebserviceInfo
boolean serviceIsCancellable;
boolean serviceIsCancellable;
- JInternalFrame frame;
+ JalviewInternalFrame frame;
private IProgressIndicator progressBar;
private IProgressIndicator progressBar;
@@
-322,7
+322,7
@@
public class WebserviceInfo extends GWebserviceInfo
void init(String title, String info, int width, int height,
boolean makeVisible)
{
void init(String title, String info, int width, int height,
boolean makeVisible)
{
- frame = new JInternalFrame();
+ frame = new JalviewInternalFrame();
frame.setFrameIcon(null);
frame.setContentPane(this);
Desktop.addInternalFrame(frame, title, makeVisible, width, height);
frame.setFrameIcon(null);
frame.setContentPane(this);
Desktop.addInternalFrame(frame, title, makeVisible, width, height);
diff --git
a/src/jalview/io/VamsasAppDatastore.java
b/src/jalview/io/VamsasAppDatastore.java
index
dd4b72c
..
6119db2
100644
(file)
--- a/
src/jalview/io/VamsasAppDatastore.java
+++ b/
src/jalview/io/VamsasAppDatastore.java
@@
-20,6
+20,17
@@
*/
package jalview.io;
*/
package jalview.io;
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Vector;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+
import jalview.bin.Console;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.bin.Console;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
@@
-36,18
+47,6
@@
import jalview.io.vamsas.Rangetype;
import jalview.project.Jalview2XML;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.project.Jalview2XML;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
-
-import java.io.IOException;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.IdentityHashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Vector;
-import java.util.jar.JarInputStream;
-import java.util.jar.JarOutputStream;
-
import uk.ac.vamsas.client.IClientAppdata;
import uk.ac.vamsas.client.IClientDocument;
import uk.ac.vamsas.client.Vobject;
import uk.ac.vamsas.client.IClientAppdata;
import uk.ac.vamsas.client.IClientDocument;
import uk.ac.vamsas.client.Vobject;
@@
-506,8
+505,8
@@
public class VamsasAppDatastore
}
// ////////////////////////////////////////////
// SAVE Alignment Sequence Features
}
// ////////////////////////////////////////////
// SAVE Alignment Sequence Features
- for (int i = 0, iSize = alignment
- .getAlignmentSequenceCount(); i < iSize; i++)
+ for (int i = 0,
+ iSize = alignment.getAlignmentSequenceCount(); i < iSize; i++)
{
AlignmentSequence valseq;
SequenceI alseq = (SequenceI) getvObj2jv(
{
AlignmentSequence valseq;
SequenceI alseq = (SequenceI) getvObj2jv(
@@
-1687,7
+1686,7
@@
public class VamsasAppDatastore
+ ((Vobject) dataset
.getDataSetAnnotations(dsa)
.getSeqRef(0)).getVorbaId()
+ ((Vobject) dataset
.getDataSetAnnotations(dsa)
.getSeqRef(0)).getVorbaId()
- .getId());
+ .getId());
}
else
{
}
else
{
@@
-1719,8
+1718,8
@@
public class VamsasAppDatastore
{
// LOAD ALIGNMENTS from DATASET
{
// LOAD ALIGNMENTS from DATASET
- for (int al = 0, nal = dataset
- .getAlignmentCount(); al < nal; al++)
+ for (int al = 0,
+ nal = dataset.getAlignmentCount(); al < nal; al++)
{
uk.ac.vamsas.objects.core.Alignment alignment = dataset
.getAlignment(al);
{
uk.ac.vamsas.objects.core.Alignment alignment = dataset
.getAlignment(al);
@@
-1837,8
+1836,8
@@
public class VamsasAppDatastore
if (newasAnnots != null && newasAnnots.size() > 0)
{
// Add the new sequence annotations in to the alignment.
if (newasAnnots != null && newasAnnots.size() > 0)
{
// Add the new sequence annotations in to the alignment.
