X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationChooser.java;h=d9768152af9164f25ea7585d7c093e6db0f44dcb;hb=155a17a423e980849fd4dc5f857da1a72b0010b9;hp=5ac76db0f0b4f1f7c54f74f3178822366f6ba664;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git
diff --git a/src/jalview/gui/AnnotationChooser.java b/src/jalview/gui/AnnotationChooser.java
index 5ac76db..d976815 100644
--- a/src/jalview/gui/AnnotationChooser.java
+++ b/src/jalview/gui/AnnotationChooser.java
@@ -1,10 +1,25 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
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;
@@ -25,6 +40,11 @@ import javax.swing.JInternalFrame;
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.
@@ -36,7 +56,8 @@ import javax.swing.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;
@@ -61,7 +82,7 @@ public class AnnotationChooser extends JPanel
private boolean applyToUnselectedSequences;
// currently selected 'annotation type' checkboxes
- private Map selectedTypes = new HashMap();
+ private Map selectedTypes = new HashMap<>();
/**
* Constructor.
@@ -174,14 +195,7 @@ public class AnnotationChooser extends JPanel
{
setAnnotationVisibility(true);
- // copied from AnnotationLabel.actionPerformed (after show/hide row)...
- // TODO should drive this functionality into AlignmentPanel
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);
}
/**
@@ -208,11 +222,6 @@ public class AnnotationChooser extends JPanel
}
}
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);
}
/**
@@ -222,15 +231,13 @@ public class AnnotationChooser extends JPanel
* type which are in the application scope (all, selected or unselected
* sequences).
*
- * @param type
+ * @param dataSourceType
*/
protected void changeShowHide_actionPerformed()
{
setAnnotationVisibility(false);
- this.ap.updateAnnotation();
- // this.ap.annotationPanel.adjustPanelHeight();
- this.ap.paintAlignment(true);
+ ap.updateAnnotation();
}
/**
@@ -335,7 +342,7 @@ public class AnnotationChooser extends JPanel
public static List getAnnotationTypes(AlignmentI alignment,
boolean sequenceSpecificOnly)
{
- List result = new ArrayList();
+ List result = new ArrayList<>();
for (AlignmentAnnotation aa : alignment.getAlignmentAnnotation())
{
if (!sequenceSpecificOnly || aa.sequenceRef != null)
@@ -595,6 +602,7 @@ public class AnnotationChooser extends JPanel
private void showFrame()
{
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
Desktop.addInternalFrame(frame,