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Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
[jalview.git]
/
src
/
jalview
/
gui
/
AnnotationChooser.java
diff --git
a/src/jalview/gui/AnnotationChooser.java
b/src/jalview/gui/AnnotationChooser.java
index
35b6032
..
d976815
100644
(file)
--- a/
src/jalview/gui/AnnotationChooser.java
+++ b/
src/jalview/gui/AnnotationChooser.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,11
+20,6
@@
*/
package jalview.gui;
*/
package jalview.gui;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceGroup;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Checkbox;
import java.awt.CheckboxGroup;
import java.awt.BorderLayout;
import java.awt.Checkbox;
import java.awt.CheckboxGroup;
@@
-45,6
+40,11
@@
import javax.swing.JInternalFrame;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceGroup;
+import jalview.util.MessageManager;
+
/**
* A panel that allows the user to select which sequence-associated annotation
* rows to show or hide.
/**
* A panel that allows the user to select which sequence-associated annotation
* rows to show or hide.
@@
-56,7
+56,8
@@
import javax.swing.JPanel;
public class AnnotationChooser extends JPanel
{
public class AnnotationChooser extends JPanel
{
- private static final Font CHECKBOX_FONT = new Font("Serif", Font.BOLD, 12);
+ private static final Font CHECKBOX_FONT = new Font("Serif", Font.BOLD,
+ 12);
private static final int MY_FRAME_WIDTH = 600;
private static final int MY_FRAME_WIDTH = 600;
@@
-81,7
+82,7
@@
public class AnnotationChooser extends JPanel
private boolean applyToUnselectedSequences;
// currently selected 'annotation type' checkboxes
private boolean applyToUnselectedSequences;
// currently selected 'annotation type' checkboxes
- private Map<String, String> selectedTypes = new HashMap<String, String>();
+ private Map<String, String> selectedTypes = new HashMap<>();
/**
* Constructor.
/**
* Constructor.
@@
-194,14
+195,7
@@
public class AnnotationChooser extends JPanel
{
setAnnotationVisibility(true);
{
setAnnotationVisibility(true);
- // copied from AnnotationLabel.actionPerformed (after show/hide row)...
- // TODO should drive this functionality into AlignmentPanel
ap.updateAnnotation();
ap.updateAnnotation();
- // this.ap.annotationPanel.adjustPanelHeight();
- // this.ap.alabels.setSize(this.ap.alabels.getSize().width,
- // this.ap.annotationPanel.getSize().height);
- // this.ap.validate();
- this.ap.paintAlignment(true);
}
/**
}
/**
@@
-228,11
+222,6
@@
public class AnnotationChooser extends JPanel
}
}
ap.updateAnnotation();
}
}
ap.updateAnnotation();
- // // this.ap.annotationPanel.adjustPanelHeight();
- // this.ap.alabels.setSize(this.ap.alabels.getSize().width,
- // this.ap.annotationPanel.getSize().height);
- // this.ap.validate();
- this.ap.paintAlignment(true);
}
/**
}
/**
@@
-242,15
+231,13
@@
public class AnnotationChooser extends JPanel
* type which are in the application scope (all, selected or unselected
* sequences).
*
* type which are in the application scope (all, selected or unselected
* sequences).
*
- * @param type
+ * @param dataSourceType
*/
protected void changeShowHide_actionPerformed()
{
setAnnotationVisibility(false);
*/
protected void changeShowHide_actionPerformed()
{
setAnnotationVisibility(false);
- this.ap.updateAnnotation();
- // this.ap.annotationPanel.adjustPanelHeight();
- this.ap.paintAlignment(true);
+ ap.updateAnnotation();
}
/**
}
/**
@@
-355,7
+342,7
@@
public class AnnotationChooser extends JPanel
public static List<String> getAnnotationTypes(AlignmentI alignment,
boolean sequenceSpecificOnly)
{
public static List<String> getAnnotationTypes(AlignmentI alignment,
boolean sequenceSpecificOnly)
{
- List<String> result = new ArrayList<String>();
+ List<String> result = new ArrayList<>();
for (AlignmentAnnotation aa : alignment.getAlignmentAnnotation())
{
if (!sequenceSpecificOnly || aa.sequenceRef != null)
for (AlignmentAnnotation aa : alignment.getAlignmentAnnotation())
{
if (!sequenceSpecificOnly || aa.sequenceRef != null)
@@
-615,6
+602,7
@@
public class AnnotationChooser extends JPanel
private void showFrame()
{
frame = new JInternalFrame();
private void showFrame()
{
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
Desktop.addInternalFrame(frame,
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
Desktop.addInternalFrame(frame,