- for (int an = 0, anSize = newasAnnots
- .size(); an < anSize; an++)
+ for (int an = 0,
+ anSize = newasAnnots.size(); an < anSize; an++)
{
jal.addAnnotation(
(AlignmentAnnotation) newasAnnots.elementAt(an));
{
jal.addAnnotation(
(AlignmentAnnotation) newasAnnots.elementAt(an));
@@
-1912,8
+1911,8
@@
public class VamsasAppDatastore
.getAction();
if (alignment.getPropertyCount() > 0)
{
.getAction();
if (alignment.getPropertyCount() > 0)
{
- for (int p = 0, pe = alignment
- .getPropertyCount(); p < pe; p++)
+ for (int p = 0,
+ pe = alignment.getPropertyCount(); p < pe; p++)
{
if (alignment.getProperty(p).getName().equals("title"))
{
{
if (alignment.getProperty(p).getName().equals("title"))
{
diff --git
a/src/jalview/jbgui/GAlignFrame.java
b/src/jalview/jbgui/GAlignFrame.java
index
2d151bc
..
b43d17f
100755
(executable)
--- a/
src/jalview/jbgui/GAlignFrame.java
+++ b/
src/jalview/jbgui/GAlignFrame.java
@@
-36,7
+36,7
@@
import java.util.Map;
import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
@@
-62,7
+62,7
@@
import jalview.util.MessageManager;
import jalview.util.Platform;
@SuppressWarnings("serial")
import jalview.util.Platform;
@SuppressWarnings("serial")
-public class GAlignFrame extends JInternalFrame
+public class GAlignFrame extends JalviewInternalFrame
{
protected JMenuBar alignFrameMenuBar = new JMenuBar();
{
protected JMenuBar alignFrameMenuBar = new JMenuBar();
diff --git
a/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
b/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
index
ef09b6a
..
3c76977
100644
(file)
--- a/
src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
+++ b/
src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
@@
-29,7
+29,7
@@
import java.awt.event.MouseEvent;
import javax.swing.JButton;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JEditorPane;
import javax.swing.JButton;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JEditorPane;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
@@
-47,7
+47,7
@@
import jalview.util.MessageManager;
* @author $author$
* @version $Revision$
*/
* @author $author$
* @version $Revision$
*/
-public class GCutAndPasteHtmlTransfer extends JInternalFrame
+public class GCutAndPasteHtmlTransfer extends JalviewInternalFrame
{
protected JEditorPane textarea = new JEditorPane("text/html", "");
{
protected JEditorPane textarea = new JEditorPane("text/html", "");
diff --git
a/src/jalview/jbgui/GCutAndPasteTransfer.java
b/src/jalview/jbgui/GCutAndPasteTransfer.java
index
3cd52ae
..
100ca95
100755
(executable)
--- a/
src/jalview/jbgui/GCutAndPasteTransfer.java
+++ b/
src/jalview/jbgui/GCutAndPasteTransfer.java
@@
-27,7
+27,7
@@
import java.awt.event.ActionListener;
import java.awt.event.MouseEvent;
import javax.swing.JButton;
import java.awt.event.MouseEvent;
import javax.swing.JButton;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
@@
-44,7
+44,7
@@
import jalview.util.MessageManager;
* @author $author$
* @version $Revision$
*/
* @author $author$
* @version $Revision$
*/
-public class GCutAndPasteTransfer extends JInternalFrame
+public class GCutAndPasteTransfer extends JalviewInternalFrame
{
protected JTextArea textarea = new JTextArea();
{
protected JTextArea textarea = new JTextArea();
diff --git
a/src/jalview/jbgui/GPCAPanel.java
b/src/jalview/jbgui/GPCAPanel.java
index
cf7bc4e
..
