X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationChooser.java;h=84883d7266fa3e1376f995bde2f7527d4868a8bc;hb=5c8c056843d24f3c0259615a05c981012e0f5d70;hp=5ac76db0f0b4f1f7c54f74f3178822366f6ba664;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git
diff --git a/src/jalview/gui/AnnotationChooser.java b/src/jalview/gui/AnnotationChooser.java
index 5ac76db..84883d7 100644
--- a/src/jalview/gui/AnnotationChooser.java
+++ b/src/jalview/gui/AnnotationChooser.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -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.
@@ -181,7 +202,7 @@ public class AnnotationChooser extends JPanel
// this.ap.alabels.setSize(this.ap.alabels.getSize().width,
// this.ap.annotationPanel.getSize().height);
// this.ap.validate();
- this.ap.paintAlignment(true);
+ this.ap.paintAlignment(true, false);
}
/**
@@ -212,7 +233,7 @@ public class AnnotationChooser extends JPanel
// this.ap.alabels.setSize(this.ap.alabels.getSize().width,
// this.ap.annotationPanel.getSize().height);
// this.ap.validate();
- this.ap.paintAlignment(true);
+ this.ap.paintAlignment(true, false);
}
/**
@@ -222,7 +243,7 @@ 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()
{
@@ -230,7 +251,7 @@ public class AnnotationChooser extends JPanel
this.ap.updateAnnotation();
// this.ap.annotationPanel.adjustPanelHeight();
- this.ap.paintAlignment(true);
+ this.ap.paintAlignment(true, false);
}
/**
@@ -335,7 +356,7 @@ 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)