1f1c728
100755
(executable)
--- a/
src/jalview/jbgui/GPCAPanel.java
+++ b/
src/jalview/jbgui/GPCAPanel.java
@@
-31,7
+31,7
@@
import java.awt.event.ActionListener;
import javax.swing.JButton;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JComboBox;
import javax.swing.JButton;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JComboBox;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
@@
-43,7
+43,7
@@
import javax.swing.event.MenuListener;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
-public class GPCAPanel extends JInternalFrame
+public class GPCAPanel extends JalviewInternalFrame
{
private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
{
private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
diff --git
a/src/jalview/jbgui/GRnaStructureViewer.java
b/src/jalview/jbgui/GRnaStructureViewer.java
index
663245f
..
df0786c
100644
(file)
--- a/
src/jalview/jbgui/GRnaStructureViewer.java
+++ b/
src/jalview/jbgui/GRnaStructureViewer.java
@@
-20,10
+20,10
@@
*/
package jalview.jbgui;
*/
package jalview.jbgui;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
@SuppressWarnings("serial")
@SuppressWarnings("serial")
-public class GRnaStructureViewer extends JInternalFrame
+public class GRnaStructureViewer extends JalviewInternalFrame
{
public GRnaStructureViewer()
{
{
public GRnaStructureViewer()
{
diff --git
a/src/jalview/jbgui/GSplitFrame.java
b/src/jalview/jbgui/GSplitFrame.java
index
4d531be
..
4faab0a
100644
(file)
--- a/
src/jalview/jbgui/GSplitFrame.java
+++ b/
src/jalview/jbgui/GSplitFrame.java
@@
-25,13
+25,13
@@
import java.awt.MouseInfo;
import java.awt.Point;
import java.awt.Rectangle;
import java.awt.Point;
import java.awt.Rectangle;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JSplitPane;
import javax.swing.plaf.basic.BasicInternalFrameUI;
import jalview.util.Platform;
import javax.swing.JSplitPane;
import javax.swing.plaf.basic.BasicInternalFrameUI;
import jalview.util.Platform;
-public class GSplitFrame extends JInternalFrame
+public class GSplitFrame extends JalviewInternalFrame
{
protected static final int DIVIDER_SIZE = 5;
{
protected static final int DIVIDER_SIZE = 5;
@@
-107,9
+107,9
@@
public class GSplitFrame extends JInternalFrame
if (Platform.isAMacAndNotJS())
{
// this saves some space - but doesn't hide the title bar
if (Platform.isAMacAndNotJS())
{
// this saves some space - but doesn't hide the title bar
- topFrame.putClientProperty("JInternalFrame.isPalette", true);
+ topFrame.putClientProperty("JalviewInternalFrame.isPalette", true);
// topFrame.getRootPane().putClientProperty("Window.style", "small");
// topFrame.getRootPane().putClientProperty("Window.style", "small");
- bottomFrame.putClientProperty("JInternalFrame.isPalette", true);
+ bottomFrame.putClientProperty("JalviewInternalFrame.isPalette", true);
}
else
{
}
else
{
diff --git
a/src/jalview/jbgui/GStructureChooser.java
b/src/jalview/jbgui/GStructureChooser.java
index
8cb5b3c
..
e9e12a5
100644
(file)
--- a/
src/jalview/jbgui/GStructureChooser.java
+++ b/
src/jalview/jbgui/GStructureChooser.java
@@
-49,7
+49,7
@@
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JFrame;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JFrame;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JPanel;
@@
-115,7
+115,7
@@
public abstract class GStructureChooser extends JPanel
protected String frameTitle = MessageManager
.getString("label.structure_chooser");
protected String frameTitle = MessageManager
.getString("label.structure_chooser");
- protected JInternalFrame mainFrame = new JInternalFrame(frameTitle);
+ protected JalviewInternalFrame mainFrame = new JalviewInternalFrame(frameTitle);
protected JComboBox<FilterOption> cmb_filterOption = new JComboBox<>();
protected JComboBox<FilterOption> cmb_filterOption = new JComboBox<>();
@@
-1067,7
+1067,7
@@
public abstract class GStructureChooser extends JPanel
protected abstract void validateSelections();
protected abstract void validateSelections();
- public JInternalFrame getFrame()
+ public JalviewInternalFrame getFrame()
{
return mainFrame;
}
{
return mainFrame;
}
diff --git
a/src/jalview/jbgui/GStructureViewer.java
b/src/jalview/jbgui/GStructureViewer.java
index
18e4c9f
..
19196f8
100644
(file)
--- a/
src/jalview/jbgui/GStructureViewer.java
+++ b/
src/jalview/jbgui/GStructureViewer.java
@@
-25,7
+25,7
@@
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
@@
-39,7
+39,7
@@
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
@SuppressWarnings("serial")
import jalview.util.MessageManager;
@SuppressWarnings("serial")
-public abstract class GStructureViewer extends JInternalFrame
+public abstract class GStructureViewer extends JalviewInternalFrame
implements JalviewStructureDisplayI, ColourChangeListener
{
// private AAStructureBindingModel bindingModel;
implements JalviewStructureDisplayI, ColourChangeListener
{
// private AAStructureBindingModel bindingModel;
diff --git
a/src/jalview/jbgui/GTreePanel.java
b/src/jalview/jbgui/GTreePanel.java
index
2a1b11f
..
a90771b
100755
(executable)
--- a/
src/jalview/jbgui/GTreePanel.java
+++ b/
src/jalview/jbgui/GTreePanel.java
@@
-26,7
+26,7
@@
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.JCheckBoxMenuItem;
import java.awt.event.ActionListener;
import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
@@
-38,7
+38,7
@@
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
@SuppressWarnings("serial")
import jalview.util.MessageManager;
@SuppressWarnings("serial")
-public class GTreePanel extends JInternalFrame
+public class GTreePanel extends JalviewInternalFrame
{
BorderLayout borderLayout1 = new BorderLayout();
{
BorderLayout borderLayout1 = new BorderLayout();
diff --git
a/src/jalview/project/Jalview2XML.java
b/src/jalview/project/Jalview2XML.java
index
6f26036
..
52d818c
100644
(file)
--- a/
src/jalview/project/Jalview2XML.java
+++ b/
src/jalview/project/Jalview2XML.java
@@
-26,7
+26,6
@@
import static jalview.math.RotatableMatrix.Axis.Z;
import java.awt.Color;
import java.awt.Font;
import java.awt.Color;
import java.awt.Font;
-import java.awt.FontMetrics;
import java.awt.Rectangle;
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
import java.awt.Rectangle;
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
@@
-2516,6
+2515,7
@@
public class Jalview2XML
return BitSet.valueOf(newlongvals);
}
return BitSet.valueOf(newlongvals);
}
+
private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
{
AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
{
AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
diff --git
a/src/jalview/ws/jws2/MsaWSThread.java
b/src/jalview/ws/jws2/MsaWSThread.java
index
ee0fbc5
..
6ab0c4f
100644
(file)
--- a/
src/jalview/ws/jws2/MsaWSThread.java
+++ b/
src/jalview/ws/jws2/MsaWSThread.java
@@
-46,7
+46,7
@@
import java.util.List;
import java.util.Map;
import java.util.Vector;
import java.util.Map;
import java.util.Vector;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
import compbio.data.msa.MsaWS;
import compbio.metadata.Argument;
import compbio.data.msa.MsaWS;
import compbio.metadata.Argument;
@@
-1045,7
+1045,7
@@
class MsaWSThread extends AWS2Thread implements WSClientI
af2.setTitle(complementTitle);
String linkedTitle = MessageManager
.getString("label.linked_view_title");
af2.setTitle(complementTitle);
String linkedTitle = MessageManager
.getString("label.linked_view_title");
- JInternalFrame splitFrame = new SplitFrame(
+ JalviewInternalFrame splitFrame = new SplitFrame(
al.isNucleotide() ? af : af2, al.isNucleotide() ? af2 : af);
Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
return;
al.isNucleotide() ? af : af2, al.isNucleotide() ? af2 : af);
Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
return;